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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/LICENSE Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,340 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Lesser General Public License instead.) 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,89 @@ +# ========================== +# BEDTools Makefile +# (c) 2009 Aaron Quinlan +# ========================== + +# define our object and binary directories +export OBJ_DIR = obj +export BIN_DIR = bin +export SRC_DIR = src +export CXX = g++ +export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC +export LIBS = -lz +export BT_ROOT = src/utils/BamTools/ + + +SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ + $(SRC_DIR)/bedToBam \ + $(SRC_DIR)/bedToIgv \ + $(SRC_DIR)/bed12ToBed6 \ + $(SRC_DIR)/closestBed \ + $(SRC_DIR)/complementBed \ + $(SRC_DIR)/coverageBed \ + $(SRC_DIR)/fastaFromBed \ + $(SRC_DIR)/flankBed \ + $(SRC_DIR)/genomeCoverageBed \ + $(SRC_DIR)/intersectBed \ + $(SRC_DIR)/linksBed \ + $(SRC_DIR)/maskFastaFromBed \ + $(SRC_DIR)/mergeBed \ + $(SRC_DIR)/multiBamCov \ + $(SRC_DIR)/multiIntersectBed \ + $(SRC_DIR)/nucBed \ + $(SRC_DIR)/overlap \ + $(SRC_DIR)/pairToBed \ + $(SRC_DIR)/pairToPair \ + $(SRC_DIR)/shuffleBed \ + $(SRC_DIR)/slopBed \ + $(SRC_DIR)/sortBed \ + $(SRC_DIR)/subtractBed \ + $(SRC_DIR)/tagBam \ + $(SRC_DIR)/unionBedGraphs \ + $(SRC_DIR)/windowBed + +UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities \ + $(SRC_DIR)/utils/bedFile \ + $(SRC_DIR)/utils/bedGraphFile \ + $(SRC_DIR)/utils/chromsweep \ + $(SRC_DIR)/utils/gzstream \ + $(SRC_DIR)/utils/fileType \ + $(SRC_DIR)/utils/bedFilePE \ + $(SRC_DIR)/utils/sequenceUtilities \ + $(SRC_DIR)/utils/tabFile \ + $(SRC_DIR)/utils/BamTools \ + $(SRC_DIR)/utils/BamTools-Ancillary \ + $(SRC_DIR)/utils/Fasta \ + $(SRC_DIR)/utils/genomeFile + +all: + [ -d $(OBJ_DIR) ] || mkdir -p $(OBJ_DIR) + [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR) + + @echo "Building BEDTools:" + @echo "=========================================================" + + @for dir in $(UTIL_SUBDIRS); do \ + echo "- Building in $$dir"; \ + $(MAKE) --no-print-directory -C $$dir; \ + echo ""; \ + done + + @for dir in $(SUBDIRS); do \ + echo "- Building in $$dir"; \ + $(MAKE) --no-print-directory -C $$dir; \ + echo ""; \ + done + + +.PHONY: all + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + @rm -Rf $(BT_ROOT)/lib + @rm -f $(BT_ROOT)/src/api/*.o + @rm -f $(BT_ROOT)/src/api/internal/*.o + @rm -Rf $(BT_ROOT)/include + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/README.rst Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,47 @@ +============================== + BEDTools +============================== + +Created by Aaron Quinlan Spring 2009. + +Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved. + +Stable releases: http://code.google.com/p/bedtools + +Repository: https://github.com/arq5x/bedtools + +Released under GNU public license version 2 (GPL v2). + + +Summary +------- +BEDTools is a collection of utilities for comparing, summarizing, and +intersecting genomic features in BED, GTF/GFF, VCF and BAM formats. + + +Manual +------ +See the extensive PDF manual included at: http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf. + +This manual covers many common usage examples. There are also examples available at: +http://code.google.com/p/bedtools/wiki/Usage +http://code.google.com/p/bedtools/wiki/UsageAdvanced + +Installation +------------ +Git +... +git clone git://github.com/arq5x/bedtools.git + +Download tarball - that big gray button on the upper right. +........................................................... +#. Unpack the source downloaded tarball. +#. cd into the expanded folder. +#. Type "make clean" and hit enter. +#. Type "make all" and hit enter. +#. If you encountered no errors, then all of the BED Tools should now be in bin/ + If not, try to troubleshoot then email me: aaronquinlan at gmail dot com +#. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin. +#. Use the tools. + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/RELEASE_HISTORY Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,646 @@ +Version 2.14.2 (2-Nov-2011) + +Bug Fixes +========= +1. Corrected the help for closestBed. It now correctly reads -io instead of -no. +2. Fixed regression in closestBed injected in version 2.13.4 whereby B features to the right of an A feature were missed. + +New tool. +============ +1. Added the multiIntersectBed tool for reporting common intervals among multiple **sorted** BED/GFF/VCF files. + + + +Version 2.13.4 (26-Oct-2011) +Bug Fixes +========= +1. The -sorted option (chromsweep) in intersectBed now obeys -s and -S. I had neglected to implement that. Thanks to Paul Ryvkin for pointing this out. +2. The -split option was mistakenly splitting of D CIGAR ops. +3. The Makefile was not including zlib properly for newer versions of GCC. Thanks to Istvan Albert for pointing this out and providing the solution. + +Improvements +============ +1. Thanks to Jacob Biesinger for a new option (-D) in closestBed that will report _signed_ distances. Moreover, the new option allows fine control over whether the distances are reported based on the reference genome or based on the strand of the A or B feature. Many thanks to Jacob. +2. Thanks to some nice analysis from Paul Ryvkin, I realized that the -sorted option was using way too much memory in certain cases where there is a chromosome change in a sorted BED file. This has been corrected. + +Version 2.13.3 (30-Sept-2011) +Bug Fixes +============ +1. intersectBed detected, but did not report overlaps when using BAM input and -bed. + +Other +===== +1. Warning that -sorted trusts, but does not enforce that data is actually sorted. + + +Version 2.13.2 (23-Sept-2011) + +New algorithm +============= +1. Preliminary release of the chrom_sweep algorithm. + +New options +=========== +1. genomeCoverageBed no longer requires a genome file when working with BAM input. It instead uses the BAM header. +2. tagBam now has a -score option for annotating alignments with the BED "scores" field in annotation files. This overrides the default behavior, which is to use the -labels associated with the annotation files passed in on the command line. + +Bug fixes +========= +1. Correct a bug that prevented proper BAM support in intersectBed. +2. Improved detection of GFF features with negative coordinates. + + + +Version 2.13.1 (6-Sept-2011) + +New options +=========== +1. tagBam now has -s and -S options for only annotating alignments with features on the same and opposite strand, respectively. +2. tagBam now has a -names option for annotating alignments with the "name" field in annotation files. This overrides the default behavior, which is to use the -labels associated with the annotation files passed in on the command line. Currently, this works well with BED files, but given the limited metadata support for GFF files, annotating with -names and GFF files may not work as well as wished, depending on the type of GFF file used. + + + +Version 2.13.0 (1-Sept-2011) + +New tools +========= +1. tagBam. This tool annotates a BAM file with custom tag fields based on overlaps with BED/GFF/VCF files. +For example: +$ tagBam -i aln.bam -files exons.bed introns.bed cpg.bed utrs.bed \ + -tags exonic intonic cpg utr \ + > aln.tagged.bam +For alignments that have overlaps, you should see new BAM tags like "YB:Z:exonic", "YB:Z:cpg;utr" + +2. multiBamCov. The new tool counts sequence coverage for multiple bams at specific loci defined in a BED/GFF/VCF file. +For example: + +$ multiBamCov -bams aln.1.bam aln.2.bam aln3.bam -bed exons.bed +chr1 861306 861409 SAMD11 1 + 181 280 236 +chr1 865533 865718 SAMD11 2 + 249 365 374 +chr1 866393 866496 SAMD11 3 + 162 298 322 + +where the last 3 columns represent the number of alignments overlapping each interval from the three BAM file. + +The following options are available to control which types of alignments are are counted. +-q Minimum mapping quality allowed. Default is 0. + +-D Include duplicate-marked reads. Default is to count non-duplicates only + +-F Include failed-QC reads. Default is to count pass-QC reads only + +-p Only count proper pairs. Default is to count all alignments with MAPQ + greater than the -q argument, regardless of the BAM FLAG field. + +3. nucBed. This new tool profiles the nucleotide content of intervals in a fasta file. The following information will be reported after each original BED/GFF/VCF entry: + 1) %AT content + 2) %GC content + 3) Number of As observed + 4) Number of Cs observed + 5) Number of Gs observed + 6) Number of Ts observed + 7) Number of Ns observed + 8) Number of other bases observed + 9) The length of the explored sequence/interval. + 10) The sequence extracted from the FASTA file. (optional, if -seq is used) + 11) The number of times a user defined pattern was observed. (optional, if -pattern is used.) + + + +For example: +$ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed | head -3 +#1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len +chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 +chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 + + +One can also report the sequence itself: +$ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -seq | head -3 +#1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len 16_seq +chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 ccagggg... +chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 TCTTTCA... + +Or, one can count the number of times that a specific pattern occur in the intervals (reported as the last column): +$ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -pattern CGTT | head +#1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len 16_user_patt_count +chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 0 +chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 0 +chr1 10757 10997 trf 434 + 0.370833 0.629167 49 70 81 40 0 0 240 0 +chr1 11225 11447 trf 273 + 0.463964 0.536036 44 86 33 59 0 0 222 0 +chr1 11271 11448 trf 187 + 0.463277 0.536723 37 69 26 45 0 0 177 0 +chr1 11283 11448 trf 199 + 0.466667 0.533333 37 64 24 40 0 0 165 0 +chr1 19305 19443 trf 242 + 0.282609 0.717391 17 57 42 22 0 0 138 1 +chr1 20828 20863 trf 70 + 0.428571 0.571429 10 7 13 5 0 0 35 0 +chr1 30862 30959 trf 79 + 0.556701 0.443299 35 22 21 19 0 0 97 0 + + + +New options +=========== +1. Support for named pipes and FIFOs. +2. "-" is now allowable to indicate that data is being sent via stdin. + +3. Multiple tools. Added new -S option to annotateBed, closestBed, coverageBed, intersectBed, pairToBed, subtractBed, and windowBed (-Sm). This new option does the opposite of the -s option: that is, overlaps are only processed if they are on _opposite_ strands. Thanks to Sol Katzman for the great suggestion. Very useful for certain RNA-seq analyses. + +4. coverageBed. Added a new -counts option to coverageBed that only reports the count of overlaps, instead of also computing fractions, etc. This is much faster and uses much less memory. + +5. fastaFromBed. Added a new -full option that uses the full BED entry when naming each output sequence. Also removed the -fo option such that all output is now written to stdout. + +6. genomeCoverageBed. + - Added new -scale option that allows the coverage values to be scaled by a constant. Useful for normalizing coverage with RPM, RPKM, etc. Thanks to Ryan Dale for the useful suggestion. + - Added new -5, -3, -trackline, -trackopts, and -dz options. Many thanks to Assaf Gordon for these improvements. + -5: Calculate coverage of 5" positions (instead of entire interval) + -3: Calculate coverage of 3" positions (instead of entire interval). + -trackline: Adds a UCSC/Genome-Browser track line definition in the first line of the output. + -trackopts: rites additional track line definition parameters in the first line. + -dz: Report the depth at each genome position with zero-based coordinates, instead of zero-based. + +7. closestBed. See below, thanks to Brent Pedersen, Assaf Gordon, Ryan Layer and Dan Webster for the helpful discussions. + - closestBed now reports _all_ features in B that overlap A by default. This allows folks to decide which is the "best" overlapping feature on their own. + + 2. closestBed now has a "-io" option that ignores overlapping features. In other words, it will only report the closest, non-overlapping feature. + + An example: + + $ cat a.bed + chr1 10 20 + + $ cat b.bed + chr1 15 16 + chr1 16 40 + chr1 100 1000 + chr1 200 1000 + + $ bin/closestBed -a a.bed -b b.bed + chr1 10 20 chr1 15 16 + chr1 10 20 chr1 16 40 + + $ bin/closestBed -a a.bed -b b.bed -io + chr1 10 20 chr1 100 1000 + +Updates +======= +1. Updated to the latest version of BamTools. This allows greater functionality and will facilitate new options and tools in the future. + + - +Bug Fixes +========= +1. GFF files cannot have zero-length features. +2. Corrected an erroneous check on the start coordinates in VCF files. Thanks to Jan Vogel for the correction. +3. mergeBed now always reports output in BED format. +3. Updated the text file Tokenizer function to yield 15% speed improvement. +4. Various tweaks and improvements. + + + + +Version 2.12.0 (April-3-2011) + +New Tool +======== +1. Added new tool called "flankBed", which allows one to extract solely the flanking regions that are upstream and downstream of a given feature. Unlike slopBed, flankBed does not include the original feature itself. A new feature is created for each flabking region. For example, imagine the following feature: + +chr1 100 200 + +The following would create features for solely the 10 bp regions flanking this feature. +$ bin/flankBed -i a.bed -b 10 -g genomes/human.hg18.genome +chr1 90 100 +chr1 200 210 + +In contrast, slopBed would return: +bin/slopBed -i a.bed -b 10 -g genomes/human.hg18.genome +chr1 90 210 + +FlankBed has all of the same features as slopBed. + + +New Features +============ +1. Added new "-scores" feature to mergeBed. This allows one to take the sum, min, max, +mean, median, mode, or antimode of merged feature scores. In addition, one can use the "collapse" operation to get a comma-separated list of the merged scores. +2. mergeBed now tolerates multiple features in a merged block to have the same feature name. +3. Thanks to Erik Garrison's "fastahack" library, fastaFromBed now reports its output in the order of the input file. +4. Added a "-n" option to bed12ToBed6, which forces the score field to be the 1-based block number from the original BED12 feature. This is useful for tracking exon numbers, for example. +5. Thanks to Can Alkan, added a new "-mc" option to maskFastaFromBed that allows one to define a custom mask character, such as "X" (-n X). + + +Bug Fixes +========= +1. Thanks to Davide Cittaro, intersectBed and windowBed now properly capture unmapped BAM alignments when using the "-v" option. +2. ClosestBed now properly handles cases where b.end == a.start +3. Thanks to John Marshall, the default constructors are much safer and less buggy. +4. Fixed bug in shuffleBed that complained about a lack of -incl and -excl. +5. Fixed bug in shuffleBed for features that would go beyond the end of a chromosome. +6. Tweaked bedToIgv to make it more Windows friendly. + + + +Version 2.11.2 (January-31-2010) +Fixed a coordinate reporting bug in coverageBed. +Added "max distance (-d)" argument back to the new implementation of mergeBed. + + + +Version 2.11.0 (January-21-2010) + +Enhancements: +============= +1. Support for zero length features (i.e., start = end) + - For example, this allows overlaps to be detected with insertions in the reference genome, as reported by dbSNP. +2. Both 8 and 9 column GFF files are now supported. +3. slopBed can now extend the size of features by a percentage of it's size (-pct) instead of just a fixed number of bases. +4. Two improvements to shuffleBed: + 3a. A -f (overlapFraction) parameter that defines the maximum overlap that a randomized feature can have with an -excl feature. + That is, if a chosen locus has more than -f overlap with an -excl feature, a new locus is sought. + 3b. A new -incl option (thanks to Michael Hoffman and Davide Cittaro) that, defines intervals in which the randomized features should be placed. This is used instead of placing the features randomly in the genome. Note that a genome file is still required so + that a randomized feature does not go beyond the end of a chromosome. +5. bamToBed can now optionally report the CIGAR string as an additional field. +6. pairToPair can now report the entire paired feature from the B file when overlaps are found. +7. complementBed now reports all chromosomes, not just those with features in the BED file. +8. Improved randomization seeding in shuffleBed. This prevents identical output for runs of shuffleBed that + occur in the same second (often the case). + + +Bug Fixes: +========== +1. Fixed the "BamAlignmentSupportData is private" compilation issue. +2. Fixed a bug in windowBed that caused positions to run off the end of a chromosome. + + +Major Changes: +============== +1. The groupBy command is now part of the filo package (https://github.com/arq5x/filo) and will no longer be distributed with BEDTools. + + + +Version 2.10.0 (September-21-2010) +==New tools== +1. annotateBed. Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed +from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. For example, the following will annotate the fraction of the variants in variants.bed that are covered by genes, conservaed regions and know variation, respectively. +$ annotateBed -i variants.bed -files genes.bed conserv.bed known_var.bed + +This tool was suggested by Can Alkan and was motivated by the example source code that he kindly provided. + +==New features== +1. New frequency operations (freqasc and freqdesc) added to groupBy. These operations report a histogram of the frequency that each value is observed in a given column. +2. Support for writing uncompressed bam with the -ubam option. +3. Shorthand arguments for groupBy (-g eq. -grp, -c eq. -opCols, -o eq. -opCols). +4. In addition, all BEDTools that require only one main input file (the -i file) will assume that input is +coming from standard input if the -i parameter is ignored. For example, the following are equivalent: +$ cat snps.bed | sortBed –i stdin +$ cat snps.bed | sortBed + +As are these: +$ cat data.txt | groupBy -i stdin -g 1,2,3 -c 5 -o mean +$ cat data.txt | groupBy -g 1,2,3 -c 5 -o mean + +==Bug fixes== +1. Increased the precision of the output from groupBy. + + + +Version 2.9.0 (August-16-2010) +==New tools== +1. unionBedGraphs. This is a very powerful new tool contributed by Assaf Gordon from CSHL. It will combine/merge multiple BEDGRAPH files into a single file, thus allowing comparisons of coverage (or any text-value) across multiple samples. + +==New features== +1. New "distance feature" (-d) added to closestBed by Erik Arner. In addition to finding the closest feature to each feature in A, the -d option will report the distance to the closest feature in B. Overlapping features have a distance of 0. +2. New "per base depth feature" (-d) added to coverageBed. This reports the per base coverage (1-based) of each feature in file B based on the coverage of features found in file A. For example, this could report the per-base depth of sequencing reads (-a) across each capture target (-b). + + +==Bug Fixes== +1. Fixed bug in closestBed preventing closest features from being found for A features with start coordinates < 2048000. Thanks to Erik Arner for pointing this out. +2. Fixed minor reporting annoyances in closestBed. Thanks to Erik Arner. +3. Fixed typo/bug in genomeCoverageBed that reported negative coverage owing to numeric overflow. Thanks to Alexander Dobin for the detailed bug report. +4. Fixed other minor parsing and reporting bugs/annoyances. + + + + +Version 2.8.3 (July-25-2010) +1. Fixed bug that caused some GFF files to be misinterpreted as VCF. This prevented the detection of overlaps. +2. Added a new "-tag" option in bamToBed that allows one to choose the _numeric_ tag that will be used to populate the score field. For example, one could populate the score field with the alignment score with "-tag AS". +3. Updated the BamTools API. + + +Version 2.8.2 (July-18-2010) +1. Fixed a bug in bedFile.h preventing GFF strands from being read properly. +2. Fixed a bug in intersectBed that occasionally caused spurious overlaps between BAM alignments and BED features. +3. Fixed bug in intersectBed causing -r to not report the same result when files are swapped. +4. Added checks to groupBy to prevent the selection of improper opCols and groups. +5. Fixed various compilation issues, esp. for groupBy, bedToBam, and bedToIgv. +6. Updated the usage statements to reflect bed/gff/vcf support. +7. Added new fileType functions for auto-detecting gzipped or regular files. Thanks to Assaf Gordon. + + +Version 2.8.1 (July-05-2010) +1. Added bedToIgv. + + +Version 2.8.0 (July-04-2010) + +1. Proper support for "split" BAM alignments and "blocked" BED (aka BED12) features. By using the "-split" option, intersectBed, coverageBed, genomeCoverageBed, and bamToBed will now correctly compute overlaps/coverage solely for the "split" portions of BAM alignments or the "blocks" of BED12 features such as genes. + +2. Added native support for the 1000 Genome Variant Calling Format (VCF) version 4.0. + +3. New bed12ToBed6 tool. This tool will convert each block of a BED12 feature into discrete BED6 features. + +4. Useful new groupBy tool. This is a very useful new tool that mimics the "groupBy" clause in SQL. Given a file or stream that is sorted by the appropriate "grouping columns", groupBy will compute summary statistics on another column in the file or stream. This will work with output from all BEDTools as well as any other tab-delimited file or stream. Example summary operations include: sum, mean, stdev, min, max, etc. Please see the help for the tools for examples. The functionality in groupBy was motivated by helpful discussions with Erik Arner at Riken. + +5. Improvements to genomeCoverageBed. Applied several code improvements provided by Gordon Assaf at CSHL. Most notably, beyond the several efficiency and organizational changes he made, he include a "-strand" option which allows one to specify that coverage should only be computed on either the "+" or the "-" strand. + +6. Fixed a bug in closestBed found by Erik Arner (Riken) which incorrectly reported "null" overlaps for features that did not have a closest feature in the B file. + +7. Fixed a careless bug in slopBed also found by Erik Arner (Riken) that caused an infinite loop when the "-excl" option was used. + +8. Reduced memory consumption by ca. 15% and run time by ca. 10% for most tools. + +9. Several code-cleanliness updates such as templated functions and common tyedefs. + +10. Tweaked the genome binning approach such that 16kb bins are the most granular. + + +Version 2.7.1 (May-06-2010) +Fixed a typo that caused some compilers to fail on closestBed. + +Version 2.7.0 (May-05-2010) + +General: +1. "Gzipped" BED and GFF files are now supported as input by all BEDTools. Such files must end in ".gz". +2. Tools that process BAM alignments now uniformly compute an ungapped alignment end position based on the BAM CIGAR string. Specifically, "M", "D" and "N" operations are observed when computing the end position. +3. bamToBed requires the BAM file to be sorted/grouped by read id when creating BEDPE output. This allows the alignments end coordinate for each end of the pair to be properly computed based on its CIGAR string. The same requirement applies to pairToBed. +4. Updated manual. +5. Many silent modifications to the code that improve clarity and sanity-checking and facilitate future additions/modifications. + + +New Tools: +1. bedToBam. This utility will convert BED files to BAM format. Both "blocked" (aka BED12) and "unblocked" (e.g. BED6) formats are acceptable. This allows one to, for example, compress large BED files such as dbSNP into BAM format for efficient visualization. + + +Changes to existing tools: + intersectBed + 1. Added -wao option to report 0 overlap for features in A that do not intersect any features in B. This is an extension of the -wo option. + + bamToBed + 1. Requires that BAM input be sorted/grouped by read name. + + pairToBed + 1. Requires that BAM input be sorted/grouped by read name. + 2. Allows use of minimum mapping quality or total edit distance for score field. + + windowBed + 1. Now supports BAM input. + + genomeCoverageBed + 1. -bga option. Thanks to Gordon Assaf for the suggestion. + 2. Eliminated potential seg fault. + +Acknowledgements: + 1. Gordon Assaf: for suggesting the -bga option in genomeCoverageBed and for testing the new bedToBam utility. + 2. Ivan Gregoretti: for helping to expedite the inclusion of gzip support. + 3. Can Alkan: for suggesting the addition of the -wao option to intersectBed. + 4. James Ward: for pointing out that bedToBam did not need to create "dummy" seq and qual entries. + + + +Version 2.6.1 (Mar-29-2010) +1. Fixed a careless command line parsing bug in coverageBed. + + +Version 2.6.0 (Mar-23-2010) +***Specific improvements / additions to tools*** +1. intersectBed + * Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files. + -- Not sure why this wasn't added sooner; it's obvious. + +2. coverageBed + * native BAM support + * can now report a histogram (-hist) of coverage for each feature in B. Useful for exome sequencing projects, for example. + -- thanks for the excellent suggestion from Jose Bras + * faster + +3. genomeCoverageBed + * native BAM support + * can now report coverage in BEDGRAPH format (-bg) + -- thanks for the code and great suggestion from Gordon Assaf, CSHL. + +4. bamToBed + * support for "blocked" BED (aka BED12) format. This facilitates the creation of BED entries for "split" alignments (e.g. RNAseq or SV) + -- thanks to Ann Loraine, UNCC for test data to support this addition. + +5. fastaFromBed + * added the ability to extract sequences from a FASTA file according to the strand in the BED file. That is, when "-" the extracted sequence is reverse complemented. + -- thanks to Thomas Doktor, U. of Southern Denmark for the code and suggestion. + +6. ***NEW*** overlap + * newly added tool for computing the overlap/distance between features on the same line. + -- For example: + $ cat test.out + chr1 10 20 A chr1 15 25 B + chr1 10 20 C chr1 25 35 D + + $ cat test.out | overlaps -i stdin -cols 2,3,6,7 + chr1 10 20 A chr1 15 25 B 5 + chr1 10 20 C chr1 25 35 D -5 + +***Bug fixes*** +1. Fixed a bug in pairToBed when comparing paired-end BAM alignments to BED annotations and using the "notboth" option. +2. Fixed an idiotic bug in intersectBed that occasionally caused segfaults when blank lines existed in BED files. +3. Fixed a minor bug in mergeBed when using the -nms option. + +***General changes*** +1. Added a proper class for genomeFiles. The code is much cleaner and the tools are less sensitive to minor problems with the formatting of genome files. Per Gordon Assaf's wise suggestion, the tools now support "chromInfo" files directly downloaded from UCSC. Thanks Gordon---I disagreed at first, but you were right. +2. Cleaned up some of the code and made the API a bit more streamlined. Will facilitate future tool development, etc. + + +Version 2.5.4 (Mar-3-2010) +1. Fixed an insidious bug that caused malform BAM output from intersectBed and pairToBed. The previous BAM files worked fine with samtools as BAM input, but when piped in as SAM, there was an extra tab that thwarted conversion from SAM back to BAM. Many thanks to Ivan Gregoretti for reporting this bug. I had never used the BAM output in this way and thus never caught the bug! + + +Version 2.5.3 (Feb-19-2010) +1. Fixed bug to "re-allow" track and "browser" lines. +2. Fixed bug in reporting BEDPE overlaps. +3. Fixed bug when using type "notboth" with BAM files in pairToBed. +4. When comparing BAM files to BED/GFF annotations with intersectBed or pairToBed, the __aligned__ sequence is used, rather than the __original__ sequence. +5. Greatly increased the speed of pairToBed when using BAM alignments. +6. Fixed a bug in bamToBed when reporting edit distance from certain aligners. + + +Version 2.5.2 (Feb-2-2010) +1. The start and end coordinates for BED and BEDPE entries created by bamToBed are now based on the __aligned__ sequence, rather than the original sequence. It's obvious, but I missed it originally...sorry. +2. Added an error message to mergeBed preventing one from using "-n" and "-nms" together. +3. Fixed a bug in pairToBed that caused neither -type "notispan" nor "notospan" to behave as described. + + +Version 2.5.1 (Jan-28-2010) +1. Fixed a bug in the new GFF/BED determinator that caused a segfault when start = 0. + + +Version 2.5.0 (Jan-27-2010) +1. Added support for custom BED fields after the 6th column. +2. Fixed a command line parsing bug in pairToBed. +3. Improved sanity checking. + + +Version 2.4.2 (Jan-23-2010) +1. Fixed a minor bug in mergeBed when -nms and -s were used together. +2. Improved the command line parsing to prevent the occasional segfault. + + +Version 2.4.1 (Jan-12-2010) +1. Updated BamTools libraries to remove some compilation issues on some systems/compilers. + + +Version 2.4.0 (Jan-11-2010) +1. Added BAM support to intersectBed and pairToBed +2. New bamToBed feature. +3. Added support for GFF features +4. Added support for "blocked" BED format (BED12) +6. Wrote complete manual and included it in distribution. +7. Fixed several minor bugs. +8. Cleaned up code and improved documentation. + + +Version 2.3.3 (12/17/2009) +Rewrote complementBed to use a slower but much simpler approach. This resolves several bugs with the previous logic. + + +Version 2.3.2 (11/25/2009) +Fixed a bug in subtractBed that prevent a file from subtracting itself when the following is used: + $ subtractBed -a test.bed -b test.bed + + +Version 2.3.1 (11/19/2009) +Fixed a typo in closestBed that caused all nearby features to be returned instead of just the closest one. + + +Version 2.3.0 (11/18/2009) +1. Added four new tools: + - shuffleBed. Randomly permutes the locations of a BED file among a genome. Useful for testing for significant overlap enrichments. + - slopBed. Adds a requested number of base pairs to each end of a BED feature. Constrained by the size of each chromosome. + - maskFastaFromBed. Masks a FASTA file based on BED coordinates. Useful making custom genome files from targeted capture experiment, etc. + - pairToPair. Returns overlaps between two paired-end BED files. This is great for finding structural variants that are private or shared among samples. + +2. Increased the speed of intersectBed by nearly 50%. +3. Improved corrected some of the help messages. +4. Improved sanity checking for BED entries. + + +Version 2.2.4 (10/27/2009) +1. Updated the mergeBed documentation to describe the -names option which allows one to report the names of the +features that were merged (separated by semicolons). + + +Version 2.2.3 (10/23/2009) +1. Changed windowBed to optionally define "left" and "right" windows based on strand. For example by default, -l 100 and -r 500 will +add 100 bases to the left (lower coordinates) of a feature in A when scanning for hits in B and 500 bases to the right (higher coordinates). + +However if one chooses the -sw option (windows bases on strandedness), the behavior changes. Assume the above example except that a feature in A +is on the negative strand ("-"). In this case, -l 100, -r 500 and -sw will add 100 bases to the right (higher coordinates) and 500 bases to the left (lower coordinates). + +In addition, there is a separate option (-sm) that can optionally force hits in B to only be tracked if they are on the same strand as A. + +***NOTE: This replaces the previous -s option and may affect existing pipelines***. + + +Version 2.2.2 (10/20/2009) +1. Improved the speed of genomeCoverageBed by roughly 100 fold. The memory usage is now less than 2.0 Gb. + + +Version 2.2.1 +1. Fixed a very obvious bug in subtractBed that caused improper behavior when a feature in A was overlapped by more than one feature in B. +Many thanks to folks in the Hannon lab at CSHL for pointing this out. + + +Version 2.2.0 +=== Notable changes in this release === +1. coverageBed will optionally only count features in BED file A (e.g. sequencing reads) that overlap with + the intervals/windows in BED file B on the same strand. This has been requested several times recently + and facilitates CHiP-Seq and RNA-Seq experiments. + +2. intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B. For example, + previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit" + to be reported. If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B. This helps + to exclude overlaps between say small features in A and large features in B: + + A ========== + B ********************************************************** + + -f 0.50 (Reported), whereas -f 0.50 -r (Not reported) + +3. The score field has been changed to be a string. While this deviates from the UCSC definition, it allows one to track + much more meaningful information about a feature/interval. For example, score could now be: + + 7.31E-05 (a p-value) + 0.334577 (mean enrichment) + 2:2.2:40:2 (several values encoded in a string) + +4. closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A. Previously, it + merely reported the first such feature that appeared in B. Here's a cartoon explaining the difference. + + **Prior behavior** + + A ============== + B.1 ++++++++++++++ + B.2 ++++++++++++++ + B.3 +++++++++ + + ----------------------------------------- + Result = B.1 ++++++++++++++ + + + **Current behavior** + + A ============== + B.1 ++++++++++++++ + B.2 ++++++++++++++ + B.3 +++++++++ + + ----------------------------------------- + Result = B.1 ++++++++++++++ + B.2 ++++++++++++++ + + Using the -t option, one can also choose to report either the first or the last entry in B in the event of a tie. + +5. Several other minor changes to the algorithms have been made to increase speed a bit. + + +VERSION 2.1.2 +1. Fixed yet another bug in the parsing of "track" or "browser" lines. Sigh... +2. Change the "score" column (i.e. column 5) to b stored as a string. While this deviates + from the UCSC convention, it allows significantly more information to be packed into the column. + + +VERSION 2.1.1 +1. Added limits.h to bedFile.h to fix compilation issues on some systems. +2. Fixed bug in testing for "track" or "browser" lines. + + +VERSION 2.1.0 +1. Fixed a bug in peIntersectBed that prevented -a from being correctly handled when passed via stdin. +2. Added new functionality to coverageBed that calculates the density of coverage. +3. Fixed bug in geneomCoverageBed. + + +VERSION 2.0.1 +1. Added the ability to retain UCSC browser track/browser headers in BED files. + + +VERSION 2.0 +1. Sped up the file parsing. ~10-20% increase in speed. +2. Created reportBed() as a common method in the bedFile class. Cleans up the code quite nicely. +3. Added the ability to compare BED files accounting for strandedness. +4. Paired-end intersect. +5. Fixed bug that prevented overlaps from being reported when the overlap fraction requested is 1.0 + + + +VERSION 1.2, 04/27/2009. (1eb06115bdf3c49e75793f764a70c3501bb53f33) +1. Added subtractBed. + A. Fixed bug that prevented "split" overlaps from being reported. + B. Prevented A from being reported if >=1 feature in B completely spans it. +2. Added linksBed. +3. Added the ability to define separate windows for upstream and downstream to windowBed. + + +VERSION 1.1, 04/23/2009. (b74eb1afddca9b70bfa90ba763d4f2981a56f432) +Initial release.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/data/knownGene.hg18.chr21.bed Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,828 @@ +chr21 9928613 10012791 uc002yip.1 0 - 9928775 9995604 0 24 298,71,93,80,106,81,62,89,82,61,65,64,100,120,162,51,60,54,54,54,54,58,109,158, 0,2082,3564,7620,9627,13341,15191,27109,27296,28194,35165,35968,36178,37925,44523,46170,52998,62332,63266,64549,66980,78302,81026,84020, +chr21 9928613 10012791 uc002yiq.1 0 - 9928775 9995604 0 23 298,71,93,80,106,81,62,89,82,61,65,64,100,120,162,51,60,54,54,54,58,109,158, 0,2082,3564,7620,9627,13341,15191,27109,27296,28194,35165,35968,36178,37925,44523,46170,52998,63266,64549,66980,78302,81026,84020, +chr21 9928613 10012791 uc002yir.1 0 - 9928775 9995604 0 22 298,71,93,80,106,81,62,89,82,61,65,64,100,120,162,51,54,54,54,58,109,158, 0,2082,3564,7620,9627,13341,15191,27109,27296,28194,35165,35968,36178,37925,44523,46170,63266,64549,66980,78302,81026,84020, +chr21 9928613 10012791 uc010gkv.1 0 - 9928775 9973168 0 19 298,71,93,80,106,81,62,89,82,61,65,64,100,120,162,51,58,109,158, 0,2082,3564,7620,9627,13341,15191,27109,27296,28194,35165,35968,36178,37925,44523,46170,78302,81026,84020, +chr21 9928613 10061300 uc002yis.1 0 - 9928613 9928613 0 33 298,71,93,80,81,62,89,82,61,65,64,100,120,162,51,60,54,54,54,58,109,120,129,213,66,130,165,197,105,102,117,120,702, 0,2082,3564,7620,13341,15191,27109,27296,28194,35165,35968,36178,37925,44523,46170,52998,63266,64549,66980,78302,81026,89277,91464,104695,106174,106728,108195,108605,114070,114367,119980,122855,131985, +chr21 10042683 10120796 uc002yit.1 0 - 10071441 10120588 0 10 105,102,117,120,702,115,172,163,101,223, 0,297,5910,8785,17915,26668,28637,37348,76733,77890, +chr21 10042683 10120808 uc002yiu.1 0 - 10080193 10120608 0 9 105,102,117,702,115,172,163,101,215, 0,297,5910,17915,26668,28637,37348,76733,77910, +chr21 10079666 10120808 uc002yiv.1 0 - 10081686 10120608 0 4 528,91,101,215, 0,1930,39750,40927, +chr21 10080031 10081687 uc002yiw.1 0 - 10080031 10080031 0 2 200,91, 0,1565, +chr21 10081660 10120796 uc002yix.2 0 - 10081660 10081660 0 3 27,101,223, 0,37756,38913, +chr21 13332351 13346202 uc002yiy.2 0 + 13332351 13332351 0 5 265,115,2492,65,215, 0,4342,4619,10805,13636, +chr21 13336975 13346202 uc002yiz.2 0 + 13336975 13336975 0 4 169,108,65,215, 0,2379,6181,9012, +chr21 13361138 13412440 uc002yja.2 0 + 13361189 13412250 0 3 102,118,411, 0,2228,50891, +chr21 13904368 13935777 uc002yjb.1 0 + 13904420 13935758 0 11 573,115,174,107,138,71,71,45,167,124,241, 0,4946,5220,8172,9981,12628,18205,19679,20764,29338,31168, +chr21 13944438 13944477 uc002yjc.1 0 + 13944438 13944438 0 1 39, 0, +chr21 13945076 13945106 uc002yjd.1 0 + 13945076 13945076 0 1 30, 0, +chr21 13973491 13975330 uc002yje.1 0 - 13973781 13974201 0 1 1839, 0, +chr21 14137333 14142556 uc002yjf.1 0 - 14137333 14137333 0 6 291,114,270,129,191,275, 0,880,1863,2871,3617,4948, +chr21 14200023 14200052 uc002yjg.1 0 + 14200023 14200023 0 1 29, 0, +chr21 14202070 14202096 uc002yjh.1 0 - 14202070 14202070 0 1 26, 0, +chr21 14237966 14274631 uc002yji.1 0 - 14237966 14237966 0 6 88,71,73,29,85,738, 0,1264,7292,7457,10291,35927, +chr21 14270940 14274631 uc002yjj.2 0 - 14270940 14270940 0 2 1809,738, 0,2953, +chr21 14321612 14438647 uc002yjk.2 0 + 14321612 14321612 0 3 177,195,699, 0,56529,116336, +chr21 14321612 14438730 uc002yjl.2 0 + 14321612 14321612 0 3 177,195,1030, 0,56529,116088, +chr21 14403005 14501125 uc002yjm.1 0 - 14403184 14501115 0 10 267,177,112,105,168,90,102,109,386,119, 0,35809,43759,54605,56409,57548,72944,77147,80220,98001, +chr21 14459414 14483611 uc010gkw.1 0 - 14459415 14483519 0 4 168,102,109,386, 0,16535,20738,23811, +chr21 14510336 14522564 uc002yjo.2 0 + 14510378 14521485 0 5 138,163,73,100,1493, 0,3418,4952,8293,10735, +chr21 14510336 14522564 uc002yjn.2 0 + 14518639 14521485 0 5 138,173,73,100,1493, 0,3408,4952,8293,10735, +chr21 14510336 14522564 uc002yjp.2 0 + 14518639 14521485 0 4 138,73,100,1493, 0,4952,8293,10735, +chr21 14567990 14585577 uc002yjq.1 0 + 14568283 14585568 0 5 359,62,148,143,100, 0,5797,13751,14605,17487, +chr21 14567990 14595563 uc002yjr.1 0 + 14568283 14593857 0 6 359,62,148,143,178,1934, 0,5797,13751,14605,17771,25639, +chr21 14567990 14595563 uc010gkx.1 0 + 14582733 14593857 0 5 359,148,143,178,1934, 0,13751,14605,17771,25639, +chr21 14567990 14632206 uc002yjs.2 0 + 14567990 14567990 0 14 359,62,148,143,178,147,85,67,188,1435,76,178,61,234, 0,5797,13751,14605,17771,31897,34572,34754,39145,42402,49713,62281,63381,63982, +chr21 14665307 14677380 uc002yjt.1 0 - 14667808 14677311 0 5 3169,168,214,341,94, 0,4536,7083,10087,11979, +chr21 14779419 14840535 uc002yju.1 0 - 14780103 14840453 0 8 887,151,207,152,130,150,72,139, 0,13214,15301,25082,27216,31664,35922,60977, +chr21 14779419 14840535 uc010gky.1 0 - 14780103 14840453 0 4 887,151,207,139, 0,13214,15301,60977, +chr21 14779419 14877594 uc002yjv.1 0 - 14780103 14876588 0 9 887,151,207,152,130,150,72,353,83, 0,13214,15301,25082,27216,31664,35922,96908,98092, +chr21 15117160 15151900 uc002yjw.1 0 - 15117160 15117160 0 3 1447,102,167, 0,2554,34573, +chr21 15255426 15262718 uc002yjx.1 0 - 15258907 15262384 0 1 7292, 0, +chr21 15258731 15358997 uc010gkz.1 0 - 15258907 15262384 0 4 3987,123,80,61, 0,49804,78955,100205, +chr21 16024366 16174248 uc002yjy.1 0 + 16024583 16172665 0 24 262,78,145,124,163,87,138,77,74,149,128,96,162,227,71,229,201,143,179,79,80,124,196,1756, 0,32714,35820,47727,61325,69580,74944,78632,80960,88521,93862,94789,96027,96800,100354,101224,103171,112221,134091,136089,139891,144226,147619,148126, +chr21 16024366 16174248 uc002yjz.1 0 + 16024583 16172665 0 25 262,78,145,124,163,87,138,77,74,149,128,96,162,227,71,229,201,143,96,179,79,80,124,196,1756, 0,32714,35820,47727,61325,69580,74944,78632,80960,88521,93862,94789,96027,96800,100354,101224,103171,112221,119600,134091,136089,139891,144226,147619,148126, +chr21 16024366 16174248 uc010gla.1 0 + 16024583 16172665 0 11 262,78,145,124,163,87,138,80,124,196,1756, 0,32714,35820,47727,61325,69580,74944,139891,144226,147619,148126, +chr21 16085691 16113036 uc010glb.1 0 + 16085691 16085691 0 5 163,87,138,74,149, 0,8255,13619,19635,27196, +chr21 16364712 16901413 uc002ykb.1 0 + 16365304 16365529 0 8 27,285,97,60,49,61,115,229, 0,592,111069,160534,416968,466857,523818,536472, +chr21 16364712 16901413 uc002yka.1 0 + 16365304 16365529 0 8 27,285,97,60,72,49,61,229, 0,592,111069,160534,321092,416968,466857,536472, +chr21 16365304 16365529 uc010glc.1 0 + 16365304 16365529 0 1 225, 0, +chr21 16488569 16901413 uc002ykc.1 0 + 16488613 16685848 0 6 255,60,72,49,61,229, 0,36677,197235,293111,343000,412615, +chr21 16833279 16833360 uc002ykd.1 0 + 16833279 16833279 0 1 81, 0, +chr21 16834014 16834106 uc002yke.1 0 + 16834014 16834014 0 1 92, 0, +chr21 16884427 16884516 uc002ykf.1 0 + 16884427 16884427 0 1 89, 0, +chr21 17733107 17743132 uc002ykg.1 0 + 17733107 17733107 0 4 79,170,118,79, 0,2755,5164,9946, +chr21 17807200 17859800 uc002ykh.1 0 + 17807318 17859798 0 5 161,167,205,156,184, 0,34015,38737,45964,52416, +chr21 17807200 17859800 uc010gld.1 0 + 17807318 17859798 0 4 161,167,205,184, 0,34015,38737,52416, +chr21 17807200 17859800 uc010gle.1 0 + 17807318 17859676 0 3 161,167,184, 0,34015,52416, +chr21 17807200 17861137 uc002yki.1 0 + 17807318 17859881 0 7 161,167,205,156,123,139,1521, 0,34015,38737,45964,47690,48326,52416, +chr21 17841215 17887768 uc002ykj.1 0 + 17841253 17887382 0 7 167,205,156,123,139,184,428, 0,4722,11949,13675,14311,18401,46125, +chr21 17887841 17907033 uc002ykk.1 0 - 17888281 17903333 0 5 680,208,138,181,146, 0,4964,11207,15319,19046, +chr21 17887841 17907033 uc002ykl.1 0 - 17888281 17903333 0 6 680,208,132,138,181,146, 0,4964,10492,11207,15319,19046, +chr21 18071593 18086697 uc002ykm.2 0 - 18071593 18071593 0 4 214,65,183,33, 0,8142,9622,15071, +chr21 18071593 18086697 uc002ykn.2 0 - 18071593 18071593 0 3 214,183,33, 0,9622,15071, +chr21 18083154 18113574 uc002ykq.2 0 - 18087602 18112506 0 5 4612,63,537,134,84, 0,6241,7615,29225,30336, +chr21 18083154 18113574 uc002yko.2 0 - 18087602 18112506 0 5 4615,63,537,134,84, 0,6241,7615,29225,30336, +chr21 18083154 18113574 uc002ykp.2 0 - 18087767 18112506 0 4 4615,537,134,84, 0,7615,29225,30336, +chr21 18195450 18561558 uc002ykr.1 0 + 18550740 18560226 0 7 162,181,310,158,87,103,1417, 0,15957,355246,355707,358937,361528,364691, +chr21 18211407 18561558 uc002yks.1 0 + 18550740 18560226 0 7 181,100,310,158,87,103,1417, 0,110653,339289,339750,342980,345571,348734, +chr21 18211407 18561558 uc002ykt.1 0 + 18550740 18560341 0 6 181,100,310,158,87,1417, 0,110653,339289,339750,342980,348734, +chr21 18211407 18561558 uc002yku.1 0 + 18550740 18560341 0 5 181,310,158,87,1417, 0,339289,339750,342980,348734, +chr21 18539020 18561558 uc002ykv.1 0 + 18539411 18560226 0 6 470,310,158,87,103,1417, 0,11676,12137,15367,17958,21121, +chr21 18563560 18697844 uc002ykw.1 0 - 18564156 18697810 0 25 752,140,96,182,175,50,96,133,111,141,126,90,136,151,106,150,141,107,109,132,36,152,68,131,179, 0,5824,9591,11667,24897,25230,28361,43572,45773,57059,59796,62711,72040,74133,74582,83530,84350,90384,95767,102820,109910,114254,128506,128826,134105, +chr21 18855455 19032214 uc010glf.1 0 - 18855455 18855455 0 4 425,58,174,102, 0,2048,8971,176657, +chr21 18855455 19054001 uc002ykx.2 0 - 18855455 18855455 0 4 425,94,102,39, 0,28260,176657,198507, +chr21 21036784 21097287 uc002yky.2 0 - 21036784 21036784 0 8 1238,107,130,120,126,92,197,104, 0,14715,35822,36047,38753,38974,39654,60399, +chr21 21036784 21097287 uc002ykz.2 0 - 21036784 21036784 0 8 1238,130,120,126,92,140,53,104, 0,35822,36047,38753,38974,39711,43440,60399, +chr21 21036784 21097287 uc002yla.2 0 - 21036784 21036784 0 7 1238,130,126,92,197,53,104, 0,35822,38753,38974,39654,43440,60399, +chr21 21036784 21097287 uc002ylb.2 0 - 21036784 21036784 0 7 1238,130,126,92,136,53,104, 0,35822,38753,38974,39711,43440,60399, +chr21 21036784 21097287 uc002ylc.2 0 - 21036784 21036784 0 7 1238,130,120,126,92,140,104, 0,35822,36047,38753,38974,39711,60399, +chr21 21292503 21833085 uc002yld.1 0 + 21292752 21832149 0 18 304,75,207,144,138,118,161,146,151,188,97,174,120,122,181,205,120,1048, 0,282265,285881,287956,293791,326070,337192,340076,375550,411961,420160,433795,468294,470350,478979,510539,536225,539534, +chr21 22041175 22091604 uc002yle.2 0 + 22041175 22041175 0 5 59,290,81,93,235, 0,1410,37988,39314,50194, +chr21 22303349 22392649 uc002ylf.2 0 - 22303349 22303349 0 6 199,111,216,164,58,147, 0,7140,32060,33785,87369,89153, +chr21 22392806 22410718 uc002ylg.1 0 + 22392806 22392806 0 6 100,103,56,139,135,193, 0,10834,13154,16143,16361,17719, +chr21 22462158 22462605 uc002ylh.1 0 - 22462158 22462158 0 1 447, 0, +chr21 24722924 24784492 uc002yli.1 0 + 24722924 24722924 0 6 165,181,185,119,63,2195, 0,9513,12429,13055,56883,59373, +chr21 25134734 25351923 uc002ylj.2 0 + 25134734 25134734 0 4 179,151,76,2306, 0,4229,189233,214883, +chr21 25680009 25725884 uc002ylk.1 0 - 25680009 25680009 0 5 513,93,96,244,524, 0,34881,38727,43939,45351, +chr21 25680009 25725884 uc010glg.1 0 - 25680009 25680009 0 4 513,93,244,524, 0,34881,43939,45351, +chr21 25856312 25869344 uc002ylm.2 0 + 25856312 25856312 0 3 128,85,1269, 0,7707,11763, +chr21 25856375 25869344 uc002yll.1 0 + 25856375 25856375 0 1 12969, 0, +chr21 25879838 25901672 uc002yln.1 0 - 25879933 25901658 0 11 99,89,48,154,66,113,68,100,140,207,87, 0,2045,3179,7156,8237,11646,14143,15712,18140,20793,21747, +chr21 25879838 25901672 uc002ylo.1 0 - 25879889 25901658 0 10 99,48,154,66,113,68,100,140,207,87, 0,3179,7156,8237,11646,14143,15712,18140,20793,21747, +chr21 25933459 26009106 uc002ylp.1 0 + 25934004 26008855 0 10 612,66,108,153,203,100,108,16,43,284, 0,44606,50589,54479,59400,62893,66702,70157,73063,75363, +chr21 25933459 26009106 uc002ylq.1 0 + 25933459 25933459 0 10 612,66,108,153,203,96,108,16,43,284, 0,44606,50589,54479,59400,62893,66702,70157,73063,75363, +chr21 25933459 26009106 uc002ylr.1 0 + 25934004 26008855 0 9 612,66,108,153,203,100,112,43,284, 0,44606,50589,54479,59400,62893,66702,73063,75363, +chr21 25933459 26009106 uc010glh.1 0 + 25933459 25933459 0 10 612,66,108,153,203,100,112,202,43,284, 0,44606,50589,54479,59400,62893,66702,72090,73063,75363, +chr21 25933459 26009106 uc010gli.1 0 + 25934004 26008850 0 8 612,66,108,153,203,100,112,284, 0,44606,50589,54479,59400,62893,66702,75363, +chr21 26018661 26029836 uc002yls.1 0 - 26018821 26023976 0 4 198,125,171,666, 0,746,5151,10509, +chr21 26018661 26029836 uc002ylt.1 0 - 26018821 26023976 0 4 198,125,171,168, 0,746,5151,11007, +chr21 26018661 26029836 uc002ylu.1 0 - 26018821 26023976 0 4 198,125,171,802, 0,746,5151,10373, +chr21 26018661 26029836 uc002ylv.1 0 - 26018821 26029137 0 4 198,125,171,716, 0,746,5151,10459, +chr21 26018661 26029836 uc002ylw.1 0 - 26018821 26023976 0 4 198,125,171,340, 0,746,5151,10835, +chr21 26028751 26066642 uc002ylx.2 0 + 26035780 26063414 0 10 501,103,145,85,246,195,54,141,193,3457, 0,7003,10640,14466,17419,23440,27742,29640,30025,34434, +chr21 26029199 26066642 uc002yly.2 0 + 26035780 26063414 0 10 561,103,145,85,246,195,54,141,193,3457, 0,6555,10192,14018,16971,22992,27294,29192,29577,33986, +chr21 26174731 26465003 uc002ylz.1 0 - 26175851 26464809 0 18 1222,147,101,54,222,100,129,159,75,134,57,168,203,194,113,130,168,251, 0,11173,17024,24475,31192,74043,75080,94522,95406,101796,116814,119469,141295,170455,172691,209398,231435,290021, +chr21 26174731 26465003 uc002yma.1 0 - 26175851 26464809 0 17 1222,147,101,54,222,100,129,159,75,134,168,203,194,113,130,168,251, 0,11173,17024,24475,31192,74043,75080,94522,95406,101796,119469,141295,170455,172691,209398,231435,290021, +chr21 26174731 26465003 uc002ymb.1 0 - 26175851 26464809 0 16 1222,147,101,54,222,100,129,159,75,134,203,194,113,130,168,251, 0,11173,17024,24475,31192,74043,75080,94522,95406,101796,141295,170455,172691,209398,231435,290021, +chr21 26174731 26465003 uc010glj.1 0 - 26175851 26464809 0 15 1222,147,101,54,222,100,129,159,75,134,203,194,113,130,251, 0,11173,17024,24475,31192,74043,75080,94522,95406,101796,141295,170455,172691,209398,290021, +chr21 26316026 26434649 uc010glk.1 0 - 26316027 26434383 0 6 203,194,113,130,168,308, 0,29160,31396,68103,90140,118315, +chr21 26460085 26461513 uc002ymc.1 0 - 26460085 26460085 0 1 1428, 0, +chr21 26760398 26867452 uc002ymd.1 0 - 26762690 26867130 0 4 2423,158,103,395, 0,14063,100057,106659, +chr21 26762117 26867452 uc002yme.2 0 - 26762690 26867130 0 4 707,158,103,395, 0,12344,98338,104940, +chr21 27130476 27139599 uc002ymf.1 0 - 27131768 27139144 0 9 1992,176,176,187,287,168,133,347,1185, 0,2152,3300,3588,3989,4711,5571,6052,7938, +chr21 27212111 27260703 uc002ymg.1 0 - 27218242 27260581 0 8 6699,176,176,184,284,168,133,1226, 0,11964,14082,14939,16544,25458,36817,47366, +chr21 27653075 27742769 uc002ymh.2 0 - 27653075 27653075 0 4 2271,86,43,202, 0,39594,40646,89492, +chr21 28307571 28317143 uc002ymj.2 0 + 28307571 28307571 0 2 51,257, 0,9315, +chr21 28342603 28431799 uc002ymk.1 0 + 28342603 28342603 0 5 124,220,93,395,920, 0,54136,82116,86900,88276, +chr21 28410287 28522857 uc002yml.2 0 - 28410287 28410287 0 6 3777,116,66,109,108,306, 0,47504,53980,96142,109786,112264, +chr21 28833510 28834547 uc002ymm.2 0 + 28833510 28833510 0 2 211,302, 0,735, +chr21 28833510 28834547 uc002ymn.2 0 + 28833510 28833510 0 2 567,302, 0,735, +chr21 29166383 29179564 uc002ymo.1 0 - 29170577 29179538 0 6 4301,142,84,91,87,160, 0,6001,7679,9969,10794,13021, +chr21 29166383 29179564 uc002ymp.1 0 - 29170577 29179538 0 5 4301,142,91,87,160, 0,6001,9969,10794,13021, +chr21 29166384 29179564 uc002ymq.1 0 - 29166384 29166384 0 7 548,180,142,84,91,87,160, 0,4120,6000,7678,9968,10793,13020, +chr21 29222336 29287095 uc002ymr.1 0 - 29224640 29286997 0 30 2367,168,195,221,172,187,75,238,214,145,136,143,105,160,187,145,154,240,190,42,810,136,191,174,181,53,231,99,204,140, 0,3011,4326,6965,8382,13076,15118,15523,16239,17663,18008,19320,24016,25073,28618,29188,30242,31314,32373,37721,38226,41322,42408,43127,52975,54172,56547,57994,58586,64619, +chr21 29260562 29281126 uc010gll.1 0 - 29260562 29260562 0 10 810,372,136,191,174,181,53,231,99,204, 0,1232,3096,4182,4901,14749,15946,18321,19768,20360, +chr21 29299950 29313554 uc002yms.1 0 - 29300608 29313469 0 5 893,363,68,227,152, 0,2002,2481,2636,13452, +chr21 29299950 29313554 uc002ymt.1 0 - 29300608 29302793 0 6 893,363,68,227,98,152, 0,2002,2481,2636,3836,13452, +chr21 29299950 29313554 uc002ymu.1 0 - 29299950 29299950 0 4 893,363,227,152, 0,2002,2636,13452, +chr21 29299950 29313554 uc002ymv.1 0 - 29300608 29302553 0 4 893,363,382,152, 0,2002,2481,13452, +chr21 29318808 29348678 uc002ymw.1 0 + 29322105 29348379 0 19 161,63,102,179,104,104,188,96,131,88,79,92,57,177,655,95,87,157,421, 0,1092,3256,5978,10220,11654,12659,13718,14409,14864,15992,17396,17855,18806,22050,24144,25475,29185,29449, +chr21 29318808 29348678 uc002ymy.1 0 + 29322105 29348379 0 18 161,102,179,104,104,188,96,131,88,79,92,57,177,655,95,87,157,421, 0,3256,5978,10220,11654,12659,13718,14409,14864,15992,17396,17855,18806,22050,24144,25475,29185,29449, +chr21 29318808 29348678 uc002ymx.1 0 + 29322105 29348379 0 18 161,102,179,104,104,185,96,131,88,79,92,57,177,655,95,87,157,421, 0,3256,5978,10220,11654,12662,13718,14409,14864,15992,17396,17855,18806,22050,24144,25475,29185,29449, +chr21 29350518 29357059 uc002ymz.1 0 - 29350666 29356379 0 5 226,120,165,72,740, 0,4214,4926,5169,5801, +chr21 29350518 29367827 uc002yna.1 0 - 29350666 29363692 0 15 226,120,165,72,116,88,67,179,138,62,181,150,80,91,130, 0,4214,4926,5169,5801,6001,6163,7025,8641,10389,10564,11229,13096,13920,17179, +chr21 29350518 29367881 uc002ynb.1 0 - 29350666 29367782 0 15 226,120,165,72,116,88,67,179,138,62,181,150,80,91,159, 0,4214,4926,5169,5801,6001,6163,7025,8641,10389,10564,11229,13096,13920,17204, +chr21 29350518 29367881 uc002ync.1 0 - 29350666 29367782 0 15 226,120,165,72,116,88,67,179,138,62,174,154,80,91,159, 0,4214,4926,5169,5801,6001,6163,7025,8641,10389,10564,11225,13096,13920,17204, +chr21 29350518 29367881 uc010glm.1 0 - 29350666 29367782 0 14 226,120,165,72,116,88,67,179,138,62,154,80,91,159, 0,4214,4926,5169,5801,6001,6163,7025,8641,10389,11225,13096,13920,17204, +chr21 29371824 29470073 uc002ynd.1 0 + 29371824 29371824 0 10 81,105,76,94,143,129,109,62,116,1170, 0,8180,13868,14035,14806,53162,55673,71556,82308,97079, +chr21 29371824 29470073 uc010gln.1 0 + 29371824 29371824 0 9 81,105,76,94,143,109,62,116,1170, 0,8180,13868,14035,14806,55673,71556,82308,97079, +chr21 29371824 29470073 uc002yne.1 0 + 29380052 29469084 0 8 81,105,76,94,143,62,116,1170, 0,8180,13868,14035,14806,71556,82308,97079, +chr21 29374743 29470073 uc002ynf.1 0 + 29380052 29469084 0 9 157,72,105,76,94,143,62,116,1170, 0,4520,5261,10949,11116,11887,68637,79389,94160, +chr21 29416245 29470073 uc010glo.1 0 + 29454165 29469084 0 4 160,62,116,1170, 0,27135,37887,52658, +chr21 29424835 29470073 uc002yng.1 0 + 29427536 29469084 0 5 280,109,62,116,1170, 0,2662,18545,29297,44068, +chr21 29439770 29470073 uc010glp.1 0 + 29439770 29439770 0 4 129,62,116,1170, 0,3610,14362,29133, +chr21 29487671 29582396 uc002ynh.2 0 + 29487671 29487671 0 4 231,146,66,221, 0,635,35481,94504, +chr21 29487685 29582396 uc002yni.2 0 + 29487685 29487685 0 2 767,221, 0,94490, +chr21 29593090 29640340 uc002ynj.1 0 + 29615472 29637025 0 5 55,294,1335,207,3750, 0,22322,27160,30588,43500, +chr21 29593607 29640340 uc002ynk.1 0 + 29615472 29637025 0 5 183,294,1335,207,3750, 0,21805,26643,30071,42983, +chr21 29599430 29656086 uc002ynl.1 0 + 29615472 29645921 0 8 84,294,1335,207,180,85,213,343, 0,15982,20820,24248,46395,47340,55792,56313, +chr21 29831124 30234153 uc002ynn.1 0 - 29831421 30233689 0 16 453,251,226,218,119,224,204,114,108,144,174,54,182,258,168,582, 0,18119,24691,40030,44491,50432,51905,54178,61896,105892,114184,117876,136049,152794,156961,402447, +chr21 29847736 30234153 uc002yno.1 0 - 29847746 30233689 0 17 160,251,226,218,119,224,204,114,45,108,144,174,54,182,258,168,582, 0,1507,8079,23418,27879,33820,35293,37566,42980,45284,89280,97572,101264,119437,136182,140349,385835, +chr21 29875615 30234153 uc010glq.1 0 - 29875616 30233689 0 10 119,224,204,114,108,144,174,54,182,582, 0,5941,7414,9687,17405,61401,69693,73385,91558,357956, +chr21 29890230 29924938 uc002ynp.1 0 + 29890230 29890230 0 3 739,125,209, 0,1530,34499, +chr21 29892990 30234153 uc002ynr.2 0 - 29892993 30233689 0 8 138,144,174,54,182,258,168,582, 0,44026,52318,56010,74183,90928,95095,340581, +chr21 30043127 30058182 uc002yns.1 0 + 30043127 30043127 0 3 208,180,415, 0,9893,14640, +chr21 30460131 30460806 uc002ynt.1 0 - 30460131 30460806 0 1 675, 0, +chr21 30508200 30510189 uc002ynu.1 0 - 30509436 30510114 0 1 1989, 0, +chr21 30575497 30577147 uc002ynv.1 0 - 30576356 30577121 0 1 1650, 0, +chr21 30583333 30583703 uc010glr.1 0 - 30583370 30583679 0 1 370, 0, +chr21 30613320 30614478 uc002ynw.1 0 - 30613591 30614224 0 1 1158, 0, +chr21 30631201 30631883 uc002ynx.1 0 - 30631233 30631857 0 1 682, 0, +chr21 30642587 30642795 uc002yny.1 0 - 30642597 30642795 0 1 208, 0, +chr21 30665579 30666428 uc002ynz.2 0 - 30665874 30666402 0 1 849, 0, +chr21 30690262 30691009 uc002yoa.1 0 + 30690275 30690794 0 1 747, 0, +chr21 30719581 30720101 uc002yob.1 0 - 30719582 30720101 0 1 520, 0, +chr21 30724464 30724947 uc002yoc.1 0 + 30724464 30724947 0 1 483, 0, +chr21 30734516 30734969 uc002yod.1 0 + 30734516 30734930 0 1 453, 0, +chr21 30774234 30774507 uc002yoe.1 0 - 30774234 30774507 0 1 273, 0, +chr21 30781379 30781538 uc002yof.1 0 - 30781379 30781538 0 1 159, 0, +chr21 30785652 30786146 uc002yog.1 0 - 30785900 30786146 0 1 494, 0, +chr21 30791044 30791299 uc002yoh.1 0 - 30791044 30791299 0 1 255, 0, +chr21 30796060 30796279 uc002yoi.1 0 - 30796060 30796279 0 1 219, 0, +chr21 30835724 30836052 uc002yok.1 0 - 30835846 30836023 0 1 328, 0, +chr21 30855287 30855479 uc002yol.1 0 - 30855287 30855479 0 1 192, 0, +chr21 30886629 30887245 uc002yom.1 0 + 30886635 30886968 0 1 616, 0, +chr21 30892875 30893064 uc002yon.1 0 - 30892875 30893064 0 1 189, 0, +chr21 30895310 30895457 uc002yoo.1 0 + 30895310 30895457 0 1 147, 0, +chr21 30907875 30908094 uc002yop.1 0 - 30907878 30908094 0 1 219, 0, +chr21 30910644 30910815 uc002yoq.1 0 + 30910644 30910815 0 1 171, 0, +chr21 30929453 30929651 uc002yor.1 0 + 30929453 30929651 0 1 198, 0, +chr21 30937053 30937326 uc010gls.1 0 + 30937078 30937213 0 1 273, 0, +chr21 31041139 31041391 uc002yos.1 0 - 31041139 31041391 0 1 252, 0, +chr21 31049327 31049567 uc002yot.1 0 - 31049327 31049567 0 1 240, 0, +chr21 31106885 31107441 uc002you.1 0 - 31107217 31107409 0 1 556, 0, +chr21 31174834 31175745 uc002yov.1 0 - 31175222 31175714 0 1 911, 0, +chr21 31332348 31332666 uc010glt.1 0 - 31332441 31332633 0 1 318, 0, +chr21 31412606 31853161 uc002yow.1 0 - 31414556 31561159 0 29 2420,173,88,103,59,109,119,180,109,126,69,180,104,225,87,82,105,171,75,147,186,225,173,448,974,177,180,53,51, 0,6104,8647,11795,12472,17515,22700,22907,28477,34218,34648,35829,46543,64002,68581,76804,84488,91625,94978,99133,104986,107306,127068,133322,147590,158312,220822,345560,440504, +chr21 31506817 31854161 uc002yox.1 0 - 31507554 31546163 0 9 842,147,186,225,173,448,180,53,59, 0,4922,10775,13095,32857,39111,126611,251349,347285, +chr21 31853428 31854471 uc002yoy.2 0 + 31853444 31854300 0 2 351,271, 0,772, +chr21 31948741 31953684 uc002yoz.1 0 - 31948741 31948741 0 3 870,294,104, 0,3376,4839, +chr21 31953805 31963114 uc002ypa.1 0 + 31953953 31962762 0 5 220,97,70,118,460, 0,4168,6827,7636,8849, +chr21 31953849 31963114 uc002ypb.1 0 + 31953953 31962762 0 5 119,97,70,118,460, 0,4124,6783,7592,8805, +chr21 31953892 31963114 uc002ypc.1 0 + 31953892 31953892 0 5 1000,97,70,118,460, 0,4081,6740,7549,8762, +chr21 31965417 32026133 uc002ypd.1 0 - 31965582 32025876 0 20 1121,192,87,166,158,157,114,101,191,86,168,109,182,177,143,136,162,45,84,287, 0,13815,14164,14334,17073,19563,20583,21115,22060,22970,23579,24879,25335,29761,30542,31010,32531,34189,35040,60429, +chr21 31965417 32026133 uc002ype.1 0 - 31965582 32025876 0 20 1121,126,87,166,158,157,114,101,191,86,168,109,182,177,143,136,162,45,84,287, 0,13815,14164,14334,17073,19563,20583,21115,22060,22970,23579,24879,25335,29761,30542,31010,32531,34189,35040,60429, +chr21 31965417 32026133 uc010glu.1 0 - 31965582 32025876 0 19 1121,192,87,166,158,157,114,101,191,86,168,109,182,177,143,136,162,84,287, 0,13815,14164,14334,17073,19563,20583,21115,22060,22970,23579,24879,25335,29761,30542,31010,32531,35040,60429, +chr21 31978178 31996102 uc002ypf.1 0 - 31979158 31990386 0 14 1246,87,166,158,157,114,101,191,86,168,109,168,177,143, 0,1403,1573,4312,6802,7822,8354,9299,10209,10818,12118,12574,17000,17781, +chr21 31994942 32026133 uc002ypg.1 0 - 31995013 32025876 0 7 413,143,136,162,45,84,287, 0,1017,1485,3006,4664,5515,30904, +chr21 32167498 32298248 uc002yph.1 0 + 32167858 32293368 0 11 621,293,56,136,128,136,163,84,48,181,5539, 0,51152,66849,72720,85527,94934,101239,110211,116814,122453,125211, +chr21 32562400 32573247 uc002ypi.1 0 - 32563218 32573196 0 5 899,97,123,67,385, 0,1488,2188,6611,10462, +chr21 32585994 32606470 uc002ypj.1 0 + 32593153 32606178 0 5 37,140,116,100,605, 0,1180,7149,14827,19871, +chr21 32585994 32606470 uc010glv.1 0 + 32585994 32585994 0 4 37,140,100,605, 0,1180,14827,19871, +chr21 32585994 32608965 uc002ypk.1 0 + 32593153 32608835 0 5 37,140,116,100,233, 0,1180,7149,14827,22738, +chr21 32593031 32606470 uc002ypl.1 0 + 32593153 32606178 0 3 228,100,605, 0,7790,12834, +chr21 32600647 32602916 uc002ypm.2 0 - 32600647 32600647 0 2 361,216, 0,2053, +chr21 32607648 32687021 uc002ypn.1 0 - 32609099 32678641 0 39 1633,600,242,198,110,144,107,112,161,103,172,64,111,194,59,187,202,856,180,219,197,171,139,117,120,113,117,130,174,138,196,125,126,86,97,133,152,140,73, 0,2999,4209,5749,7063,8333,9010,11023,11761,19848,20694,23625,23935,25238,27997,31101,31905,33487,35835,37235,39241,40464,41390,41980,44068,46327,47538,48423,49687,53149,54934,59038,60178,61929,64976,69953,70844,72076,79300, +chr21 32671366 32671502 uc002ypo.1 0 - 32671366 32671366 0 1 136, 0, +chr21 32706622 32762234 uc002ypq.1 0 + 32707032 32762080 0 4 570,197,124,360, 0,40868,45153,55252, +chr21 32706622 32809568 uc002ypr.1 0 + 32707032 32809371 0 8 570,197,124,153,144,81,90,574, 0,40868,45153,55252,82585,88973,91484,102372, +chr21 32706622 32809568 uc002yps.1 0 + 32706622 32706622 0 7 570,124,153,144,81,90,574, 0,45153,55252,82585,88973,91484,102372, +chr21 32706622 32809568 uc010glw.1 0 + 32707032 32809371 0 8 570,197,124,153,144,72,90,574, 0,40868,45153,55252,82585,88973,91484,102372, +chr21 32706622 32809568 uc002ypt.1 0 + 32706622 32706622 0 6 570,153,144,124,90,574, 0,55252,82585,88973,91484,102372, +chr21 32746363 32809568 uc002ypu.1 0 + 32747615 32809371 0 7 1324,124,153,144,81,90,574, 0,5412,15511,42844,49232,51743,62631, +chr21 32866419 32870062 uc002ypv.1 0 - 32866419 32866419 0 4 357,85,29,1306, 0,1045,1857,2337, +chr21 32870732 32879714 uc002ypw.2 0 - 32870954 32878485 0 5 372,138,216,145,113, 0,2142,5648,7609,8869, +chr21 32876380 32901897 uc002ypx.1 0 - 32876380 32901883 0 3 216,159,68, 0,21925,25449, +chr21 32876380 32906537 uc002ypy.1 0 - 32876380 32906424 0 7 216,96,132,159,68,168,252, 0,20072,20961,21925,25449,27638,29905, +chr21 32876380 32906537 uc002ypz.1 0 - 32876380 32906424 0 6 216,132,159,68,168,252, 0,20961,21925,25449,27638,29905, +chr21 32895854 32898694 uc002yqa.2 0 - 32897269 32898482 0 2 1619,389, 0,2451, +chr21 32895854 32906537 uc002yqb.2 0 - 32897269 32906424 0 5 1619,159,68,168,252, 0,2451,5975,8164,10431, +chr21 32895977 32906537 uc002yqc.1 0 - 32896043 32906424 0 7 177,96,132,159,68,168,252, 0,475,1364,2328,5852,8041,10308, +chr21 32895977 32906537 uc002yqd.1 0 - 32896043 32906424 0 6 177,132,159,68,168,252, 0,1364,2328,5852,8041,10308, +chr21 32895977 32906537 uc010glx.1 0 - 32896043 32904096 0 6 177,96,132,159,168,252, 0,475,1364,2328,8041,10308, +chr21 32922943 32936331 uc002yqe.2 0 - 32925175 32925772 0 6 3039,24,218,109,71,56, 0,6098,10145,10908,13133,13332, +chr21 32922943 33022105 uc002yqf.1 0 - 32929044 33021077 0 32 3039,24,218,109,71,39,39,144,210,163,79,216,118,157,159,193,141,85,192,24,157,153,82,170,97,62,84,226,268,87,146,87, 0,6098,10145,10908,13133,13332,16205,16883,17630,21421,24525,27924,28240,28953,36150,37180,37670,41525,44577,47569,49882,52733,55275,56985,58215,59543,65465,66294,71075,73198,98010,99075, +chr21 32922943 33022105 uc002yqg.1 0 - 32925175 33021077 0 28 3039,218,109,71,144,210,163,79,216,118,157,159,193,141,85,192,166,153,82,170,97,62,84,226,268,87,146,87, 0,10145,10908,13133,16883,17630,21421,24525,27924,28240,28953,36150,37180,37670,41525,44577,49882,52733,55275,56985,58215,59543,65465,66294,71075,73198,98010,99075, +chr21 32922943 33022148 uc002yqh.1 0 - 32925175 33021077 0 32 3039,218,109,71,39,48,39,144,210,163,79,216,118,157,159,193,141,85,192,24,157,153,82,170,97,62,84,226,268,87,146,21, 0,10145,10908,13133,13332,14647,16205,16883,17630,21421,24525,27924,28240,28953,36150,37180,37670,41525,44577,47569,49882,52733,55275,56985,58215,59543,65465,66294,71075,73198,98010,99184, +chr21 32922943 33022148 uc002yqi.1 0 - 32929044 33021077 0 33 3039,24,218,109,71,39,48,39,144,210,163,79,216,118,157,159,193,141,85,192,24,157,153,82,170,97,62,84,226,268,87,146,21, 0,6098,10145,10908,13133,13332,14647,16205,16883,17630,21421,24525,27924,28240,28953,36150,37180,37670,41525,44577,47569,49882,52733,55275,56985,58215,59543,65465,66294,71075,73198,98010,99184, +chr21 33022296 33027093 uc002yqj.1 0 + 33022296 33022296 0 2 2547,393, 0,4404, +chr21 33022296 33037303 uc002yqk.2 0 + 33022296 33022296 0 4 2547,69,70,860, 0,5474,10157,14147, +chr21 33028080 33046092 uc002yql.1 0 - 33029131 33045434 0 10 1169,155,147,67,77,122,145,200,116,792, 0,3355,4274,9349,9779,10893,11675,14600,17018,17220, +chr21 33028080 33050976 uc002yqm.1 0 - 33029131 33045389 0 11 1169,155,147,67,77,122,145,200,116,100,1582, 0,3355,4274,9349,9779,10893,11675,14600,17018,17220,21314, +chr21 33028080 33066040 uc002yqn.1 0 - 33029131 33065850 0 18 1169,155,147,67,77,122,145,200,116,100,124,190,218,104,222,177,129,533, 0,3355,4274,9349,9779,10893,11675,14600,17018,17220,21331,25181,25878,27160,28197,30449,35915,37427, +chr21 33028080 33066040 uc002yqo.1 0 - 33028080 33028080 0 18 1169,155,147,67,77,122,145,200,116,100,141,190,218,104,222,177,129,533, 0,3355,4274,9349,9779,10893,11675,14600,17018,17220,21314,25181,25878,27160,28197,30449,35915,37427, +chr21 33035520 33066040 uc002yqp.1 0 - 33035690 33065850 0 16 284,67,77,122,145,200,116,100,124,190,218,104,222,177,129,533, 0,1909,2339,3453,4235,7160,9578,9780,13891,17741,18438,19720,20757,23009,28475,29987, +chr21 33049593 33066040 uc002yqq.1 0 - 33050523 33065850 0 8 957,190,218,104,222,177,129,533, 0,3668,4365,5647,6684,8936,14402,15914, +chr21 33053537 33066040 uc002yqr.2 0 - 33053954 33065850 0 6 639,104,222,177,129,533, 0,1703,2740,4992,10458,11970, +chr21 33066281 33091884 uc002yqs.2 0 + 33066281 33066281 0 4 209,123,90,766, 0,12697,16512,24837, +chr21 33066306 33091884 uc002yqt.2 0 + 33066306 33066306 0 2 148,766, 0,24812, +chr21 33066387 33091884 uc002yqu.2 0 + 33066387 33066387 0 4 115,123,90,766, 0,12591,16406,24731, +chr21 33084854 33107876 uc002yqv.1 0 - 33087858 33088602 0 3 3812,81,105, 0,19899,22917, +chr21 33084854 33107876 uc010gly.1 0 - 33087858 33088602 0 4 3812,75,81,105, 0,16967,19899,22917, +chr21 33084854 33107876 uc002yqw.1 0 - 33087858 33088602 0 2 3812,105, 0,22917, +chr21 33087858 33088602 uc010glz.1 0 - 33087858 33088602 0 1 744, 0, +chr21 33320108 33323370 uc002yqx.1 0 + 33321040 33322012 0 2 96,2392, 0,870, +chr21 33321040 33322012 uc002yqy.2 0 + 33321040 33322012 0 1 972, 0, +chr21 33364442 33366596 uc002yqz.1 0 + 33364470 33365238 0 1 2154, 0, +chr21 33459786 33464411 uc002yra.1 0 - 33459786 33459786 0 4 81,139,138,96, 0,2831,4084,4529, +chr21 33524100 33556932 uc002yrb.1 0 + 33536097 33556891 0 9 291,92,42,124,173,146,169,131,197, 0,11960,13747,15025,16792,18783,22736,30671,32635, +chr21 33524100 33556932 uc002yrc.1 0 + 33536097 33556891 0 9 291,138,42,124,173,146,169,131,197, 0,11914,13747,15025,16792,18783,22736,30671,32635, +chr21 33524100 33558690 uc002yrd.1 0 + 33536097 33557675 0 9 291,92,42,124,173,146,169,131,1723, 0,11960,13747,15025,16792,18783,22736,30671,32867, +chr21 33524100 33558690 uc002yre.1 0 + 33536097 33557675 0 9 291,138,42,124,173,146,169,131,1723, 0,11914,13747,15025,16792,18783,22736,30671,32867, +chr21 33524100 33558690 uc002yrf.1 0 + 33536097 33556978 0 8 291,138,42,124,173,146,169,1723, 0,11914,13747,15025,16792,18783,22736,32867, +chr21 33539667 33556932 uc002yrg.1 0 + 33541064 33556891 0 6 313,173,146,169,131,197, 0,1225,3216,7169,15104,17068, +chr21 33542883 33577416 uc002yrh.1 0 + 33542939 33577415 0 6 146,169,124,158,167,148, 0,3953,19685,27887,31043,34385, +chr21 33542883 33577416 uc002yri.1 0 + 33546973 33577415 0 5 146,169,158,167,148, 0,3953,27887,31043,34385, +chr21 33558047 33560435 uc002yrj.1 0 - 33558047 33558047 0 2 2030,198, 0,2190, +chr21 33560541 33591390 uc002yrk.1 0 + 33560640 33590532 0 7 148,124,158,167,148,158,1032, 0,2027,10229,13385,16727,21737,29817, +chr21 33562102 33591390 uc002yrl.1 0 + 33562513 33590532 0 6 590,158,167,148,158,1032, 0,8668,11824,15166,20176,28256, +chr21 33619083 33653998 uc002yrn.1 0 + 33619230 33649725 0 11 223,124,176,155,142,115,200,155,151,146,4507, 0,10616,16091,18360,18627,20338,24183,24481,27850,28730,30408, +chr21 33697071 33731698 uc002yrp.2 0 + 33697719 33731139 0 7 721,133,206,149,160,158,694, 0,11993,18585,23989,29282,29819,33933, +chr21 33697071 33731698 uc002yrq.2 0 + 33697719 33731139 0 8 721,57,133,206,149,160,158,694, 0,7940,11993,18585,23989,29282,29819,33933, +chr21 33697071 33731698 uc010gma.1 0 + 33715687 33731139 0 8 721,52,133,206,149,160,158,694, 0,7945,11993,18585,23989,29282,29819,33933, +chr21 33709055 33731698 uc002yrr.2 0 + 33715687 33731139 0 6 142,206,149,160,158,694, 0,6601,12005,17298,17835,21949, +chr21 33726662 33774151 uc002yrs.1 0 - 33726662 33726662 0 9 317,84,2082,58,93,68,113,140,137, 0,6728,16296,23241,27927,32856,34524,36301,47352, +chr21 33742958 33774151 uc002yrt.1 0 - 33744994 33763062 0 7 2082,58,93,68,113,140,137, 0,6945,11631,16560,18228,20005,31056, +chr21 33742958 33774151 uc010gmb.1 0 - 33742958 33742958 0 8 2082,58,94,93,68,113,140,137, 0,6945,7222,11631,16560,18228,20005,31056, +chr21 33782107 33785660 uc002yrv.1 0 - 33782403 33783570 0 2 1494,418, 0,3135, +chr21 33782107 33785893 uc002yrw.1 0 - 33782403 33783570 0 2 1494,115, 0,3671, +chr21 33782403 33783570 uc010gmc.1 0 - 33782403 33783570 0 1 1167, 0, +chr21 33798141 33836286 uc002yrx.1 0 - 33798300 33833491 0 22 351,116,142,131,138,207,153,252,199,110,95,232,169,86,88,126,69,112,175,96,186,46, 0,447,1596,2009,5818,7287,13024,13392,16399,16941,18223,20804,24201,24553,24884,26793,27523,28379,30613,31259,35205,38099, +chr21 33798141 33836995 uc002yry.1 0 - 33798300 33833491 0 22 351,116,142,131,138,207,153,252,199,110,95,232,169,86,88,126,69,112,175,96,186,160, 0,447,1596,2009,5818,7287,13024,13392,16399,16941,18223,20804,24201,24553,24884,26793,27523,28379,30613,31259,35205,38694, +chr21 33798141 33837006 uc002yrz.1 0 - 33798300 33833491 0 22 351,116,142,131,138,207,153,252,199,110,95,232,169,86,88,126,69,112,175,96,153,244, 0,447,1596,2009,5818,7287,13024,13392,16399,16941,18223,20804,24201,24553,24884,26793,27523,28379,30613,31259,35205,38621, +chr21 33798141 33837065 uc010gmd.1 0 - 33798300 33822394 0 22 351,116,142,131,138,207,153,252,199,110,95,232,169,90,88,126,69,112,175,96,186,299, 0,447,1596,2009,5818,7287,13024,13392,16399,16941,18223,20804,24201,24549,24884,26793,27523,28379,30613,31259,35205,38625, +chr21 33818186 33836286 uc002ysa.1 0 - 33818941 33833491 0 11 991,169,86,88,126,69,112,175,96,186,46, 0,4156,4508,4839,6748,7478,8334,10568,11214,15160,18054, +chr21 33837219 33851844 uc002ysb.1 0 + 33837268 33851727 0 5 126,167,5916,161,123, 0,3169,6432,14112,14502, +chr21 33837219 33854843 uc002ysc.1 0 + 33837268 33854307 0 7 126,167,5916,161,147,189,791, 0,3169,6432,14112,16186,16543,16833, +chr21 33837219 33871654 uc002ysd.2 0 + 33846434 33870752 0 13 126,167,1814,3144,161,147,189,111,117,148,72,116,1061, 0,3169,6432,9204,14112,16186,16543,24113,25927,30264,32552,32734,33374, +chr21 33837219 33871682 uc002yse.1 0 + 33837268 33870600 0 12 126,167,5916,161,147,189,111,117,148,72,116,1142, 0,3169,6432,14112,16186,16543,24113,25927,30264,32552,32734,33321, +chr21 33837219 33871682 uc002ysf.1 0 + 33837268 33870600 0 11 126,167,161,147,189,111,117,148,72,116,1142, 0,3169,14112,16186,16543,24113,25927,30264,32552,32734,33321, +chr21 33846423 33861642 uc002ysg.2 0 + 33846434 33861524 0 5 3144,161,147,189,310, 0,4908,6982,7339,14909, +chr21 33866544 33871654 uc002ysh.2 0 + 33867519 33870752 0 5 262,148,72,116,1061, 0,939,3227,3409,4049, +chr21 33869652 33880357 uc002ysi.1 0 - 33872482 33878830 0 9 332,146,213,199,105,82,179,137,204, 0,2822,3873,5825,6474,6688,8011,9113,10501, +chr21 33872080 33881778 uc002ysj.1 0 - 33872482 33876176 0 8 540,213,199,105,82,179,204,81, 0,1445,3397,4046,4260,6685,8073,9617, +chr21 33872080 33883137 uc010gme.1 0 - 33872482 33882817 0 9 540,213,199,105,82,179,179,204,641, 0,1445,3397,4046,4260,5583,6685,8073,10416, +chr21 33872080 33883137 uc002ysk.1 0 - 33872482 33882817 0 10 540,213,199,105,82,179,179,204,81,641, 0,1445,3397,4046,4260,5583,6685,8073,9617,10416, +chr21 33872080 33883137 uc002ysl.1 0 - 33872482 33876176 0 9 540,213,199,105,82,179,83,81,641, 0,1445,3397,4046,4260,6685,8073,9617,10416, +chr21 33872080 33889790 uc002ysm.1 0 - 33872482 33882817 0 13 540,213,199,105,82,179,179,204,81,641,81,210,259, 0,1445,3397,4046,4260,5583,6685,8073,9617,10416,11936,13257,17451, +chr21 33878765 34206573 uc002ysn.1 0 - 33878767 34201565 0 5 179,204,113,130,111, 0,1388,322749,324490,327697, +chr21 33883517 33936030 uc010gmf.1 0 - 33883997 33925727 0 13 580,46,106,122,99,112,134,69,45,73,78,72,174, 0,1820,6389,7938,9808,12892,14062,24196,27364,32654,35341,42144,52339, +chr21 33888837 33889792 uc002ysp.2 0 - 33888837 33888837 0 1 955, 0, +chr21 33889437 33891577 uc002ysq.2 0 - 33889437 33889437 0 2 267,122, 0,2018, +chr21 33889906 33936030 uc002ysr.1 0 - 33889907 33935420 0 12 106,122,99,112,134,69,45,73,78,72,127,174, 0,1549,3419,6503,7673,17807,20975,26265,28952,35755,45448,45950, +chr21 33889906 33936030 uc002yss.1 0 - 33889906 33889906 0 11 106,122,136,112,134,69,45,73,78,72,174, 0,1549,3419,6503,7673,17807,20975,26265,28952,35755,45950, +chr21 33889906 33936030 uc002yst.1 0 - 33889906 33889906 0 10 106,122,136,112,134,69,73,78,72,174, 0,1549,3419,6503,7673,17807,26265,28952,35755,45950, +chr21 33910469 33936030 uc002ysu.2 0 - 33910699 33925727 0 6 310,45,73,78,72,174, 0,412,5702,8389,15192,25387, +chr21 33933921 33936030 uc002ysv.2 0 - 33933921 33933921 0 3 443,127,174, 0,1433,1935, +chr21 33936653 34132672 uc002yth.2 0 + 33936653 33936653 0 28 236,60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,46,122,118,192,1512, 0,76318,78699,80109,92565,107664,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,175787,176761,184338,187144,191827,193961,194507, +chr21 33936653 34132672 uc002ysz.1 0 + 34013003 34131162 0 27 236,60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,122,118,192,1512, 0,76318,78699,80109,92565,107664,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,175787,176761,187144,191827,193961,194507, +chr21 33936653 34132672 uc010gmg.1 0 + 34013003 34131162 0 27 236,60,93,64,161,69,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,122,118,192,1512, 0,76318,78699,80109,92565,107775,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,175787,176761,187144,191827,193961,194507, +chr21 33936653 34132672 uc010gmh.1 0 + 33936653 33936653 0 26 236,60,93,64,161,69,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,83,122,118,192,1512, 0,76318,78699,80109,92565,107775,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,176761,187144,191827,193961,194507, +chr21 33936653 34132672 uc002ysw.1 0 + 34013003 34131162 0 30 236,60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,15,248,160,206,83,167,46,122,118,192,1512, 0,76318,78699,80109,92565,107664,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,159950,168495,171433,175787,176761,181007,184338,187144,191827,193961,194507, +chr21 33936653 34132672 uc010gmi.1 0 + 34013003 34131162 0 30 236,60,93,64,161,69,97,101,64,138,116,263,150,141,88,140,128,230,122,15,248,160,206,83,167,46,122,118,192,1512, 0,76318,78699,80109,92565,107775,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,159950,168495,171433,175787,176761,181007,184338,187144,191827,193961,194507, +chr21 33936653 34132672 uc010gmj.1 0 + 34044319 34131162 0 28 236,60,93,64,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,167,46,122,118,192,1512, 0,76318,78699,80109,107664,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,175787,176761,181007,184338,187144,191827,193961,194507, +chr21 33936653 34132672 uc002ysy.1 0 + 34013003 34131162 0 29 236,60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,167,46,122,118,192,1512, 0,76318,78699,80109,92565,107664,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,175787,176761,181007,184338,187144,191827,193961,194507, +chr21 33936653 34132672 uc002ysx.1 0 + 34013003 34131162 0 29 236,60,93,64,161,69,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,167,46,122,118,192,1512, 0,76318,78699,80109,92565,107775,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,175787,176761,181007,184338,187144,191827,193961,194507, +chr21 33936653 34183479 uc002yta.1 0 + 34013003 34182474 0 40 236,60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,15,248,160,206,83,167,46,122,118,192,122,107,184,99,168,213,122,83,84,174,1154, 0,76318,78699,80109,92565,107664,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,159950,168495,171433,175787,176761,181007,184338,187144,191827,193961,214256,216206,222671,224753,232874,239763,241070,242561,242959,243807,245672, +chr21 33936653 34183479 uc002ytb.1 0 + 34013003 34182474 0 39 236,60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,167,46,122,118,192,122,107,184,99,168,213,122,83,84,174,1154, 0,76318,78699,80109,92565,107664,109331,112818,119443,123395,125233,129581,132249,132488,138981,139514,151861,154899,157328,168495,171433,175787,176761,181007,184338,187144,191827,193961,214256,216206,222671,224753,232874,239763,241070,242561,242959,243807,245672, +chr21 34012971 34111788 uc002ytc.1 0 + 34013003 34111755 0 21 60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,384, 0,2381,3791,16247,31346,33013,36500,43125,47077,48915,53263,55931,56170,62663,63196,75543,78581,81010,92177,95115,98433, +chr21 34012971 34132672 uc002ytd.1 0 + 34012971 34012971 0 29 60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,167,46,83,122,118,192,1512, 0,2381,3791,16247,31346,33013,36500,43125,47077,48915,53263,55931,56170,62663,63196,75543,78581,81010,92177,95115,99469,100443,104689,108020,110170,110826,115509,117643,118189, +chr21 34012971 34132672 uc010gmk.1 0 + 34013003 34131162 0 27 60,93,64,161,69,97,101,64,138,116,263,150,141,88,140,128,230,122,15,248,160,206,83,122,118,192,1512, 0,2381,3791,16247,31457,33013,36500,43125,47077,48915,53263,55931,56170,62663,63196,75543,78581,81010,83632,92177,95115,99469,100443,110826,115509,117643,118189, +chr21 34012971 34132672 uc010gml.1 0 + 34012971 34012971 0 25 60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,83,122,118,192,1512, 0,2381,3791,16247,31346,33013,36500,43125,47077,48915,53263,55931,56170,62663,63196,75543,78581,81010,92177,95115,100443,110826,115509,117643,118189, +chr21 34012971 34183479 uc002ytj.2 0 + 34013003 34182474 0 37 60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,167,46,122,118,192,122,107,184,99,213,122,83,84,174,1154, 0,2381,3791,16247,31346,33013,36500,43125,47077,48915,53263,55931,56170,62663,63196,75543,78581,81010,92177,95115,99469,100443,104689,108020,110826,115509,117643,137938,139888,146353,148435,163445,164752,166243,166641,167489,169354, +chr21 34012971 34183479 uc010gmm.1 0 + 34012971 34012971 0 37 60,93,64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,248,160,206,83,46,122,118,192,122,107,184,99,168,213,122,83,84,174,1154, 0,2381,3791,16247,31346,33013,36500,43125,47077,48915,53263,55931,56170,62663,63196,75543,78581,81010,92177,95115,99469,100443,108020,110826,115509,117643,137938,139888,146353,148435,156556,163445,164752,166243,166641,167489,169354, +chr21 34016762 34132672 uc002yte.1 0 + 34029231 34131162 0 25 64,161,180,97,101,64,138,116,263,150,141,88,140,128,230,122,15,248,160,206,83,122,118,192,1512, 0,12456,27555,29222,32709,39334,43286,45124,49472,52140,52379,58872,59405,71752,74790,77219,79841,88386,91324,95678,96652,107035,111718,113852,114398, +chr21 34096603 34111788 uc002ytf.1 0 + 34096603 34096603 0 4 15,248,160,384, 0,8545,11483,14801, +chr21 34112440 34123224 uc002ytg.1 0 + 34112554 34123154 0 4 206,83,46,83, 0,974,8551,10701, +chr21 34123141 34151031 uc002yti.1 0 + 34123141 34123141 0 5 83,122,118,192,122, 0,656,5339,7473,27768, +chr21 34169527 34179696 uc002ytk.1 0 + 34169527 34169527 0 3 168,83,84, 0,9687,10085, +chr21 34169527 34180634 uc010gmn.1 0 + 34169527 34169527 0 5 168,122,83,84,174, 0,8196,9687,10085,10933, +chr21 34197626 34210028 uc002ytl.1 0 - 34197699 34209937 0 7 187,87,113,130,111,51,127, 0,482,3888,5629,8836,10997,12275, +chr21 34206462 34209898 uc002ytm.1 0 - 34206462 34206462 0 3 111,51,589, 0,2161,2847, +chr21 34225295 34265357 uc002ytn.2 0 + 34225295 34225295 0 3 621,86,1950, 0,14688,38112, +chr21 34367692 34400431 uc002yto.1 0 + 34389367 34391524 0 2 223,11400, 0,21339, +chr21 34367692 34437204 uc002ytp.2 0 + 34367870 34436770 0 3 223,140,627, 0,51818,68885, +chr21 34389367 34391524 uc002ytq.2 0 + 34389367 34391524 0 1 2157, 0, +chr21 34474917 34477415 uc002ytr.2 0 + 34474917 34474917 0 2 47,537, 0,1961, +chr21 34474917 34484090 uc002yts.1 0 + 34474917 34474917 0 2 47,1152, 0,8021, +chr21 34658192 34665310 uc002ytt.1 0 + 34664647 34665019 0 2 128,675, 0,6443, +chr21 34664647 34665019 uc010gmo.1 0 + 34664647 34665019 0 1 372, 0, +chr21 34669618 34683322 uc002ytu.2 0 + 34673673 34679810 0 4 118,89,167,526, 0,3978,10027,13178, +chr21 34669618 34696944 uc002ytv.2 0 + 34669618 34669618 0 4 118,89,189,686, 0,3978,24260,26640, +chr21 34669618 34696944 uc002ytw.2 0 + 34669618 34669618 0 5 118,89,167,189,686, 0,3978,10027,24260,26640, +chr21 34712882 34718134 uc002yty.1 0 - 34713385 34718007 0 2 916,134, 0,5118, +chr21 34740857 34749933 uc010gmp.1 0 - 34743412 34743802 0 2 2995,380, 0,8696, +chr21 34740857 34753772 uc002ytz.1 0 - 34743412 34743802 0 3 2995,83,76, 0,11964,12839, +chr21 34740857 34753772 uc010gmq.1 0 - 34743412 34743802 0 3 2995,111,76, 0,11964,12839, +chr21 34740857 34805483 uc010gmr.1 0 - 34743412 34743802 0 3 2995,111,215, 0,11964,64411, +chr21 34740857 34806443 uc002yua.1 0 - 34740857 34740857 0 4 2995,111,215,249, 0,11964,64411,65337, +chr21 34743412 34743802 uc010gms.1 0 - 34743412 34743802 0 1 390, 0, +chr21 34810653 34821131 uc002yub.1 0 - 34812251 34820917 0 4 1771,160,174,301, 0,5013,7051,10177, +chr21 34810653 34908012 uc002yuc.1 0 - 34812251 34907964 0 4 1771,160,174,57, 0,5013,7051,97302, +chr21 34810653 34908615 uc002yud.1 0 - 34812251 34817725 0 4 1771,160,174,169, 0,5013,7051,97793, +chr21 34810653 34909252 uc002yue.1 0 - 34812251 34909180 0 4 1771,160,174,324, 0,5013,7051,98275, +chr21 34963557 35012389 uc002yuf.1 0 + 34963557 35010650 0 6 1374,110,126,107,182,1901, 0,37890,38554,39310,39967,46931, +chr21 34963557 35012389 uc010gmt.1 0 + 34963557 35010650 0 7 1374,54,110,126,107,182,1901, 0,36637,37890,38554,39310,39967,46931, +chr21 35040013 35079036 uc002yug.2 0 + 35040013 35040013 0 3 170,66,2289, 0,36278,36734, +chr21 35081967 35182857 uc002yuh.1 0 - 35086301 35181279 0 6 4810,162,192,105,157,1848, 0,11500,46609,71673,92756,99042, +chr21 35081967 35182857 uc002yui.1 0 - 35086301 35181279 0 5 4810,162,105,157,1848, 0,11500,71673,92756,99042, +chr21 35081967 35343437 uc010gmu.1 0 - 35086301 35343066 0 9 4810,162,192,105,157,254,39,117,190, 0,11500,46609,71673,92756,99042,105124,261041,261280, +chr21 35081967 35343465 uc010gmv.1 0 - 35086301 35343066 0 9 4810,162,192,105,157,254,39,117,131, 0,11500,46609,71673,92756,99042,105124,261041,261367, +chr21 35081967 35343465 uc002yuj.2 0 - 35086301 35174835 0 7 4810,162,192,105,157,117,131, 0,11500,46609,71673,92756,261041,261367, +chr21 35081967 35343511 uc002yuk.2 0 - 35086301 35343066 0 8 4810,162,192,105,157,254,39,503, 0,11500,46609,71673,92756,99042,105124,261041, +chr21 35091579 35128768 uc002yul.1 0 - 35092221 35128676 0 3 680,162,192, 0,1888,36997, +chr21 35091579 35343125 uc002yum.1 0 - 35092221 35174835 0 5 680,162,105,157,117, 0,1888,62061,83144,251429, +chr21 35115443 35124138 uc002yun.1 0 - 35115443 35115443 0 2 420,120, 0,8575, +chr21 35115443 35182857 uc002yuo.1 0 - 35115834 35181279 0 5 420,192,105,157,1848, 0,13133,38197,59280,65566, +chr21 35117630 35120573 uc002yup.1 0 - 35117630 35117630 0 1 2943, 0, +chr21 35127127 35343465 uc010gmw.1 0 - 35128286 35343066 0 7 1641,105,157,254,39,117,131, 0,26513,47596,53882,59964,215881,216207, +chr21 35153500 35174880 uc002yur.1 0 - 35153500 35174835 0 2 245,157, 0,21223, +chr21 35153640 35153741 uc002yus.1 0 + 35153640 35153640 0 1 101, 0, +chr21 35181009 36278917 uc002yut.1 0 - 35181009 35181009 0 11 254,39,117,137,65,270,56,183,93,166,178, 0,6082,161999,178093,575119,693818,767978,977443,1083233,1094909,1097730, +chr21 36328708 36354789 uc002yuu.1 0 - 36328708 36328708 0 11 1420,167,124,81,82,175,430,38,96,109,275, 0,1544,3609,6034,7266,9241,11041,19042,22568,24275,25806, +chr21 36328708 36358576 uc002yuv.1 0 - 36330284 36353056 0 14 1420,167,124,81,82,175,430,89,38,96,109,275,61,195, 0,1544,3609,6034,7266,9241,11041,13767,19042,22568,24275,25806,28965,29673, +chr21 36328709 36354429 uc002yuw.1 0 - 36330284 36353056 0 10 1710,124,81,82,175,430,89,38,96,1446, 0,3608,6033,7265,9240,11040,13766,19041,22567,24274, +chr21 36328709 36354789 uc002yux.1 0 - 36330284 36351552 0 12 1710,124,81,82,175,430,89,38,96,94,158,275, 0,3608,6033,7265,9240,11040,13766,19041,22567,22842,24274,25805, +chr21 36337851 36354481 uc002yuy.1 0 - 36337926 36353056 0 7 273,430,89,38,96,158,32, 0,1898,4624,9899,13425,15132,16598, +chr21 36337851 36354481 uc002yuz.1 0 - 36337926 36351552 0 8 273,430,89,38,96,94,158,32, 0,1898,4624,9899,13425,13700,15132,16598, +chr21 36337851 36373557 uc002yva.1 0 - 36337926 36351552 0 8 273,430,89,38,96,94,109,85, 0,1898,4624,9899,13425,13700,15132,35621, +chr21 36364154 36365751 uc010gmx.1 0 + 36364283 36365365 0 2 418,634, 0,963, +chr21 36364154 36367332 uc002yvb.1 0 + 36364283 36367050 0 3 418,108,719, 0,963,2459, +chr21 36364154 36367334 uc010gmy.1 0 + 36364283 36366107 0 3 418,108,1352, 0,963,1828, +chr21 36425934 36450475 uc002yvc.1 0 - 36425934 36425934 0 4 1308,75,100,91, 0,1920,14489,24450, +chr21 36425934 36450475 uc002yvd.1 0 - 36425934 36425934 0 3 1308,100,91, 0,14489,24450, +chr21 36429132 36440730 uc002yve.1 0 + 36429360 36440680 0 3 517,108,487, 0,2860,11111, +chr21 36435563 36450475 uc002yvf.1 0 - 36435563 36435563 0 3 551,100,91, 0,4860,14821, +chr21 36458708 36588442 uc002yvg.1 0 + 36458901 36587739 0 37 53,164,182,171,190,99,124,110,115,121,120,103,192,685,272,153,101,191,1630,112,189,123,138,56,105,67,145,80,110,147,62,129,137,56,162,130,955, 0,167,34529,35790,44174,47012,47433,49540,49901,54831,58690,61024,63145,65909,68263,72721,74060,75224,80507,82976,83839,86621,89231,96136,99005,99207,105472,112480,113434,113668,115744,116942,123473,124215,124504,127563,128779, +chr21 36539215 36556078 uc002yvh.2 0 + 36539595 36554904 0 6 1630,112,189,123,138,1234, 0,2469,3332,6114,8724,15629, +chr21 36614375 36670814 uc002yvi.1 0 + 36614432 36669464 0 17 96,73,133,215,148,148,129,120,98,105,123,75,46,167,889,158,1504, 0,13438,16666,17524,18566,21191,24371,24704,29103,36412,39747,39976,41975,43885,48780,52166,54935, +chr21 36632941 36633667 uc010gmz.1 0 + 36632941 36632941 0 1 726, 0, +chr21 36679558 36710995 uc002yvj.1 0 + 36680304 36710534 0 14 61,203,133,118,104,97,85,94,70,92,142,432,95,553, 0,669,2207,6160,9156,12024,14130,17367,23370,23983,26072,27493,29904,30884, +chr21 36754789 36760595 uc002yvk.1 0 - 36755143 36755863 0 2 1155,61, 0,5745, +chr21 36754789 36774258 uc002yvl.1 0 - 36755143 36755863 0 3 1155,190,596, 0,16752,18873, +chr21 36754789 36774258 uc002yvm.1 0 - 36755143 36755863 0 2 1155,596, 0,18873, +chr21 36754789 36836768 uc002yvn.1 0 - 36755143 36755863 0 3 1155,138,36, 0,49741,81943, +chr21 36754789 36870737 uc002yvo.1 0 - 36755143 36755863 0 3 1155,138,159, 0,49741,115789, +chr21 36755143 36755863 uc010gna.1 0 - 36755143 36755863 0 1 720, 0, +chr21 36993860 37004772 uc002yvp.2 0 + 36993916 37003675 0 2 231,1435, 0,9477, +chr21 36993860 37040485 uc002yvq.1 0 + 36993916 37039444 0 10 231,83,90,109,86,200,107,148,169,1587, 0,9477,12842,20131,23355,26429,31355,42027,43697,45038, +chr21 36993860 37044088 uc002yvr.1 0 + 36993916 37042263 0 11 231,83,90,109,86,200,107,148,169,409,2253, 0,9477,12842,20131,23355,26429,31355,42027,43697,45038,47975, +chr21 37045058 37256340 uc010gnb.1 0 - 37048416 37233053 0 11 3530,214,115,161,68,272,183,944,163,955,135, 0,5654,8839,14124,16330,145971,179362,185560,187943,196444,211147, +chr21 37045058 37284373 uc002yvs.1 0 - 37048416 37233053 0 12 3530,214,115,161,68,272,183,944,163,146,135,46, 0,5654,8839,14124,16330,145971,179362,185560,187943,195120,211147,239269, +chr21 37224420 37260808 uc010gnc.1 0 - 37224420 37260808 0 5 183,944,163,135,195, 0,6198,8581,31785,36193, +chr21 37300319 37313828 uc002yvu.1 0 + 37312056 37312377 0 4 84,67,68,1785, 0,2007,7401,11724, +chr21 37300319 37313828 uc010gnd.1 0 + 37312144 37312468 0 3 84,67,1785, 0,2007,11724, +chr21 37300732 37313828 uc002yvv.1 0 + 37300942 37312377 0 4 314,67,68,1785, 0,1594,6988,11311, +chr21 37359533 37366973 uc002yvw.1 0 - 37359751 37366757 0 4 349,119,73,370, 0,1898,4188,7070, +chr21 37359533 37367328 uc002yvx.1 0 - 37359751 37366685 0 5 349,119,73,104,159, 0,1898,4188,7070,7636, +chr21 37359533 37367328 uc002yvy.1 0 - 37359751 37366318 0 6 349,119,73,166,104,159, 0,1898,4188,6781,7070,7636, +chr21 37367440 37497278 uc002yvz.1 0 + 37381427 37495745 0 46 94,155,43,151,88,54,121,86,95,63,55,163,46,124,64,61,85,135,81,113,121,123,102,93,65,137,327,252,47,57,74,165,1066,66,150,140,69,97,101,91,102,362,127,144,93,1668, 0,13976,14562,14925,15528,16962,18022,20734,22079,23310,35121,48546,49712,51348,52809,55732,59411,62109,65363,67290,71254,74210,75275,76807,77549,78622,79680,83386,86430,87533,88721,90782,92281,94286,99326,109505,112436,113779,115225,118064,118842,122405,124300,124612,126962,128170, +chr21 37367444 37438815 uc010gne.1 0 + 37381427 37438815 0 21 199,155,43,151,88,54,121,86,95,63,55,163,46,124,64,61,85,135,81,113,121, 0,13972,14558,14921,15524,16958,18018,20730,22075,23306,35117,48542,49708,51344,52805,55728,59407,62105,65359,67286,71250, +chr21 37377116 37497278 uc002ywa.1 0 + 37381427 37495745 0 46 1385,155,43,151,88,54,121,86,95,63,55,163,46,124,64,61,85,135,81,113,121,123,102,93,65,137,327,252,47,57,74,165,1066,66,150,140,69,97,101,91,102,362,127,144,93,1668, 0,4300,4886,5249,5852,7286,8346,11058,12403,13634,25445,38870,40036,41672,43133,46056,49735,52433,55687,57614,61578,64534,65599,67131,67873,68946,70004,73710,76754,77857,79045,81106,82605,84610,89650,99829,102760,104103,105549,108388,109166,112729,114624,114936,117286,118494, +chr21 37379959 37497278 uc002ywb.1 0 + 37381427 37495745 0 45 1612,43,151,88,54,121,86,95,63,55,163,46,124,64,61,85,135,81,113,121,123,102,93,65,137,327,252,47,57,74,165,1066,66,150,140,69,97,101,91,102,362,127,144,93,1668, 0,2043,2406,3009,4443,5503,8215,9560,10791,22602,36027,37193,38829,40290,43213,46892,49590,52844,54771,58735,61691,62756,64288,65030,66103,67161,70867,73911,75014,76202,78263,79762,81767,86807,96986,99917,101260,102706,105545,106323,109886,111781,112093,114443,115651, +chr21 37379959 37497278 uc010gnf.1 0 + 37389537 37495745 0 44 1612,43,151,88,54,121,95,63,55,163,46,124,64,61,85,135,81,113,121,123,102,93,65,137,327,252,47,57,74,165,1066,66,150,140,69,97,101,91,102,362,127,144,93,1668, 0,2043,2406,3009,4443,5503,9560,10791,22602,36027,37193,38829,40290,43213,46892,49590,52844,54771,58735,61691,62756,64288,65030,66103,67161,70867,73911,75014,76202,78263,79762,81767,86807,96986,99917,101260,102706,105545,106323,109886,111781,112093,114443,115651, +chr21 37401907 37497278 uc002ywc.1 0 + 37416016 37495745 0 36 709,163,46,124,64,61,85,135,81,113,121,123,102,93,65,137,327,252,47,57,74,165,1066,66,150,140,69,97,101,91,102,362,127,144,93,1668, 0,14079,15245,16881,18342,21265,24944,27642,30896,32823,36787,39743,40808,42340,43082,44155,45213,48919,51963,53066,54254,56315,57814,59819,64859,75038,77969,79312,80758,83597,84375,87938,89833,90145,92495,93703, +chr21 37450826 37480250 uc002ywd.1 0 + 37450894 37479982 0 10 252,47,57,74,165,1066,66,150,140,374, 0,3044,4147,5335,7396,8895,10900,15940,26119,29050, +chr21 37502673 37514868 uc010gng.1 0 + 37502673 37502673 0 5 42,103,58,89,460, 0,151,5593,7902,11735, +chr21 37502673 37514868 uc010gnh.1 0 + 37502673 37502673 0 4 42,103,89,460, 0,151,7902,11735, +chr21 37502673 37514868 uc010gni.1 0 + 37502673 37502673 0 4 42,103,58,460, 0,151,5593,11735, +chr21 37502673 37514868 uc010gnj.1 0 + 37502673 37502673 0 3 42,103,460, 0,151,11735, +chr21 37514496 37515910 uc010gnk.1 0 + 37514496 37514496 0 1 1414, 0, +chr21 37517595 37534810 uc010gnl.1 0 - 37519714 37534741 0 6 2202,153,151,75,150,144, 0,4229,4798,8952,15035,17071, +chr21 37517595 37561703 uc002ywf.1 0 - 37519714 37561465 0 8 2202,153,151,75,81,150,144,295, 0,4229,4798,8952,9937,15035,17071,43813, +chr21 37517595 37561703 uc010gnm.1 0 - 37517595 37517595 0 10 2202,153,151,78,483,269,81,150,144,295, 0,4229,4798,5720,8068,8952,9937,15035,17071,43813, +chr21 37517595 37561703 uc010gnn.1 0 - 37519714 37534741 0 9 2202,153,151,75,81,150,144,56,295, 0,4229,4798,8952,9937,15035,17071,43367,43813, +chr21 37661728 37767052 uc010gno.1 0 + 37661728 37661728 0 4 72,76,86,197, 0,47933,52742,105127, +chr21 37661728 37767052 uc002ywg.1 0 + 37661728 37661728 0 3 72,86,197, 0,52742,105127, +chr21 37661728 37780786 uc002ywh.1 0 + 37766932 37780785 0 5 72,197,93,189,148, 0,105127,110651,113081,118910, +chr21 37661728 37809549 uc002ywi.1 0 + 37714546 37800480 0 13 72,101,86,197,120,189,148,287,147,141,307,256,3466, 0,43013,52742,105127,110624,113081,118910,122618,125460,128561,137727,138543,144355, +chr21 37713076 37809549 uc002ywj.1 0 + 37714546 37806704 0 11 1480,197,93,189,148,287,147,141,307,125,3466, 0,53779,59303,61733,67562,71270,74112,77213,86379,87195,93007, +chr21 37714470 37809549 uc002ywk.1 0 + 37714546 37806704 0 11 86,197,120,189,148,287,147,141,307,125,3466, 0,52385,57882,60339,66168,69876,72718,75819,84985,85801,91613, +chr21 37714470 37809549 uc002ywm.1 0 + 37714546 37806127 0 10 86,197,120,189,148,287,147,141,307,3466, 0,52385,57882,60339,66168,69876,72718,75819,84985,91613, +chr21 37714470 37809549 uc002ywl.1 0 + 37714546 37800521 0 11 86,197,120,189,148,287,147,141,306,84,3466, 0,52385,57882,60339,66168,69876,72718,75819,84985,85973,91613, +chr21 37901635 37904535 uc002ywn.1 0 - 37901635 37901635 0 1 2900, 0, +chr21 37918656 38210566 uc002ywo.1 0 - 37919330 38134854 0 4 1000,921,52,510, 0,89727,216173,291400, +chr21 38348182 38415324 uc002ywp.1 0 - 38348818 38415219 0 3 763,102,233, 0,66088,66909, +chr21 38415436 38450474 uc002ywt.2 0 + 38415436 38415436 0 4 129,357,97,207, 0,839,32960,34831, +chr21 38415436 38450474 uc010gnp.1 0 + 38415436 38415436 0 4 129,100,97,207, 0,839,32960,34831, +chr21 38415436 38450474 uc010gnq.1 0 + 38415436 38415436 0 4 129,100,115,207, 0,839,32942,34831, +chr21 38415436 38450474 uc010gnr.1 0 + 38415436 38415436 0 3 129,357,207, 0,839,34831, +chr21 38415436 38450474 uc010gns.1 0 + 38415436 38415436 0 3 129,100,207, 0,839,34831, +chr21 38500119 38502606 uc010gnt.1 0 + 38500119 38500119 0 3 205,145,508, 0,316,1979, +chr21 38550533 38595616 uc002ywv.1 0 + 38593053 38594181 0 4 46,140,98,2581, 0,304,40184,42502, +chr21 38550739 38595616 uc002yww.1 0 + 38593053 38594181 0 3 238,98,2581, 0,39978,42296, +chr21 38566298 38595616 uc002ywx.1 0 + 38593053 38594181 0 3 51,98,2581, 0,24419,26737, +chr21 38567267 38569311 uc002ywy.2 0 + 38567267 38567267 0 1 2044, 0, +chr21 38593053 38594181 uc010gnu.1 0 + 38593053 38594181 0 1 1128, 0, +chr21 38661052 38955488 uc002ywz.1 0 - 38661426 38869494 0 12 388,48,57,69,72,81,204,152,218,86,102,37, 0,23734,24398,25115,33313,35296,36245,56149,78144,208403,217585,294399, +chr21 38675670 38792267 uc002yxa.1 0 - 38677194 38792174 0 10 2045,48,57,69,72,81,204,152,218,111, 0,9116,9780,10497,18695,20678,21627,41531,63526,116486, +chr21 38675670 38878739 uc010gnv.1 0 - 38677194 38717313 0 9 2045,48,57,69,81,204,152,86,102, 0,9116,9780,10497,20678,21627,41531,193785,202967, +chr21 38675670 38954461 uc010gnw.1 0 - 38677194 38869494 0 12 2045,48,57,69,72,81,204,152,218,86,102,146, 0,9116,9780,10497,18695,20678,21627,41531,63526,193785,202967,278645, +chr21 38675670 38954461 uc010gnx.1 0 - 38677194 38869494 0 11 2045,48,57,69,81,204,152,218,86,102,146, 0,9116,9780,10497,20678,21627,41531,63526,193785,202967,278645, +chr21 38675670 38955488 uc002yxb.1 0 - 38677194 38869494 0 11 2045,48,57,69,81,204,152,218,86,102,37, 0,9116,9780,10497,20678,21627,41531,63526,193785,202967,279781, +chr21 38686167 38697501 uc010gny.1 0 - 38686167 38686167 0 2 69,204, 0,11130, +chr21 38693868 38955488 uc002yxc.2 0 - 38694153 38869494 0 8 569,81,204,152,218,86,102,37, 0,2480,3429,23333,45328,175587,184769,261583, +chr21 38764567 38955488 uc010gnz.1 0 - 38764567 38764567 0 5 1306,95,86,102,37, 0,3252,104888,114070,190884, +chr21 39032820 39046051 uc010goa.1 0 - 39032820 39032820 0 4 303,99,118,51, 0,1289,7272,13180, +chr21 39032820 39067271 uc002yxd.2 0 - 39032820 39032820 0 7 303,99,185,52,118,64,29, 0,1289,1857,2294,7272,8370,34422, +chr21 39099100 39118748 uc002yxf.1 0 + 39099140 39116683 0 11 310,150,72,112,120,201,84,222,264,119,2281, 0,664,4728,7696,8966,9474,11701,13118,14196,16279,17367, +chr21 39099718 39118748 uc002yxg.1 0 + 39103828 39116683 0 10 196,72,112,120,201,84,222,264,119,2281, 0,4110,7078,8348,8856,11083,12500,13578,15661,16749, +chr21 39171084 39232223 uc002yxh.1 0 - 39172299 39172710 0 4 3082,65,56,620, 0,24610,46347,60519, +chr21 39469253 39477310 uc002yxi.1 0 - 39469385 39477181 0 7 207,137,199,63,152,107,263, 0,1977,2991,4466,4827,6314,7794, +chr21 39469253 39477310 uc002yxj.1 0 - 39469385 39477181 0 6 207,137,199,152,107,263, 0,1977,2991,4827,6314,7794, +chr21 39469253 39477310 uc010gob.1 0 - 39469385 39474212 0 6 207,137,199,63,152,263, 0,1977,2991,4466,4827,7794, +chr21 39479273 39558815 uc010goc.1 0 - 39480821 39503916 0 26 1940,918,900,168,221,167,153,144,42,73,126,132,62,112,83,125,108,126,190,95,132,94,184,186,226,129, 0,11020,13285,14741,16847,20630,24517,25308,27188,28003,29759,33051,38930,39608,43022,43834,46699,46895,51117,53001,62223,65318,70167,73009,78982,79413, +chr21 39479273 39607426 uc002yxk.1 0 - 39480821 39607287 0 42 1940,918,900,168,221,167,153,144,42,73,126,121,156,62,112,83,125,108,126,190,95,132,94,184,186,226,129,135,151,99,41,101,71,101,222,161,99,151,60,30,59,188, 0,11020,13285,14741,16847,20630,24517,25308,27188,28003,29759,32674,33027,38930,39608,43022,43834,46699,46895,51117,53001,62223,65318,70167,73009,78982,79413,84421,84805,88896,90695,91773,93265,94670,108333,110265,110787,112954,127363,127594,127763,127965, +chr21 39484017 39607426 uc002yxl.1 0 - 39490054 39607287 0 42 821,6366,900,168,221,167,153,144,42,73,126,121,156,62,112,83,125,108,126,190,95,132,94,184,186,226,129,135,151,99,41,101,71,101,222,161,99,151,60,30,59,188, 0,828,8541,9997,12103,15886,19773,20564,22444,23259,25015,27930,28283,34186,34864,38278,39090,41955,42151,46373,48257,57479,60574,65423,68265,74238,74669,79677,80061,84152,85951,87029,88521,89926,103589,105521,106043,108210,122619,122850,123019,123221, +chr21 39496120 39523232 uc010god.1 0 - 39496121 39523130 0 12 221,167,153,42,73,126,121,156,62,112,83,125, 0,3783,7670,10341,11156,12912,15827,16180,22083,22761,26175,26987, +chr21 39530390 39574044 uc010goe.1 0 - 39530390 39530390 0 15 190,95,132,94,184,186,105,129,135,151,99,41,101,71,101, 0,1884,11106,14201,19050,21892,27865,28296,33304,33688,37779,39578,40656,42148,43553, +chr21 39530390 39574044 uc010gof.1 0 - 39530390 39558799 0 15 190,95,132,94,184,186,226,34,135,151,99,41,101,71,101, 0,1884,11106,14201,19050,21892,27865,28391,33304,33688,37779,39578,40656,42148,43553, +chr21 39530390 39574044 uc010gog.1 0 - 39530390 39530390 0 15 190,95,132,94,164,186,226,129,135,151,99,41,101,71,101, 0,1884,11106,14201,19070,21892,27865,28296,33304,33688,37779,39578,40656,42148,43553, +chr21 39530390 39574044 uc010goh.1 0 - 39530390 39530390 0 14 190,95,132,94,186,226,129,135,151,99,41,101,71,101, 0,1884,11106,14201,21892,27865,28296,33304,33688,37779,39578,40656,42148,43553, +chr21 39530390 39574044 uc010goi.1 0 - 39530390 39574035 0 14 190,95,94,184,186,226,129,135,151,99,41,101,71,101, 0,1884,14201,19050,21892,27865,28296,33304,33688,37779,39578,40656,42148,43553, +chr21 39590234 39607426 uc002yxm.1 0 - 39592213 39607287 0 5 2144,60,30,59,188, 0,16402,16633,16802,17004, +chr21 39636110 39642917 uc002yxo.1 0 - 39636907 39642713 0 6 845,129,48,30,33,219, 0,2831,5977,6107,6230,6588, +chr21 39636110 39642917 uc002yxp.1 0 - 39636594 39639642 0 8 845,129,129,100,48,30,33,219, 0,2831,3515,5064,5977,6107,6230,6588, +chr21 39636110 39642917 uc002yxq.1 0 - 39636594 39639642 0 7 845,129,129,48,30,33,219, 0,2831,3515,5977,6107,6230,6588, +chr21 39636110 39643140 uc002yxr.1 0 - 39636110 39636110 0 8 845,129,1463,105,48,30,33,54, 0,2831,3515,5064,5977,6107,6230,6976, +chr21 39674139 39691486 uc002yxs.1 0 + 39674180 39690735 0 5 143,166,68,115,825, 0,10354,11425,12822,16522, +chr21 39681560 39691486 uc010goj.1 0 + 39681560 39681560 0 5 91,779,68,115,825, 0,2933,4004,5401,9101, +chr21 39681560 39691486 uc002yxt.2 0 + 39684493 39690735 0 5 91,166,68,115,825, 0,2933,4004,5401,9101, +chr21 39699639 39737997 uc002yxu.1 0 - 39699677 39722289 0 10 769,118,104,85,138,515,332,81,154,67, 0,4135,4420,5874,14862,17132,22328,23287,29576,38291, +chr21 39699639 39739529 uc002yxv.1 0 - 39699677 39722289 0 10 769,118,104,85,138,515,332,81,154,284, 0,4135,4420,5874,14862,17132,22328,23287,29576,39606, +chr21 39715354 39739601 uc002yxw.1 0 - 39716741 39722289 0 5 1932,332,81,154,81, 0,6613,7572,13861,24166, +chr21 39715354 39739601 uc002yxx.1 0 - 39716741 39717194 0 4 1932,81,67,81, 0,7572,22576,24166, +chr21 39715868 39732732 uc002yxy.2 0 - 39715868 39715868 0 4 1836,1086,81,253, 0,5345,7058,16611, +chr21 39739666 39809303 uc002yxz.1 0 + 39756269 39805572 0 7 59,186,81,93,30,130,419, 0,16504,29264,53952,63128,65810,69218, +chr21 39745649 39809303 uc002yya.1 0 + 39745703 39805572 0 7 288,186,81,93,30,130,419, 0,10521,23281,47969,57145,59827,63235, +chr21 39850238 39956685 uc002yyb.1 0 + 39954356 39955289 0 5 69,132,231,160,2329, 0,48652,89950,103311,104118, +chr21 39890946 39906618 uc010gok.1 0 - 39890946 39890946 0 3 840,83,525, 0,12433,15147, +chr21 39899406 39906618 uc002yyd.2 0 - 39899406 39899406 0 3 738,83,525, 0,3973,6687, +chr21 39906841 39953709 uc002yyf.1 0 + 39906841 39906841 0 4 23,108,231,160, 0,2178,33347,46708, +chr21 39906841 39956685 uc002yye.2 0 + 39954356 39955289 0 3 23,160,2329, 0,46708,47515, +chr21 39924087 39953709 uc002yyg.1 0 + 39924087 39924087 0 3 200,231,160, 0,16101,29462, +chr21 39924087 39953709 uc010gol.1 0 + 39924087 39924087 0 2 200,160, 0,29462, +chr21 39936181 39953709 uc002yyh.1 0 + 39936181 39936181 0 3 92,231,160, 0,4007,17368, +chr21 39936181 39953709 uc010gom.1 0 + 39936181 39936181 0 2 92,160, 0,17368, +chr21 39951123 39956685 uc002yyi.1 0 + 39954356 39955289 0 4 273,109,160,2329, 0,458,2426,3233, +chr21 39951123 39956685 uc002yyj.1 0 + 39954356 39955289 0 3 140,160,2329, 0,2426,3233, +chr21 39951123 39956685 uc002yyk.1 0 + 39954356 39955289 0 3 273,160,2329, 0,2426,3233, +chr21 39951123 39956685 uc002yyl.1 0 + 39954356 39955289 0 3 273,109,2329, 0,458,3233, +chr21 39951123 39956685 uc002yym.1 0 + 39954356 39955289 0 2 273,3136, 0,2426, +chr21 39954356 39955289 uc010gon.1 0 + 39954356 39955289 0 1 933, 0, +chr21 40021551 40024477 uc002yyn.1 0 + 40021551 40021551 0 3 238,127,1177, 0,1378,1749, +chr21 40039203 40095893 uc002yyo.1 0 + 40039306 40095154 0 9 120,83,318,300,216,22,92,80,835, 0,809,20128,25509,33683,42760,46601,48127,55855, +chr21 40161216 40223192 uc002yyp.1 0 + 40161297 40222906 0 3 90,52,414, 0,31054,61562, +chr21 40306212 41140909 uc002yyq.1 0 - 40306830 41140457 0 33 971,303,198,150,116,31,177,291,189,99,164,118,154,134,156,147,241,71,168,129,97,197,174,120,279,276,297,276,279,147,147,318,495, 0,29955,31662,39542,43309,50453,62621,66271,67736,71492,73186,74754,81305,111779,121438,130142,132075,154802,166511,174715,175475,176626,263681,283639,299665,325685,326703,335254,341049,356683,680393,696037,834202, +chr21 40306212 41140909 uc002yyr.1 0 - 40306212 40306212 0 33 971,303,198,150,116,31,17,260,189,99,164,118,154,134,156,147,241,71,168,129,97,197,174,120,279,276,297,276,279,147,147,318,495, 0,29955,31662,39542,43309,50453,62621,66302,67736,71492,73186,74754,81305,111779,121438,130142,132075,154802,166511,174715,175475,176626,263681,283639,299665,325685,326703,335254,341049,356683,680393,696037,834202, +chr21 40676879 40679152 uc002yys.2 0 + 40676879 40676879 0 3 373,487,777, 0,569,1496, +chr21 40676879 40679152 uc002yyt.2 0 + 40676879 40676879 0 3 326,79,777, 0,423,1496, +chr21 40676879 40679152 uc002yyu.2 0 + 40676879 40676879 0 2 373,777, 0,1496, +chr21 41435296 41441861 uc002yyv.1 0 - 41435296 41435296 0 2 1916,103, 0,6462, +chr21 41461597 41570394 uc002yyw.1 0 + 41462060 41569421 0 9 775,89,217,129,135,102,150,169,1227, 0,58465,69712,74018,75575,78161,82951,89357,107570, +chr21 41461597 41570394 uc002yyx.1 0 + 41462060 41569421 0 8 775,89,217,129,135,102,169,1227, 0,58465,69712,74018,75575,78161,89357,107570, +chr21 41461597 41570394 uc002yyy.1 0 + 41462060 41569224 0 8 775,89,217,129,135,102,150,1227, 0,58465,69712,74018,75575,78161,82951,107570, +chr21 41469027 41479036 uc002yyz.1 0 - 41472972 41473425 0 1 10009, 0, +chr21 41539758 41570394 uc010goo.1 0 + 41539758 41539758 0 2 102,1227, 0,29409, +chr21 41598067 41651524 uc002yza.1 0 + 41598067 41598067 0 10 40,1521,144,124,59,51,199,88,133,620, 0,15187,18652,34107,40205,41415,41938,42742,44321,52837, +chr21 41610530 41651524 uc002yzb.1 0 + 41610676 41650994 0 8 165,144,124,59,51,88,133,620, 0,6189,21644,27742,28952,30279,31858,40374, +chr21 41610530 41651524 uc002yzc.1 0 + 41610676 41650994 0 7 165,124,59,51,88,133,620, 0,21644,27742,28952,30279,31858,40374, +chr21 41616616 41651524 uc002yzd.1 0 + 41616631 41650994 0 7 247,124,59,51,88,133,620, 0,15558,21656,22866,24193,25772,34288, +chr21 41655819 41661103 uc002yze.1 0 + 41655819 41655819 0 2 33,4038, 0,1246, +chr21 41655819 41702739 uc002yzf.1 0 + 41670703 41702030 0 14 33,320,193,135,155,139,199,79,123,142,159,77,255,952, 0,14813,15766,17994,20387,28542,33564,35590,36874,37173,39947,41244,44721,45968, +chr21 41683339 41702739 uc002yzg.1 0 + 41684460 41702030 0 9 1161,199,79,123,142,159,77,255,952, 0,6044,8070,9354,9653,12427,13724,17201,18448, +chr21 41692693 41702739 uc010gop.1 0 + 41695906 41702030 0 5 123,159,77,255,952, 0,3073,4370,7847,9094, +chr21 41714311 41753008 uc002yzh.1 0 + 41725867 41752555 0 19 303,258,156,99,112,76,126,193,138,155,139,199,79,123,142,159,77,249,684, 0,1323,2241,6691,7240,10018,11535,15322,16500,19179,20372,21201,23273,24933,25485,28622,30652,32106,38013, +chr21 41720023 41753008 uc002yzi.1 0 + 41725867 41752555 0 17 37,99,112,76,126,193,138,155,139,199,79,123,142,159,77,249,684, 0,979,1528,4306,5823,9610,10788,13467,14660,15489,17561,19221,19773,22910,24940,26394,32301, +chr21 41720023 41753008 uc010goq.1 0 + 41725867 41752555 0 15 37,112,126,193,138,155,139,199,79,123,142,159,77,249,684, 0,1528,5823,9610,10788,13467,14660,15489,17561,19221,19773,22910,24940,26394,32301, +chr21 41758350 41801779 uc010gor.1 0 - 41759938 41791930 0 14 1600,153,143,96,176,172,44,111,127,120,87,223,71,33, 0,3180,3842,6094,7252,8771,12023,14618,15922,23840,24953,29802,33565,43396, +chr21 41758350 41801948 uc002yzj.1 0 - 41759938 41791930 0 14 1600,153,143,96,176,172,44,111,127,120,87,223,71,71, 0,3180,3842,6094,7252,8771,12023,14618,15922,23840,24953,29802,33565,43527, +chr21 41761530 41824913 uc010gos.1 0 - 41761530 41791930 0 14 153,143,96,176,172,44,111,127,120,87,223,71,246,132, 0,662,2914,4072,5591,8843,11438,12742,20660,21773,26622,30385,62239,63251, +chr21 42004748 42009004 uc010got.1 0 - 42006111 42007538 0 7 1481,122,81,113,81,164,34, 0,2031,2336,2500,2714,3600,4222, +chr21 42009664 42010809 uc002yzm.1 0 + 42009664 42009664 0 3 109,174,239, 0,565,906, +chr21 42032597 42060318 uc002yzn.1 0 - 42034066 42060270 0 8 2629,259,104,159,50,149,292,230, 0,4513,6390,7244,9785,11728,17156,27491, +chr21 42091453 42172660 uc002yzo.1 0 - 42094468 42172549 0 24 3498,210,81,176,84,132,120,80,164,135,132,95,168,88,95,182,130,231,102,253,154,94,46,213, 0,4487,6309,12125,12724,17676,21553,22066,23038,23874,25289,27931,30137,37161,37837,38192,39658,41347,48814,56290,58900,61316,62051,80994, +chr21 42091453 42172660 uc002yzp.1 0 - 42094468 42172549 0 25 3498,210,81,176,84,132,120,80,164,135,132,95,168,60,88,95,182,130,231,102,253,154,94,46,213, 0,4487,6309,12125,12724,17676,21553,22066,23038,23874,25289,27931,30137,36229,37161,37837,38192,39658,41347,48814,56290,58900,61316,62051,80994, +chr21 42094222 42172660 uc002yzq.1 0 - 42094468 42172549 0 31 729,210,81,176,84,132,120,80,164,135,132,95,168,88,95,182,130,231,102,253,154,198,94,46,189,83,78,128,166,145,213, 0,1718,3540,9356,9955,14907,18784,19297,20269,21105,22520,25162,27368,34392,35068,35423,36889,38578,46045,53521,56131,57986,58547,59282,60518,60880,66255,70449,77650,77951,78225, +chr21 42094222 42172660 uc002yzr.1 0 - 42094468 42172549 0 25 729,210,81,176,84,132,120,80,164,135,132,95,168,60,88,95,182,130,231,102,253,154,94,46,213, 0,1718,3540,9356,9955,14907,18784,19297,20269,21105,22520,25162,27368,33460,34392,35068,35423,36889,38578,46045,53521,56131,58547,59282,78225, +chr21 42178287 42194927 uc002yzs.1 0 - 42182301 42192507 0 3 4235,295,128, 0,13943,16512, +chr21 42178287 42201421 uc002yzt.1 0 - 42182301 42200335 0 6 4235,310,128,114,175,584, 0,13943,16512,20614,21882,22550, +chr21 42178287 42212211 uc002yzu.1 0 - 42182301 42212126 0 11 4235,310,128,114,175,125,65,109,124,123,178, 0,13943,16512,20614,21882,22550,24349,27222,29488,32995,33746, +chr21 42178287 42219868 uc002yzv.1 0 - 42182301 42215176 0 13 4235,310,128,114,175,125,65,109,124,123,105,114,119, 0,13943,16512,20614,21882,22550,24349,27222,29488,32995,33746,36862,41462, +chr21 42178287 42247068 uc002yzw.1 0 - 42182301 42246826 0 14 4235,310,128,114,175,125,65,109,124,123,105,114,99,521, 0,13943,16512,20614,21882,22550,24349,27222,29488,32995,33746,36862,57037,68260, +chr21 42194130 42219868 uc002yzx.1 0 - 42194727 42215176 0 11 797,114,175,125,65,109,124,123,105,114,119, 0,4771,6039,6707,8506,11379,13645,17152,17903,21019,25619, +chr21 42280008 42303565 uc002yzz.2 0 - 42284072 42287273 0 4 5059,1616,65,136, 0,5662,16066,23421, +chr21 42280008 42303565 uc002zab.2 0 - 42284072 42287273 0 3 7278,65,136, 0,16066,23421, +chr21 42280008 42303565 uc002yzy.2 0 - 42284072 42287273 0 2 7278,136, 0,23421, +chr21 42280008 42303565 uc002zaa.2 0 - 42284072 42287273 0 4 7278,154,65,136, 0,15519,16066,23421, +chr21 42284072 42287273 uc010gou.1 0 - 42284072 42287273 0 1 3201, 0, +chr21 42285670 42303565 uc010gov.1 0 - 42285671 42287273 0 4 1616,65,131,136, 0,10404,16974,17759, +chr21 42285670 42303565 uc002zac.2 0 - 42285671 42287273 0 4 1616,214,65,136, 0,9857,10404,17759, +chr21 42356136 42436174 uc002zad.1 0 + 42369322 42430799 0 23 256,243,162,122,187,141,255,113,220,138,242,205,258,113,214,138,320,146,237,160,85,203,900, 0,13046,21126,22333,25336,27340,35968,39208,40910,46604,47922,48548,50615,52915,56153,58129,59873,63387,64048,64714,66755,74481,79138, +chr21 42356136 42436174 uc002zae.1 0 + 42369322 42430799 0 22 256,243,162,122,187,141,255,113,220,138,831,258,113,214,138,320,146,237,160,85,203,900, 0,13046,21126,22333,25336,27340,35968,39208,40910,46604,47922,50615,52915,56153,58129,59873,63387,64048,64714,66755,74481,79138, +chr21 42364494 42436174 uc002zaf.1 0 + 42364494 42430799 0 23 76,243,162,122,187,141,255,113,220,138,242,205,258,113,214,138,320,146,237,160,85,203,900, 0,4688,12768,13975,16978,18982,27610,30850,32552,38246,39564,40190,42257,44557,47795,49771,51515,55029,55690,56356,58397,66123,70780, +chr21 42364494 42436174 uc002zag.1 0 + 42364494 42430799 0 22 76,243,162,122,187,141,255,113,220,138,831,258,113,214,138,320,146,237,160,85,203,900, 0,4688,12768,13975,16978,18982,27610,30850,32552,38246,39564,42257,44557,47795,49771,51515,55029,55690,56356,58397,66123,70780, +chr21 42368072 42370042 uc002zah.1 0 - 42368072 42368072 0 1 1970, 0, +chr21 42378469 42397266 uc010gow.1 0 + 42381493 42397265 0 7 122,97,187,141,255,113,220, 0,1239,3003,5007,13635,16875,18577, +chr21 42378469 42397266 uc002zai.1 0 + 42378469 42378469 0 8 122,180,141,119,154,255,113,220, 0,3003,5007,8113,8580,13635,16875,18577, +chr21 42378469 42397266 uc010gox.1 0 + 42378469 42378469 0 7 122,187,141,255,110,113,220, 0,3003,5007,13635,16417,16875,18577, +chr21 42378469 42397266 uc010goy.1 0 + 42392220 42397265 0 7 122,141,119,154,255,113,220, 0,5007,8113,8580,13635,16875,18577, +chr21 42378469 42397266 uc002zaj.1 0 + 42378469 42378469 0 7 122,187,141,154,255,113,220, 0,3003,5007,8580,13635,16875,18577, +chr21 42378481 42397266 uc010goz.1 0 + 42381493 42397265 0 5 172,187,255,113,220, 0,2991,13623,16863,18565, +chr21 42395312 42401630 uc002zak.1 0 - 42396812 42401561 0 2 1902,156, 0,6162, +chr21 42413697 42436174 uc002zal.1 0 + 42419526 42430799 0 9 433,138,320,146,237,160,85,203,900, 0,568,2312,5826,6487,7153,9194,16920,21577, +chr21 42420850 42430820 uc010gpa.1 0 + 42421303 42430799 0 4 160,142,85,203, 0,332,2041,9767, +chr21 42492867 42590423 uc002zam.1 0 + 42518873 42589571 0 17 161,147,41,244,118,133,51,146,124,115,149,102,169,101,159,119,1081, 0,1888,7257,25982,71381,73614,77206,82585,84871,86191,88200,88522,90361,91403,91809,94853,96475, +chr21 42492867 42590423 uc002zan.1 0 + 42494854 42589571 0 16 161,147,244,118,133,51,146,124,115,149,102,169,101,159,119,1081, 0,1888,25982,71381,73614,77206,82585,84871,86191,88200,88522,90361,91403,91809,94853,96475, +chr21 42509255 42590423 uc002zao.1 0 + 42509334 42589571 0 15 112,244,118,133,51,146,124,115,149,102,169,101,159,119,1081, 0,9594,54993,57226,60818,66197,68483,69803,71812,72134,73973,75015,75421,78465,80087, +chr21 42512335 42590423 uc002zap.1 0 + 42512441 42589571 0 15 148,244,118,133,51,146,124,115,149,102,169,101,159,119,1081, 0,6514,51913,54146,57738,63117,65403,66723,68732,69054,70893,71935,72341,75385,77007, +chr21 42512335 42590423 uc002zaq.1 0 + 42512441 42589571 0 15 148,244,118,133,51,146,124,115,185,102,169,101,159,119,1081, 0,6514,51913,54146,57738,63117,65403,66723,68732,69054,70893,71935,72341,75385,77007, +chr21 42513076 42590423 uc002zar.1 0 + 42513150 42589571 0 15 149,244,118,133,51,146,124,115,149,102,169,101,159,119,1081, 0,5773,51172,53405,56997,62376,64662,65982,67991,68313,70152,71194,71600,74644,76266, +chr21 42579058 42588512 uc010gpb.1 0 + 42581401 42587843 0 6 115,424,169,101,159,792, 0,2009,4170,5212,5618,8662, +chr21 42592172 42593987 uc002zau.2 0 + 42592172 42592172 0 1 1815, 0, +chr21 42605231 42608775 uc002zav.1 0 - 42605434 42608703 0 3 217,147,304, 0,1432,3240, +chr21 42639535 42644176 uc002zaw.1 0 - 42639710 42644135 0 4 189,147,150,120, 0,1128,3523,4521, +chr21 42655459 42659713 uc002zax.1 0 - 42655656 42659673 0 3 214,153,125, 0,973,4129, +chr21 42665067 42676929 uc002zay.1 0 - 42665939 42675468 0 5 890,153,143,96,1687, 0,3826,4651,8227,10175, +chr21 42665067 42682296 uc002zaz.1 0 - 42665939 42681645 0 10 890,153,146,96,170,166,44,126,124,190, 0,3826,4651,8227,10175,11143,12080,13519,16513,17039, +chr21 42665067 42683596 uc002zba.1 0 - 42665939 42681645 0 11 890,153,146,96,170,166,44,126,124,117,492, 0,3826,4651,8227,10175,11143,12080,13519,16513,17039,18037, +chr21 42665067 42689269 uc002zbb.1 0 - 42665939 42688595 0 13 890,153,146,96,170,166,44,126,124,117,111,145,150, 0,3826,4651,8227,10175,11143,12080,13519,16513,17039,18037,23434,24052, +chr21 42665067 42689269 uc002zbc.1 0 - 42665939 42688595 0 13 890,153,143,96,170,166,44,126,124,117,111,145,150, 0,3826,4651,8227,10175,11143,12080,13519,16513,17039,18037,23434,24052, +chr21 42675053 42689269 uc002zbd.1 0 - 42675159 42688595 0 9 359,166,44,126,124,117,111,145,150, 0,1157,2094,3533,6527,7053,8051,13448,14066, +chr21 42697087 42740843 uc002zbe.1 0 + 42697123 42740373 0 15 149,54,187,199,114,170,209,124,100,123,93,145,107,110,608, 0,2398,5512,9114,9500,12532,14491,22787,28193,30923,33579,38543,39403,40625,43148, +chr21 42697087 42740843 uc002zbf.1 0 + 42697123 42740373 0 14 149,54,187,199,170,209,124,100,123,93,145,107,110,608, 0,2398,5512,9114,12532,14491,22787,28193,30923,33579,38543,39403,40625,43148, +chr21 42697087 42740843 uc010gpc.1 0 + 42697087 42697087 0 14 149,54,187,199,170,209,124,100,123,93,145,265,110,608, 0,2398,5512,9114,12532,14491,22787,28193,30923,33579,38543,39245,40625,43148, +chr21 42697087 42740843 uc010gpd.1 0 + 42697087 42697087 0 14 149,54,187,199,170,209,124,100,678,55,145,107,110,608, 0,2398,5512,9114,12532,14491,22787,28193,30923,33633,38543,39403,40625,43148, +chr21 42697087 42740843 uc010gpe.1 0 + 42697123 42740299 0 12 149,54,187,199,170,209,124,100,123,93,145,608, 0,2398,5512,9114,12532,14491,22787,28193,30923,33579,38543,43148, +chr21 42765665 42789470 uc002zbg.1 0 - 42765996 42789365 0 9 384,150,154,72,136,91,106,114,159, 0,3411,4804,10150,13182,13884,20271,20479,23646, +chr21 42789186 42811689 uc002zbh.1 0 + 42789186 42789186 0 3 222,122,234, 0,6288,22269, +chr21 42792810 42874619 uc002zbi.1 0 + 42811633 42873539 0 21 112,122,234,82,133,79,136,77,167,38,81,132,91,63,86,49,74,79,98,65,1096, 0,2664,18645,26144,35066,35840,39880,42772,43804,47471,54430,59326,62446,64183,65076,66195,67353,68728,75186,80104,80713, +chr21 42807092 42874619 uc002zbj.1 0 + 42811633 42873539 0 20 804,234,82,133,79,136,77,167,38,81,132,91,63,86,49,74,79,98,65,1096, 0,4363,11862,20784,21558,25598,28490,29522,33189,40148,45044,48164,49901,50794,51913,53071,54446,60904,65822,66431, +chr21 42892458 42908237 uc002zbk.1 0 - 42892458 42892458 0 2 1569,206, 0,15573, +chr21 42941483 42944423 uc002zbl.2 0 - 42941483 42941483 0 2 2139,681, 0,2259, +chr21 42946930 43068687 uc002zbm.1 0 + 42946993 43068472 0 20 132,71,78,44,180,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,32440,34165,45216,78018,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbn.1 0 + 42947045 43068472 0 17 132,44,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,45216,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbo.1 0 + 42946993 43068472 0 19 132,71,78,76,44,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,32440,34165,43663,45216,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbp.1 0 + 43037007 43068472 0 17 132,180,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,78018,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbq.1 0 + 42946993 43068472 0 17 132,78,44,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,34165,45216,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbs.1 0 + 43037007 43068472 0 17 132,71,44,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,32440,45216,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbr.1 0 + 43037007 43068472 0 16 132,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbt.1 0 + 42946993 43068472 0 16 132,44,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,45216,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbu.1 0 + 42947045 43068472 0 16 132,78,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,34165,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbv.1 0 + 42947045 43068472 0 15 132,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbw.1 0 + 43026603 43068472 0 15 132,44,71,82,75,87,105,83,157,114,105,129,96,82,229, 0,45216,79604,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbx.1 0 + 42946993 43068472 0 19 132,71,78,44,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,32440,34165,45216,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zby.1 0 + 43026603 43068472 0 14 132,71,82,75,87,105,83,157,114,105,129,96,82,229, 0,79604,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zbz.1 0 + 42990595 43068472 0 20 132,71,78,76,44,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,32440,34165,43663,45216,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zca.1 0 + 42947045 43068472 0 19 132,78,44,180,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,34165,45216,78018,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zcb.1 0 + 42946993 43068472 0 19 132,71,44,180,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,32440,45216,78018,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zcc.1 0 + 42947045 43068472 0 18 132,78,44,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,34165,45216,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zcd.1 0 + 42946993 43068472 0 18 132,71,44,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,32440,45216,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zce.1 0 + 42947045 43068472 0 18 132,44,180,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,45216,78018,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zcf.1 0 + 43037007 43068472 0 18 132,78,44,180,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,34165,45216,78018,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 42946930 43068687 uc002zcg.1 0 + 43037007 43068472 0 18 132,44,79,55,71,85,82,75,87,105,83,157,114,105,129,96,82,229, 0,45216,70804,78318,79604,90024,97364,100238,105247,106576,107073,108331,111629,114436,115275,116951,118687,121528, +chr21 43024936 43068687 uc002zch.1 0 + 43026603 43068472 0 15 192,55,71,82,75,87,105,83,157,114,105,129,96,82,229, 0,312,1598,19358,22232,27241,28570,29067,30325,33623,36430,37269,38945,40681,43522, +chr21 43036742 43059157 uc010gpf.1 0 + 43037007 43058799 0 9 106,85,82,75,87,105,83,157,598, 0,212,7552,10426,15435,16764,17261,18519,21817, +chr21 43136272 43172747 uc002zci.1 0 - 43143227 43172674 0 12 188,202,70,184,65,99,61,113,157,141,66,162, 0,6947,9161,10475,11468,12588,16568,19188,20346,30457,33608,36313, +chr21 43136869 43139149 uc002zcj.1 0 - 43136869 43136869 0 1 2280, 0, +chr21 43142404 43172747 uc002zck.1 0 - 43143227 43172674 0 11 1017,70,184,65,99,61,113,157,141,66,162, 0,3029,4343,5336,6456,10436,13056,14214,24325,27476,30181, +chr21 43142404 43172747 uc010gpg.1 0 - 43143227 43172674 0 11 1017,70,184,62,99,61,113,157,141,66,162, 0,3029,4343,5336,6456,10436,13056,14214,24325,27476,30181, +chr21 43142404 43172747 uc002zcl.1 0 - 43143227 43156633 0 11 1017,70,184,65,99,61,113,157,89,66,56, 0,3029,4343,5336,6456,10436,13056,14214,24377,27476,30287, +chr21 43143219 43172747 uc010gph.1 0 - 43143227 43156633 0 11 202,70,184,65,99,61,113,157,89,66,162, 0,2214,3528,4521,5641,9621,12241,13399,23562,26661,29366, +chr21 43186446 43202842 uc002zcm.1 0 + 43186512 43202200 0 4 114,121,1095,800, 0,3659,9914,15596, +chr21 43186446 43202842 uc002zcn.1 0 + 43186512 43202200 0 3 114,121,800, 0,3659,15596, +chr21 43209994 43218800 uc002zco.1 0 - 43211702 43212185 0 2 2476,276, 0,8530, +chr21 43267711 43322136 uc002zcp.1 0 + 43297560 43322136 0 10 132,107,128,172,171,100,98,129,77,256, 0,29793,32958,35520,38535,42375,43600,46770,50338,54169, +chr21 43267711 43326757 uc002zcq.1 0 + 43297560 43323280 0 11 132,107,128,172,171,100,98,129,77,173,3689, 0,29793,32958,35520,38535,42375,43600,46770,50338,54169,55357, +chr21 43297504 43311226 uc002zcr.2 0 + 43297560 43310221 0 5 107,128,172,171,1140, 0,3165,5727,8742,12582, +chr21 43346369 43361583 uc002zcs.1 0 - 43347058 43360957 0 14 793,85,109,135,78,106,85,126,92,70,135,80,135,627, 0,3612,4954,5643,6035,7250,9120,9762,10709,12012,12196,12425,13052,14587, +chr21 43346369 43369020 uc002zct.1 0 - 43347058 43365372 0 17 793,85,109,135,78,106,85,126,92,70,135,80,135,107,217,38,72, 0,3612,4954,5643,6035,7250,9120,9762,10709,12012,12196,12425,13052,15318,18794,20075,22579, +chr21 43346369 43369020 uc002zcu.1 0 - 43347058 43365372 0 17 793,85,109,135,78,106,85,126,92,70,135,80,135,107,217,76,72, 0,3612,4954,5643,6035,7250,9120,9762,10709,12012,12196,12425,13052,15318,18794,20075,22579, +chr21 43346369 43369493 uc002zcv.1 0 - 43347058 43365372 0 17 793,85,109,135,78,106,85,126,92,70,135,80,135,107,217,76,90, 0,3612,4954,5643,6035,7250,9120,9762,10709,12012,12196,12425,13052,15318,18794,20075,23034, +chr21 43346371 43369493 uc002zcw.2 0 - 43347058 43365372 0 18 455,122,85,109,135,78,106,85,126,92,70,135,80,135,107,217,76,90, 0,669,3610,4952,5641,6033,7248,9118,9760,10707,12010,12194,12423,13050,15316,18792,20073,23032, +chr21 43348252 43353725 uc002zcx.1 0 - 43349129 43353621 0 6 1026,85,109,135,78,106, 0,1729,3071,3760,4152,5367, +chr21 43386134 43398431 uc002zcy.1 0 - 43386280 43388902 0 7 294,93,134,99,50,67,938, 0,1515,1699,2482,2738,7497,11359, +chr21 43386134 43400757 uc002zcz.1 0 - 43386280 43388902 0 9 294,93,134,99,50,67,67,88,128, 0,1515,1699,2482,2738,7497,8410,11359,14495, +chr21 43386134 43400757 uc002zda.1 0 - 43386280 43400673 0 8 294,93,134,99,50,67,88,128, 0,1515,1699,2482,2738,8410,11359,14495, +chr21 43386134 43400757 uc002zdb.1 0 - 43386280 43400673 0 8 294,93,134,99,50,67,88,128, 0,1515,1699,2482,2738,7497,11359,14495, +chr21 43386141 43400757 uc010gpi.1 0 - 43387645 43400673 0 7 1601,134,99,50,67,88,128, 0,1692,2475,2731,7490,11352,14488, +chr21 43390818 43400757 uc002zdc.1 0 - 43394458 43400673 0 3 3793,88,128, 0,6675,9811, +chr21 43462209 43465982 uc002zdd.1 0 + 43462278 43465459 0 3 258,123,733, 0,1486,3040, +chr21 43658826 43671430 uc002zdf.1 0 - 43661049 43670486 0 14 2599,232,282,217,126,147,224,124,125,162,64,117,170,113, 0,3024,3741,4502,4834,5340,5715,6491,6724,7119,7455,10888,11504,12491, +chr21 43694331 43698210 uc002zdg.1 0 + 43694331 43694331 0 3 898,1333,782, 0,1149,3097, +chr21 43706401 43722531 uc002zdh.1 0 - 43706401 43706401 0 4 168,183,68,160, 0,9418,13878,15970, +chr21 43773499 43903802 uc002zdi.1 0 - 43774061 43902405 0 9 771,104,118,133,150,104,151,260,108, 0,63034,84639,101131,104081,115098,127396,128870,130195, +chr21 43809497 43809957 uc002zdj.1 0 + 43809497 43809497 0 1 460, 0, +chr21 43903859 43940388 uc002zdk.1 0 + 43903973 43937692 0 16 244,83,58,86,62,130,65,182,95,98,20,132,725,153,64,2890, 0,10333,12757,14319,15085,15483,16721,17182,23728,25002,26219,27253,27965,30737,31888,33639, +chr21 43930440 43940388 uc002zdl.1 0 + 43932084 43937692 0 5 804,725,153,64,2890, 0,1384,4156,5307,7058, +chr21 43963405 44006616 uc002zdm.2 0 + 43963603 44000372 0 11 285,55,105,84,47,86,46,112,137,67,6357, 0,14972,22570,24627,26982,29898,31403,33421,34486,36601,36854, +chr21 43963405 44006616 uc010gpj.1 0 + 43963603 44000280 0 10 285,55,105,84,47,86,46,112,137,6357, 0,14972,22570,24627,26982,29898,31403,33421,34486,36854, +chr21 43963405 44006616 uc002zdn.2 0 + 43963603 44000372 0 10 285,55,105,47,86,46,112,137,67,6357, 0,14972,22570,26982,29898,31403,33421,34486,36601,36854, +chr21 43973208 43983140 uc002zdo.1 0 + 43973208 43973208 0 4 111,304,55,1251, 0,3239,5169,8681, +chr21 43973208 43983169 uc002zdp.2 0 + 43976686 43981384 0 4 111,509,55,1907, 0,3239,5169,8054, +chr21 43985728 44006616 uc002zdq.2 0 + 43986052 44000372 0 10 168,88,84,47,86,46,112,137,67,6357, 0,264,2304,4659,7575,9080,11098,12163,14278,14531, +chr21 44018258 44020687 uc002zdr.1 0 - 44018510 44020578 0 3 381,102,175, 0,708,2254, +chr21 44033845 44048411 uc002zds.2 0 + 44033938 44048083 0 13 226,83,58,86,62,130,65,194,80,98,20,114,591, 0,1813,3135,3782,5652,7885,8094,8370,10033,10980,11325,12737,13975, +chr21 44033845 44048411 uc010gpk.1 0 + 44041758 44048083 0 12 226,83,58,86,130,65,194,80,98,20,114,591, 0,1813,3135,3782,7885,8094,8370,10033,10980,11325,12737,13975, +chr21 44037239 44048411 uc010gpl.1 0 + 44037659 44048083 0 10 474,62,130,65,194,80,98,20,114,591, 0,2258,4491,4700,4976,6639,7586,7931,9343,10581, +chr21 44041669 44048411 uc010gpm.1 0 + 44041707 44048083 0 8 191,65,194,80,98,20,114,591, 0,270,546,2209,3156,3501,4913,6151, +chr21 44050068 44054670 uc002zdt.1 0 - 44050068 44050068 0 4 829,276,651,131, 0,1204,3041,4471, +chr21 44050068 44054670 uc010gpn.1 0 - 44050068 44050068 0 2 829,131, 0,4471, +chr21 44050068 44056876 uc002zdu.1 0 - 44050068 44050068 0 2 829,3767, 0,3041, +chr21 44109543 44231903 uc002zdv.1 0 + 44203990 44226701 0 10 111,63,226,170,162,154,103,76,199,5291, 0,38722,94399,102711,103883,105418,106153,112811,115754,117069, +chr21 44169706 44231903 uc002zdw.1 0 + 44203990 44226701 0 9 54,226,170,162,154,103,76,199,5291, 0,34236,42548,43720,45255,45990,52648,55591,56906, +chr21 44191238 44231903 uc002zdx.1 0 + 44199338 44226701 0 11 129,56,693,226,170,162,154,103,76,199,5291, 0,1344,7620,12704,21016,22188,23723,24458,31116,34059,35374, +chr21 44203942 44231903 uc002zdy.1 0 + 44212262 44226701 0 9 226,148,170,162,154,103,76,199,5291, 0,998,8312,9484,11019,11754,18412,21355,22670, +chr21 44256633 44304536 uc002zdz.2 0 + 44256802 44303814 0 7 236,82,136,197,196,112,763, 0,19766,25467,39955,43373,46778,47140, +chr21 44256633 44350860 uc002zea.1 0 + 44256802 44347840 0 23 236,82,136,197,196,112,248,147,115,77,92,141,113,515,142,159,230,101,127,171,178,195,3259, 0,19766,25467,39955,43373,46778,51213,61999,62714,64227,65368,67239,67690,70463,71797,74477,75374,77508,79598,81738,86032,90453,90968, +chr21 44256633 44350860 uc010gpo.1 0 + 44307923 44347840 0 24 236,82,136,197,196,112,116,248,147,115,77,92,141,113,515,142,159,230,101,127,171,178,195,3259, 0,19766,25467,39955,43373,46778,50728,51213,61999,62714,64227,65368,67239,67690,70463,71797,74477,75374,77508,79598,81738,86032,90453,90968, +chr21 44351635 44375491 uc002zeb.1 0 + 44351725 44375081 0 21 108,113,95,100,144,136,230,144,71,137,149,148,151,181,148,109,66,219,151,75,585, 0,1657,6426,6852,7298,7937,8364,10493,11436,12060,13021,13304,13625,14850,17253,18684,19573,20605,20920,21225,23271, +chr21 44377921 44390033 uc002zec.2 0 + 44378007 44389259 0 7 227,53,114,120,93,157,903, 0,490,2448,3565,6638,9593,11209, +chr21 44377921 44390033 uc002zed.2 0 + 44378007 44389259 0 6 227,53,114,120,157,903, 0,490,2448,3565,9593,11209, +chr21 44471149 44485262 uc002zee.1 0 - 44473344 44485128 0 7 2206,36,165,291,351,41,148, 0,3215,4441,8433,10028,11609,13965, +chr21 44471149 44485262 uc002zef.1 0 - 44473344 44485128 0 6 2206,36,165,291,41,148, 0,3215,4441,8433,11609,13965, +chr21 44473907 44485262 uc010gpp.1 0 - 44473909 44485128 0 6 493,165,291,351,41,148, 0,1683,5675,7270,8851,11207, +chr21 44490650 44506527 uc002zeh.1 0 - 44490707 44505570 0 12 226,86,140,76,89,88,172,113,80,45,113,477, 0,2686,4470,5283,8277,9727,12183,13097,13292,14455,14814,15400, +chr21 44490650 44506527 uc002zeg.1 0 - 44490707 44505570 0 12 223,86,140,76,89,88,172,113,80,45,113,477, 0,2686,4470,5283,8277,9727,12183,13097,13292,14455,14814,15400, +chr21 44530190 44542530 uc002zei.1 0 + 44530317 44542038 0 14 259,175,156,75,114,146,81,116,100,183,122,103,63,564, 0,677,1098,1637,2465,3777,4108,5215,6422,7113,7909,8521,10503,11776, +chr21 44534575 44542530 uc002zej.1 0 + 44535117 44542038 0 8 183,456,100,183,122,103,63,564, 0,490,2037,2728,3524,4136,6118,7391, +chr21 44534575 44542530 uc010gpq.1 0 + 44534575 44534575 0 9 183,456,100,33,68,122,103,63,564, 0,490,2037,2728,2843,3524,4136,6118,7391, +chr21 44534701 44542530 uc010gpr.1 0 + 44534904 44542038 0 7 820,100,183,122,103,63,564, 0,1911,2602,3398,4010,5992,7265, +chr21 44544357 44571684 uc002zek.1 0 + 44549638 44571173 0 25 144,181,161,136,74,78,190,166,45,109,96,93,126,65,64,147,71,88,153,165,62,112,100,106,659, 0,4228,5210,5753,6634,10959,12058,12931,13591,13866,16197,16385,18423,19304,20037,21682,22086,22915,23719,24444,24809,25106,25914,26112,26668, +chr21 44544357 44571684 uc002zel.1 0 + 44544416 44571173 0 22 144,74,78,190,166,45,109,96,93,126,65,64,147,71,88,153,165,62,112,100,106,659, 0,6634,10959,12058,12931,13591,13866,16197,16385,18423,19304,20037,21682,22086,22915,23719,24444,24809,25106,25914,26112,26668, +chr21 44563661 44571684 uc002zem.1 0 + 44566087 44571173 0 11 797,147,71,88,153,165,62,112,100,106,659, 0,2378,2782,3611,4415,5140,5505,5802,6610,6808,7364, +chr21 44563661 44571684 uc002zen.1 0 + 44566087 44571173 0 10 2525,71,88,153,165,62,112,100,106,659, 0,2782,3611,4415,5140,5505,5802,6610,6808,7364, +chr21 44573254 44578835 uc010gps.1 0 - 44574508 44575334 0 4 1383,1552,230,464, 0,1519,4089,5117, +chr21 44573254 44583095 uc002zeo.1 0 - 44574508 44580097 0 8 1383,94,172,221,47,97,19,551, 0,1879,2899,4089,6814,7880,8705,9290, +chr21 44573254 44583713 uc002zep.2 0 - 44574508 44583505 0 7 1383,97,172,230,47,19,285, 0,1879,2899,4089,6814,8705,10174, +chr21 44573254 44583713 uc002zeq.2 0 - 44574508 44583505 0 7 1383,454,172,230,47,19,285, 0,1519,2899,4089,6814,8705,10174, +chr21 44573254 44583713 uc002zer.2 0 - 44574508 44583505 0 7 1383,94,172,230,47,19,285, 0,1879,2899,4089,6814,8705,10174, +chr21 44578846 44583095 uc002zes.1 0 - 44580078 44582743 0 3 1269,19,551, 0,3113,3698, +chr21 44594473 44687392 uc002zet.1 0 + 44598011 44686128 0 33 113,265,89,169,181,167,181,62,201,103,122,354,138,130,146,113,217,119,133,172,184,182,133,88,88,158,77,102,87,106,102,117,1390, 0,3438,4485,13951,16591,19014,25670,27549,28834,32555,40741,41109,45251,47584,49133,50096,51518,54979,55742,56431,63728,67764,68260,73482,74689,75507,76497,76847,84968,86899,88904,90626,91529, +chr21 44597566 44687392 uc002zeu.1 0 + 44598011 44686128 0 32 610,89,169,181,167,181,62,201,103,122,354,138,130,146,113,217,119,133,172,184,182,133,88,88,158,77,102,87,106,102,117,1390, 0,1392,10858,13498,15921,22577,24456,25741,29462,37648,38016,42158,44491,46040,47003,48425,51886,52649,53338,60635,64671,65167,70389,71596,72414,73404,73754,81875,83806,85811,87533,88436, +chr21 44597911 44687392 uc002zew.1 0 + 44598011 44686128 0 32 265,89,169,181,167,181,62,201,103,122,354,138,130,146,113,217,119,133,172,184,182,133,88,88,158,77,102,87,106,102,117,1390, 0,1047,10513,13153,15576,22232,24111,25396,29117,37303,37671,41813,44146,45695,46658,48080,51541,52304,52993,60290,64326,64822,70044,71251,72069,73059,73409,81530,83461,85466,87188,88091, +chr21 44597911 44687392 uc010gpt.1 0 + 44598011 44686128 0 33 265,89,169,181,167,181,62,201,103,122,354,138,130,146,113,217,119,133,172,184,182,133,150,88,88,158,77,102,87,106,102,117,1390, 0,1047,10513,13153,15576,22232,24111,25396,29117,37303,37671,41813,44146,45695,46658,48080,51541,52304,52993,60290,64326,64822,68669,70044,71251,72069,73059,73409,81530,83461,85466,87188,88091, +chr21 44613431 44687392 uc002zex.1 0 + 44613525 44686128 0 28 223,181,62,201,103,122,354,138,130,146,113,217,119,133,172,184,182,133,88,88,158,77,102,87,106,102,117,1390, 0,6712,8591,9876,13597,21783,22151,26293,28626,30175,31138,32560,36021,36784,37473,44770,48806,49302,54524,55731,56549,57539,57889,66010,67941,69946,71668,72571, +chr21 44635582 44687392 uc002zey.1 0 + 44635603 44686128 0 21 354,138,130,146,113,217,119,133,172,184,182,133,88,88,158,77,87,106,102,117,1390, 0,4142,6475,8024,8987,10409,13870,14633,15322,22619,26655,27151,32373,33580,34398,35388,43859,45790,47795,49517,50420, +chr21 44658905 44661051 uc002zez.1 0 - 44658905 44658905 0 2 350,1706, 0,440, +chr21 44699820 44703167 uc002zfa.1 0 + 44700955 44701729 0 2 146,2359, 0,988, +chr21 44700955 44701729 uc010gpu.1 0 + 44700955 44701729 0 1 774, 0, +chr21 44722649 44722699 uc002zfb.1 0 - 44722649 44722649 0 1 50, 0, +chr21 44728608 44728644 uc002zfc.1 0 - 44728608 44728608 0 1 36, 0, +chr21 44737584 44737655 uc002zfd.1 0 - 44737584 44737584 0 1 71, 0, +chr21 44742202 44955923 uc002zfe.1 0 - 44744093 44955857 0 12 2045,102,188,230,187,227,132,157,91,239,221,148, 0,6888,11307,23991,27761,29400,30560,31906,33151,35793,69894,213573, +chr21 44742202 44955923 uc010gpv.1 0 - 44744093 44812195 0 13 2045,102,188,230,187,227,132,157,91,239,221,62,148, 0,6888,11307,23991,27761,29400,30560,31906,33151,35793,69894,192685,213573, +chr21 44761525 44765140 uc002zff.2 0 + 44761525 44761525 0 3 621,74,2202, 0,1044,1413, +chr21 44761525 44765140 uc002zfg.2 0 + 44761525 44761525 0 2 621,2202, 0,1413, +chr21 44783495 44784506 uc002zfh.1 0 - 44783612 44784461 0 1 1011, 0, +chr21 44794745 44795816 uc002zfi.1 0 - 44795001 44795769 0 1 1071, 0, +chr21 44802333 44803071 uc002zfj.1 0 - 44802360 44803026 0 1 738, 0, +chr21 44818033 44819415 uc002zfk.1 0 + 44818063 44819269 0 1 1382, 0, +chr21 44823991 44824909 uc002zfl.1 0 - 44824067 44824883 0 1 918, 0, +chr21 44835576 44836814 uc002zfm.1 0 - 44835695 44836793 0 1 1238, 0, +chr21 44844924 44846519 uc002zfn.2 0 + 44844949 44846077 0 2 159,1421, 0,174, +chr21 44856423 44857299 uc002zfo.1 0 + 44856445 44857225 0 1 876, 0, +chr21 44871467 44872723 uc002zfp.2 0 + 44871516 44872395 0 1 1256, 0, +chr21 44881700 44882800 uc002zfq.1 0 + 44881762 44882518 0 1 1100, 0, +chr21 44890758 44891994 uc002zfr.2 0 + 44890803 44891700 0 1 1236, 0, +chr21 44898557 44899004 uc002zfs.1 0 - 44898620 44898959 0 1 447, 0, +chr21 44902276 44902686 uc002zft.1 0 + 44902324 44902615 0 1 410, 0, +chr21 44910533 44911272 uc002zfu.1 0 - 44910790 44911231 0 1 739, 0, +chr21 44925918 44926506 uc002zfv.1 0 - 44926175 44926466 0 1 588, 0, +chr21 44941514 44942387 uc002zfw.1 0 + 44941544 44942282 0 1 873, 0, +chr21 45013382 45046166 uc002zfx.1 0 - 45015719 45032303 0 7 2450,141,119,46,36,115,118, 0,4507,8259,18880,19020,32244,32666, +chr21 45013382 45046166 uc002zfy.1 0 - 45015719 45046091 0 6 2450,141,119,46,36,118, 0,4507,8259,18880,19020,32666, +chr21 45049959 45062472 uc002zfz.1 0 - 45051293 45062311 0 4 1424,72,129,182, 0,3430,8359,12331, +chr21 45049959 45062472 uc002zga.1 0 - 45051247 45062311 0 4 1424,122,129,182, 0,3380,8359,12331, +chr21 45093940 45118169 uc002zgb.1 0 - 45095923 45117959 0 6 2030,47,172,109,53,325, 0,5612,6595,11565,15797,23904, +chr21 45130296 45155169 uc002zgd.1 0 - 45130710 45155125 0 15 477,167,203,220,245,188,141,90,96,156,242,171,181,89,102, 0,782,2739,3322,4024,5855,7450,9017,13113,14366,15538,17411,20961,24330,24771, +chr21 45130296 45155785 uc002zge.1 0 - 45130710 45155125 0 16 477,167,203,220,245,188,141,90,96,156,242,171,181,89,61,67, 0,782,2739,3322,4024,5855,7450,9017,13113,14366,15538,17411,20961,24330,24771,25422, +chr21 45130296 45165393 uc002zgf.2 0 - 45130710 45155125 0 16 477,167,203,220,245,188,141,90,96,156,242,171,181,89,61,230, 0,782,2739,3322,4024,5855,7450,9017,13113,14366,15538,17411,20961,24330,24771,34867, +chr21 45130296 45165393 uc010gpw.1 0 - 45130710 45155125 0 15 477,167,203,220,245,188,141,90,96,156,242,181,89,61,230, 0,782,2739,3322,4024,5855,7450,9017,13113,14366,15538,20961,24330,24771,34867, +chr21 45130296 45173181 uc002zgg.1 0 - 45130710 45155125 0 16 477,167,203,220,245,188,141,90,96,156,242,171,181,89,61,185, 0,782,2739,3322,4024,5855,7450,9017,13113,14366,15538,17411,20961,24330,24771,42700, +chr21 45165393 45174016 uc002zgh.2 0 + 45165393 45165393 0 4 277,137,43,1820, 0,5817,6574,6803, +chr21 45177156 45179316 uc002zgi.1 0 - 45177156 45177156 0 2 1555,40, 0,2120, +chr21 45179070 45184188 uc002zgj.2 0 - 45179154 45181947 0 4 369,264,144,253, 0,899,2811,4865, +chr21 45179070 45184188 uc002zgk.2 0 - 45179154 45184010 0 3 369,264,253, 0,899,4865, +chr21 45184382 45221316 uc002zgl.1 0 + 45184400 45221146 0 6 147,154,69,148,69,294, 0,3644,20060,26994,33157,36640, +chr21 45184382 45221316 uc002zgm.1 0 + 45184400 45221146 0 6 147,109,69,148,69,294, 0,3644,20060,26994,33157,36640, +chr21 45235614 45238429 uc002zgn.1 0 - 45235614 45235614 0 2 561,183, 0,2632, +chr21 45243556 45249070 uc002zgo.2 0 - 45243556 45243556 0 2 443,284, 0,5230, +chr21 45318942 45390638 uc002zgp.1 0 + 45318942 45318942 0 10 194,106,56,166,172,92,124,118,332,1132, 0,42333,43964,46194,53802,57615,58959,60115,70031,70564, +chr21 45318942 45470902 uc002zgq.1 0 + 45415999 45466540 0 13 194,172,75,935,115,169,149,120,169,182,179,1560,1013, 0,53802,97010,101130,105730,107985,108762,109874,110323,129955,146236,147418,150947, +chr21 45318942 45470902 uc010gpx.1 0 + 45318942 45318942 0 11 194,172,75,115,169,149,169,182,179,1560,1013, 0,53802,97010,105730,107985,108762,110323,129955,146236,147418,150947, +chr21 45318942 45470902 uc002zgr.1 0 + 45415999 45469898 0 13 194,172,75,935,115,169,149,120,169,182,179,90,1013, 0,53802,97010,101130,105730,107985,108762,109874,110323,129955,146236,147418,150947, +chr21 45318942 45470902 uc002zgs.1 0 + 45379138 45466540 0 13 194,172,118,75,935,115,169,149,169,182,179,1560,1013, 0,53802,60115,97010,101130,105730,107985,108762,110323,129955,146236,147418,150947, +chr21 45318942 45470902 uc002zgt.1 0 + 45415999 45466540 0 11 194,172,75,935,115,169,149,169,182,179,4542, 0,53802,97010,101130,105730,107985,108762,110323,129955,146236,147418, +chr21 45318942 45470902 uc002zgv.1 0 + 45318942 45318942 0 12 194,172,75,935,115,169,149,169,182,179,1560,1013, 0,53802,97010,101130,105730,107985,108762,110323,129955,146236,147418,150947, +chr21 45318942 45470902 uc002zgw.1 0 + 45415999 45469898 0 12 194,172,75,935,115,169,149,169,182,179,90,1013, 0,53802,97010,101130,105730,107985,108762,110323,129955,146236,147418,150947, +chr21 45318942 45470902 uc002zgu.1 0 + 45318942 45318942 0 12 194,172,75,935,115,169,149,169,182,179,263,1013, 0,53802,97010,101130,105730,107985,108762,110323,129955,146236,147418,150947, +chr21 45415952 45470902 uc002zgy.1 0 + 45415999 45466540 0 10 75,935,115,169,149,120,169,182,179,4542, 0,4120,8720,10975,11752,12864,13313,32945,49226,50408, +chr21 45478694 45503073 uc002zgz.1 0 + 45478694 45478694 0 3 155,95,280, 0,9180,24099, +chr21 45508270 45521753 uc002zha.1 0 - 45508270 45508270 0 6 1708,206,124,181,126,178, 0,2094,3662,5911,13089,13305, +chr21 45508270 45532239 uc002zhb.1 0 - 45508270 45508270 0 10 1708,206,124,181,126,67,111,145,251,156, 0,2094,3662,5911,13089,14175,18421,19455,21750,23813, +chr21 45508270 45532239 uc002zhc.1 0 - 45509824 45532214 0 9 1708,124,181,126,67,111,145,251,156, 0,3662,5911,13089,14175,18421,19455,21750,23813, +chr21 45508270 45532239 uc002zhd.1 0 - 45511793 45532214 0 8 3786,181,126,67,111,145,251,156, 0,5911,13089,14175,18421,19455,21750,23813, +chr21 45532394 45536081 uc002zhe.1 0 + 45532394 45532394 0 3 193,88,1268, 0,1299,2419, +chr21 45539291 45541696 uc002zhf.1 0 + 45539291 45539291 0 1 2405, 0, +chr21 45649524 45758062 uc002zhg.1 0 + 45649573 45756740 0 42 60,95,545,87,60,130,77,216,27,63,87,54,159,63,27,132,63,27,36,72,36,90,30,27,63,75,27,54,75,69,43,63,44,141,145,74,129,33,246,198,116,1533, 0,197,63059,68712,70293,71168,72228,72567,73144,74719,74887,75284,75517,76780,77612,81678,82264,83235,84303,85092,85653,86042,87352,87504,87980,88318,89362,89679,90175,91317,91867,92416,98828,99233,99951,100175,100655,102378,104173,104881,105928,107005, +chr21 45664058 45669413 uc002zhh.1 0 - 45665698 45666907 0 3 1904,250,187, 0,2696,5168, +chr21 45699851 45758062 uc002zhi.1 0 + 45699872 45756740 0 41 667,545,87,60,130,77,216,27,63,87,54,159,63,27,132,63,27,36,72,36,90,30,27,63,75,27,54,75,69,43,63,44,141,145,74,129,33,246,198,116,1533, 0,12732,18385,19966,20841,21901,22240,22817,24392,24560,24957,25190,26453,27285,31351,31937,32908,33976,34765,35326,35715,37025,37177,37653,37991,39035,39352,39848,40990,41540,42089,48501,48906,49624,49848,50328,52051,53846,54554,55601,56678, +chr21 45742542 45788753 uc010gpy.1 0 - 45742609 45782301 0 6 412,142,202,760,238,275, 0,27616,32569,33188,39570,45936, +chr21 45748757 45758062 uc002zhj.1 0 + 45749755 45756740 0 9 141,145,74,132,33,246,198,116,1533, 0,718,942,1419,3145,4940,5648,6695,7772, +chr21 45751841 45758062 uc002zhk.1 0 + 45754444 45756740 0 5 94,246,198,116,1533, 0,1856,2564,3611,4688, +chr21 45759056 45786779 uc002zhl.1 0 - 45759999 45782301 0 6 1426,142,202,760,238,70, 0,11102,16055,16674,23056,27653, +chr21 45759056 45786779 uc010gpz.1 0 - 45759999 45776316 0 6 1426,142,202,760,242,70, 0,11102,16055,16674,23052,27653, +chr21 45759056 45786779 uc002zhm.1 0 - 45759317 45782301 0 6 438,142,202,760,238,70, 0,11102,16055,16674,23056,27653, +chr21 45837995 45841691 uc002zhn.1 0 + 45837995 45837995 0 2 55,959, 0,2737, +chr21 45877516 45878815 uc010gqa.1 0 + 45877516 45877516 0 1 1299, 0, +chr21 45888110 46180046 uc010gqb.1 0 + 46094427 46179854 0 14 100,38,135,155,24,33,117,132,129,75,42,79,60,452, 0,91623,206192,252439,255830,256822,257228,265586,267133,270182,273819,286148,287017,291484, +chr21 46072302 46080761 uc002zho.1 0 - 46072302 46072302 0 3 3281,51,134, 0,4647,8325, +chr21 46092504 46186795 uc002zhp.1 0 + 46094427 46186048 0 14 239,135,155,24,33,117,132,129,75,42,79,53,170,784, 0,1798,48045,51436,52428,52834,61192,62739,65788,69425,81754,87090,91867,93507, +chr21 46094302 46162867 uc010gqc.1 0 + 46094427 46162054 0 8 135,155,24,33,117,132,403,938, 0,46247,49638,50630,51036,59394,60941,67627, +chr21 46094302 46186795 uc002zhq.1 0 + 46140635 46186048 0 14 135,155,24,33,117,132,129,75,42,79,60,53,170,784, 0,46247,49638,50630,51036,59394,60941,63990,67627,79956,80825,85292,90069,91709, +chr21 46094302 46186795 uc002zhr.1 0 + 46094427 46186048 0 14 135,155,24,33,117,132,129,75,42,76,60,53,170,784, 0,46247,49638,50630,51036,59394,60941,63990,67627,79959,80825,85292,90069,91709, +chr21 46094302 46186795 uc002zhs.1 0 + 46094427 46186048 0 13 135,155,24,33,117,132,129,42,76,60,53,170,784, 0,46247,49638,50630,51036,59394,60941,67627,79959,80825,85292,90069,91709, +chr21 46140549 46186795 uc002zht.1 0 + 46140635 46186048 0 13 155,24,33,117,132,129,144,42,76,60,53,170,784, 0,3391,4383,4789,13147,14694,17743,21380,33712,34578,39045,43822,45462, +chr21 46226090 46249391 uc002zhu.1 0 + 46226192 46248355 0 35 199,130,201,160,129,21,21,45,54,45,27,27,45,54,63,63,54,36,63,63,63,63,51,36,63,66,36,37,9,134,110,184,184,30,1659, 0,885,2520,4777,5195,5406,5750,5861,7335,7859,8003,8509,8629,9024,9230,10261,10415,10614,10999,12418,15672,15951,16372,16649,17148,17404,17908,18582,19010,19504,20212,20469,20778,21371,21642, +chr21 46242041 46249391 uc010gqd.1 0 + 46246353 46248355 0 13 63,51,36,63,66,36,41,134,110,184,184,30,1659, 0,421,698,1197,1453,1957,2631,3553,4261,4518,4827,5420,5691, +chr21 46245538 46249391 uc002zhv.1 0 + 46246353 46248355 0 6 190,110,184,184,30,1659, 0,764,1021,1330,1923,2194, +chr21 46246830 46249391 uc002zhw.1 0 + 46247986 46248355 0 3 222,30,1659, 0,631,902, +chr21 46281393 46283633 uc002zhx.1 0 + 46281393 46281393 0 2 847,835, 0,1405, +chr21 46342460 46374147 uc002zhy.1 0 + 46355818 46373270 0 28 55,142,599,21,66,54,45,27,27,45,54,63,63,90,63,63,63,63,51,36,63,63,36,46,153,453,39,903, 0,13331,13860,14685,15889,17753,17890,18258,18532,18651,19281,19755,20495,20911,21669,22396,22942,23437,23989,24377,24756,26532,26766,27147,27346,27666,28384,30784, +chr21 46342460 46374147 uc002zhz.1 0 + 46355818 46373833 0 28 55,142,599,21,66,54,45,27,27,45,54,63,63,90,63,63,63,63,51,36,63,63,36,46,153,453,39,610, 0,13331,13860,14685,15889,17753,17890,18258,18532,18651,19281,19755,20495,20911,21669,22396,22942,23437,23989,24377,24756,26532,26766,27147,27346,27666,28384,31077, +chr21 46342460 46377191 uc002zia.1 0 + 46355818 46376894 0 28 55,142,599,21,66,54,45,27,27,45,54,63,63,90,63,63,63,63,51,36,63,63,36,46,153,453,39,896, 0,13331,13860,14685,15889,17753,17890,18258,18532,18651,19281,19755,20495,20911,21669,22396,22942,23437,23989,24377,24756,26532,26766,27147,27346,27666,28384,33835, +chr21 46342460 46377191 uc002zib.1 0 + 46369619 46376894 0 9 55,32,63,36,46,153,453,39,896, 0,24787,26532,26766,27147,27346,27666,28384,33835, +chr21 46370831 46377191 uc002zic.1 0 + 46370831 46370831 0 2 52,896, 0,5464, +chr21 46374170 46377189 uc010gqe.1 0 + 46374170 46374170 0 1 3019, 0, +chr21 46380603 46387083 uc002zie.1 0 - 46380603 46380603 0 5 233,159,96,139,633, 0,653,977,2246,5847, +chr21 46380603 46399909 uc002zif.1 0 - 46381328 46399865 0 15 233,89,96,139,44,162,130,62,132,138,180,89,129,184,98, 0,723,977,2246,2618,9155,9556,10004,13857,14126,15296,15630,16645,17887,19208, +chr21 46380603 46399909 uc002zig.1 0 - 46380795 46399865 0 15 233,139,96,139,44,162,130,62,132,138,180,89,129,184,98, 0,653,977,2246,2618,9155,9556,10004,13857,14126,15296,15630,16645,17887,19208, +chr21 46381121 46399909 uc002zih.1 0 - 46381328 46399865 0 14 294,96,139,44,162,130,62,132,138,180,89,129,184,98, 0,459,1728,2100,8637,9038,9486,13339,13608,14778,15112,16127,17369,18690, +chr21 46381121 46399909 uc010gqf.1 0 - 46381587 46399865 0 13 294,96,139,162,130,62,132,138,180,89,129,184,98, 0,459,1728,8637,9038,9486,13339,13608,14778,15112,16127,17369,18690, +chr21 46381326 46399909 uc010gqg.1 0 - 46381328 46396296 0 14 89,96,139,44,162,130,62,132,138,180,114,129,184,98, 0,254,1523,1895,8432,8833,9281,13134,13403,14573,14907,15922,17164,18485, +chr21 46405497 46428729 uc002zii.1 0 - 46405720 46412731 0 4 550,152,351,32, 0,760,7152,23200, +chr21 46432787 46473119 uc002zij.1 0 - 46435445 46473087 0 23 376,170,79,171,81,66,106,97,150,51,72,57,28,98,119,109,136,97,122,109,139,166,46, 0,2620,3435,6045,7230,7756,17390,18226,18982,19805,21108,22242,24579,25292,26734,27239,27943,31030,33408,34184,39106,39988,40286, +chr21 46433466 46473079 uc002zik.1 0 - 46435445 46471972 0 21 2111,79,171,81,66,106,97,150,51,72,57,28,98,119,109,136,97,122,109,139,304, 0,2756,5366,6551,7077,16711,17547,18303,19126,20429,21563,23900,24613,26055,26560,27264,30351,32729,33505,38427,39309, +chr21 46433466 46473119 uc002zil.1 0 - 46435445 46473087 0 22 2111,79,171,81,66,106,97,150,51,72,57,28,98,119,109,136,97,122,109,139,166,46, 0,2756,5366,6551,7077,16711,17547,18303,19126,20429,21563,23900,24613,26055,26560,27264,30351,32729,33505,38427,39309,39607, +chr21 46473585 46496032 uc002zim.2 0 + 46473585 46473585 0 3 23,186,2105, 0,11590,20342, +chr21 46473585 46496032 uc002zin.2 0 + 46474701 46493945 0 4 23,201,186,2105, 0,1083,11590,20342, +chr21 46479475 46491502 uc002zio.1 0 - 46479609 46490780 0 7 293,151,207,130,258,391,854, 0,1695,5677,7668,8331,9673,11173, +chr21 46479475 46503607 uc002zip.1 0 - 46479609 46501285 0 13 293,151,207,130,258,391,98,259,154,135,69,198,327, 0,1695,5677,7668,8331,9673,11173,11494,16395,19258,19642,21655,23805, +chr21 46479475 46511294 uc002ziq.1 0 - 46479609 46509677 0 18 293,151,207,130,258,391,98,259,154,135,69,198,153,114,132,101,203,1028, 0,1695,5677,7668,8331,9673,11173,11494,16395,19258,19642,21655,23805,25659,26146,28983,30187,30791, +chr21 46479475 46529664 uc002zir.1 0 - 46479609 46529628 0 28 293,151,207,130,258,391,98,259,154,135,69,198,153,114,132,101,203,242,161,163,269,198,140,191,145,79,224,1255, 0,1695,5677,7668,8331,9673,11173,11494,16395,19258,19642,21655,23805,25659,26146,28983,30187,30791,31848,35267,37427,38254,40052,42393,44859,45363,48481,48934, +chr21 46480565 46496171 uc002zis.1 0 + 46480565 46480565 0 3 103,186,281, 0,4610,15325, +chr21 46530694 46536539 uc002zit.1 0 + 46531255 46535831 0 3 63,254,864, 0,517,4981, +chr21 46530694 46536539 uc002ziu.1 0 + 46531255 46535831 0 3 385,254,864, 0,517,4981, +chr21 46530694 46542093 uc002ziv.1 0 + 46531255 46541976 0 5 385,254,129,69,213, 0,517,4981,9809,11186, +chr21 46530694 46542093 uc002ziw.1 0 + 46531255 46541976 0 5 63,119,129,69,213, 0,517,4981,9809,11186, +chr21 46530694 46542093 uc002zix.1 0 + 46531255 46541976 0 5 63,254,129,69,213, 0,517,4981,9809,11186, +chr21 46530694 46542093 uc002ziy.1 0 + 46531255 46541976 0 4 385,254,69,213, 0,517,9809,11186, +chr21 46530694 46542093 uc010gqh.1 0 + 46531255 46541976 0 4 63,119,69,213, 0,517,9809,11186, +chr21 46537349 46539139 uc010gqi.1 0 + 46537349 46537349 0 2 570,257, 0,1533, +chr21 46544772 46562562 uc002ziz.2 0 - 46545115 46562413 0 7 364,92,112,165,74,61,209, 0,2054,11025,14285,15043,16777,17581, +chr21 46544772 46565167 uc002zja.2 0 - 46546340 46559348 0 9 364,158,92,112,334,74,141,209,189, 0,1566,2054,11025,14285,15043,16777,17581,20206, +chr21 46545474 46563479 uc002zjc.1 0 - 46546340 46559348 0 7 1022,92,112,334,74,141,1126, 0,1352,10323,13583,14341,16075,16879, +chr21 46545474 46568213 uc002zjf.1 0 - 46546340 46567080 0 8 1022,92,112,165,74,61,209,1233, 0,1352,10323,13583,14341,16075,16879,21506, +chr21 46545477 46568213 uc010gqj.1 0 - 46545477 46545477 0 9 578,158,92,112,334,74,141,209,1233, 0,861,1349,10320,13580,14338,16072,16876,21503, +chr21 46559057 46568213 uc002zjg.1 0 - 46559057 46559057 0 6 334,74,61,209,177,1233, 0,758,2492,3296,4069,7923, +chr21 46568463 46690110 uc002zji.2 0 + 46568570 46689668 0 47 161,213,372,81,256,56,175,137,112,223,82,175,218,455,556,147,152,143,233,163,213,230,117,21,207,171,153,879,156,771,103,155,141,174,196,223,151,687,245,103,174,120,230,77,139,128,486, 0,2255,10275,22006,22621,23335,24890,25562,27307,28982,29865,31331,32853,39359,42463,57573,61711,64621,65078,66549,67043,73143,73892,74113,75468,77429,78209,87067,88715,91947,94082,97848,101709,103500,104273,105888,106385,107407,111781,112856,114041,115960,116732,118374,119687,120571,121161, +chr21 46569229 46690110 uc002zjj.1 0 + 46578825 46689668 0 47 323,213,372,81,256,56,175,137,112,223,82,175,218,455,556,147,152,143,233,163,213,230,117,21,207,171,153,879,156,771,103,155,141,174,196,223,151,450,245,103,174,120,230,77,139,128,486, 0,1489,9509,21240,21855,22569,24124,24796,26541,28216,29099,30565,32087,38593,41697,56807,60945,63855,64312,65783,66277,72377,73126,73347,74702,76663,77443,86301,87949,91181,93316,97082,100943,102734,103507,105122,105619,106641,111015,112090,113275,115194,115966,117608,118921,119805,120395, +chr21 46578738 46594162 uc010gqk.1 0 + 46578738 46578738 0 6 372,81,259,56,175,137, 0,11731,12326,13060,14615,15287, +chr21 46699327 46703021 uc002zjk.1 0 - 46699327 46699327 0 2 932,597, 0,3097, +chr21 46703317 46790647 uc002zjl.1 0 + 46703472 46790347 0 20 246,72,120,120,252,129,120,198,92,111,124,110,103,65,94,120,115,140,137,426, 0,25780,31623,38011,39605,45384,50280,52440,70115,73150,74547,75027,75608,78247,78469,79506,80900,82779,86160,86904, +chr21 46703317 46791548 uc002zjm.1 0 + 46703472 46791387 0 21 246,72,120,120,252,129,120,198,92,111,124,110,103,65,94,120,115,140,137,81,293, 0,25780,31623,38011,39605,45384,50280,52440,70115,73150,74547,75027,75608,78247,78469,79506,80900,82779,86160,86904,87938, +chr21 46703317 46791548 uc010gql.1 0 + 46703472 46791387 0 20 246,72,120,120,252,120,198,92,111,124,110,103,65,94,120,115,140,137,81,293, 0,25780,31623,38011,39605,50280,52440,70115,73150,74547,75027,75608,78247,78469,79506,80900,82779,86160,86904,87938, +chr21 46703317 46794451 uc002zjn.1 0 + 46703472 46794259 0 22 246,72,120,120,252,129,120,198,92,111,124,110,103,65,94,120,115,140,137,81,128,340, 0,25780,31623,38011,39605,45384,50280,52440,70115,73150,74547,75027,75608,78247,78469,79506,80900,82779,86160,86904,87938,90794, +chr21 46703317 46813028 uc002zjo.1 0 + 46703472 46811963 0 38 246,72,120,120,252,129,120,198,92,111,124,110,103,65,94,120,115,140,137,81,128,115,202,110,81,124,122,112,110,131,169,171,62,58,75,175,124,1318, 0,25780,31623,38011,39605,45384,50280,52440,70115,73150,74547,75027,75608,78247,78469,79506,80900,82779,86160,86904,87938,90794,91566,92657,92847,95192,95598,95845,97005,97962,98608,99246,101745,102771,104881,106736,107583,108393, +chr21 46748653 46789614 uc002zjp.1 0 + 46748811 46789614 0 14 177,120,198,92,111,124,110,103,65,94,120,115,140,137, 0,4944,7104,24779,27814,29211,29691,30272,32911,33133,34170,35564,37443,40824, +chr21 46783075 46791548 uc002zjq.1 0 + 46784120 46791387 0 5 1257,140,137,81,293, 0,3021,6402,7146,8180, +chr21 46797251 46803437 uc002zjr.2 0 + 46798578 46802830 0 7 1382,122,112,110,131,169,874, 0,1664,1911,3071,4028,4674,5312, +chr21 46805625 46813028 uc002zjs.1 0 + 46806017 46811963 0 5 521,75,175,124,1318, 0,2573,4428,5275,6085, +chr21 46808123 46813028 uc002zjt.1 0 + 46808123 46808123 0 4 150,175,124,1318, 0,1930,2777,3587, +chr21 46842958 46849463 uc002zju.1 0 - 46843703 46846756 0 3 886,139,110, 0,3660,6395, +chr21 46842958 46849463 uc002zjv.1 0 - 46843791 46846756 0 4 886,94,139,110, 0,1664,3660,6395, +chr21 46879954 46904483 uc002zjw.2 0 + 46881291 46903264 0 7 149,95,105,183,162,165,1399, 0,1281,7920,8691,12843,13960,23130, +chr21 46879954 46909291 uc002zjx.1 0 + 46881291 46908667 0 12 149,109,95,105,183,162,165,176,130,137,172,657, 0,824,1281,7920,8691,12843,13960,23130,25218,26185,27768,28680, +chr21 46879954 46909291 uc002zjy.1 0 + 46881291 46908667 0 11 149,95,105,183,162,165,176,130,137,172,657, 0,1281,7920,8691,12843,13960,23130,25218,26185,27768,28680, +chr21 46879954 46909291 uc010gqm.1 0 + 46881291 46908667 0 9 149,95,105,183,162,165,137,172,657, 0,1281,7920,8691,12843,13960,26185,27768,28680, +chr21 46887625 46906276 uc002zjz.1 0 + 46892812 46905317 0 6 354,183,162,165,176,1104, 0,1020,5172,6289,15459,17547,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/data/rmsk.hg18.chr21.bed Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,57261 @@ +chr21 9719768 9721892 ALR/Alpha 1004 + +chr21 9721905 9725582 ALR/Alpha 1010 + +chr21 9725582 9725977 L1PA3 3288 + +chr21 9726021 9729309 ALR/Alpha 1051 + +chr21 9729320 9729809 L1PA3 3897 - +chr21 9729809 9730866 L1P1 8367 + +chr21 9730866 9734026 ALR/Alpha 1036 - +chr21 9734037 9757471 ALR/Alpha 1182 - +chr21 9757520 9758476 ALR/Alpha 1092 - +chr21 9758521 9764575 L1PA3 26286 - +chr21 9764577 9778787 ALR/Alpha 1141 - +chr21 9778798 9788657 ALR/Alpha 1188 - +chr21 9788657 9794680 L1PA3 27485 - +chr21 9794680 9795266 ALR/Alpha 1011 - +chr21 9795278 9795587 ALR/Alpha 979 - +chr21 9795589 9795713 (GAATG)n 308 + +chr21 9795736 9795894 (GAATG)n 683 + +chr21 9795911 9796007 (GAATG)n 345 + +chr21 9796028 9796187 (GAATG)n 756 + +chr21 9796202 9796615 (GAATG)n 891 + +chr21 9796637 9796824 (GAATG)n 621 + +chr21 9796824 9796866 HSATII 242 - +chr21 9796866 9797049 (GAATG)n 621 + +chr21 9797067 9797436 (GAATG)n 900 + +chr21 9797482 9797839 (GAATG)n 1008 + +chr21 9797866 9798044 (GAATG)n 858 + +chr21 9798051 9798118 (GAGTG)n 259 + +chr21 9798118 9798658 (GAATG)n 969 + +chr21 9798626 9798765 (AAATG)n 201 + +chr21 9798770 9798950 (GAGTG)n 571 + +chr21 9798908 9799265 (GAATG)n 942 + +chr21 9799280 9799460 (GAATG)n 813 + +chr21 9799500 9800262 (GAATG)n 933 + +chr21 9800289 9800469 (GAATG)n 666 + +chr21 9800481 9800797 (GAATG)n 977 + +chr21 9800840 9800878 (GAGTG)n 225 + +chr21 9800913 9801092 (GAGTG)n 930 + +chr21 9801092 9801169 (GAATG)n 298 + +chr21 9801182 9801639 (GAATG)n 747 + +chr21 9801651 9801769 (GAATG)n 330 + +chr21 9801781 9802265 (GAATG)n 747 + +chr21 9802265 9802310 (GAGTG)n 245 + +chr21 9802310 9802490 (GAATG)n 1203 + +chr21 9802490 9802503 (GAGTG)n 245 + +chr21 9802508 9802679 (GAATG)n 660 + +chr21 9802699 9803425 (GAATG)n 1008 + +chr21 9803427 9803488 (GAGTG)n 332 + +chr21 9803490 9803789 (GAATG)n 708 + +chr21 9803803 9804202 (GAATG)n 897 + +chr21 9804215 9804262 (GAATG)n 261 + +chr21 9804276 9804450 (GAATG)n 771 + +chr21 9804469 9804637 (GAATG)n 756 + +chr21 9804660 9804840 (GAATG)n 729 + +chr21 9804905 9805085 (GAATG)n 726 + +chr21 9805118 9805404 (GAATG)n 930 + +chr21 9805416 9805716 (GAATG)n 708 + +chr21 9805730 9806084 (GAATG)n 1050 + +chr21 9806147 9806522 (GAATG)n 765 + +chr21 9806555 9806812 (GAATG)n 661 + +chr21 9806824 9807184 (GAATG)n 1080 + +chr21 9807228 9807661 (GAATG)n 888 + +chr21 9807669 9807698 (GAGTG)n 231 + +chr21 9807698 9808290 (GAATG)n 807 + +chr21 9808301 9808897 (GAATG)n 984 + +chr21 9808920 9809796 (GAATG)n 960 + +chr21 9809843 9810023 (GAATG)n 972 + +chr21 9810043 9810492 (GAATG)n 690 + +chr21 9810503 9810553 (GAATG)n 208 + +chr21 9810554 9810733 (GAGTG)n 828 + +chr21 9810696 9811576 (GAATG)n 1005 + +chr21 9811606 9811772 (GAATG)n 604 + +chr21 9811778 9812022 (GAGTG)n 858 + +chr21 9812022 9812464 (GAATG)n 1017 + +chr21 9812479 9812900 (GAATG)n 729 + +chr21 9812901 9812954 (GAGTG)n 235 + +chr21 9812958 9813124 (GAATG)n 740 + +chr21 9813179 9813356 (GAGTG)n 819 + +chr21 9813335 9813790 (GAATG)n 837 + +chr21 9813801 9813973 (GAATG)n 582 + +chr21 9814004 9814407 (GAATG)n 780 + +chr21 9814408 9814467 (GAGTG)n 300 + +chr21 9814467 9814824 (GAATG)n 921 + +chr21 9814871 9815045 (GAATG)n 654 + +chr21 9815045 9815117 (GAGTG)n 423 + +chr21 9815118 9815297 (GAATG)n 926 + +chr21 9815356 9815455 (GAATG)n 325 + +chr21 9815463 9815640 (GAGTG)n 981 + +chr21 9815642 9815982 (GAATG)n 805 + +chr21 9816000 9816174 (GAATG)n 660 + +chr21 9816197 9816535 (GAATG)n 919 + +chr21 9816595 9816936 (GAATG)n 867 + +chr21 9816995 9817175 (GAATG)n 510 + +chr21 9817189 9817257 (GAGTG)n 269 + +chr21 9817258 9817854 (GAATG)n 1092 + +chr21 9817883 9818578 (GAATG)n 966 + +chr21 9818589 9818768 (GAATG)n 552 + +chr21 9818798 9818860 (GAATG)n 213 + +chr21 9818872 9819215 (GAATG)n 894 + +chr21 9819230 9819370 (GAATG)n 312 + +chr21 9819426 9819773 (GAATG)n 897 + +chr21 9819798 9819976 (GAATG)n 878 + +chr21 9819990 9820169 (GAATG)n 680 + +chr21 9820188 9820366 (GAATG)n 738 + +chr21 9820322 9820507 (GAGTG)n 641 + +chr21 9820507 9820756 (GAATG)n 708 + +chr21 9820767 9821118 (GAATG)n 933 + +chr21 9821145 9821567 (GAATG)n 933 + +chr21 9821569 9821606 (GAGTG)n 202 + +chr21 9821607 9822248 (GAATG)n 945 + +chr21 9822259 9822654 (GAATG)n 759 + +chr21 9822680 9822860 (GAATG)n 813 + +chr21 9822873 9823442 (GAATG)n 907 + +chr21 9823449 9823698 (GAGTG)n 726 + +chr21 9823702 9824048 (GAATG)n 645 + +chr21 9824084 9824327 (GAATG)n 882 + +chr21 9824344 9824517 (GAATG)n 597 + +chr21 9824555 9824792 (GAATG)n 807 + +chr21 9824798 9824978 (GAGTG)n 879 + +chr21 9825000 9825032 HSATII 182 - +chr21 9825043 9825400 (GAATG)n 702 + +chr21 9825423 9825466 (AATAG)n 245 + +chr21 9825466 9825642 (GAATG)n 900 + +chr21 9825642 9825706 (AATAG)n 245 + +chr21 9825728 9825888 (GAGTG)n 806 + +chr21 9825888 9826067 (GAATG)n 957 + +chr21 9826067 9826214 (GAGTG)n 806 + +chr21 9826217 9826396 (GAATG)n 924 + +chr21 9826460 9826952 (GAATG)n 1038 + +chr21 9826972 9827489 (GAATG)n 1050 + +chr21 9827517 9827697 (GAATG)n 861 + +chr21 9827712 9827897 (GAATG)n 688 + +chr21 9827940 9828084 (GAATG)n 618 + +chr21 9828112 9828291 (GAATG)n 876 + +chr21 9828340 9828448 (GAATG)n 489 + +chr21 9828467 9828647 (GAATG)n 945 + +chr21 9828648 9828685 (GAGTG)n 227 + +chr21 9828688 9828858 (GAATG)n 757 + +chr21 9828907 9829266 (GAATG)n 1284 + +chr21 9829272 9829311 HSATII 216 - +chr21 9829322 9829502 (GAATG)n 811 + +chr21 9829530 9829703 (GAATG)n 957 + +chr21 9829722 9830072 (GAATG)n 768 + +chr21 9830084 9830345 (GAATG)n 744 + +chr21 9830380 9830560 (GAATG)n 855 + +chr21 9830581 9830744 (GAATG)n 558 + +chr21 9830751 9830930 (GAGTG)n 702 + +chr21 9830890 9831840 (GAATG)n 855 + +chr21 9831853 9831940 (GAATG)n 300 + +chr21 9831951 9832237 (GAATG)n 732 + +chr21 9832263 9832436 (GAATG)n 762 + +chr21 9832448 9832625 (GAATG)n 819 + +chr21 9832660 9832841 (GAATG)n 561 + +chr21 9832883 9833070 (GAATG)n 613 + +chr21 9833084 9833443 (GAATG)n 783 + +chr21 9833474 9833645 (GAGTG)n 603 + +chr21 9833658 9833903 (GAATG)n 867 + +chr21 9833943 9834119 (GAATG)n 684 + +chr21 9834151 9834318 (GAATG)n 558 + +chr21 9834373 9834557 (GAATG)n 733 + +chr21 9834607 9834787 (GAATG)n 804 + +chr21 9834812 9835075 (GAATG)n 897 + +chr21 9835087 9835265 (GAATG)n 753 + +chr21 9835288 9835705 (GAATG)n 780 + +chr21 9835716 9836049 (GAATG)n 1023 + +chr21 9836061 9836241 (GAATG)n 714 + +chr21 9836288 9836971 (GAATG)n 879 + +chr21 9837006 9837353 (GAATG)n 957 + +chr21 9837376 9838332 (GAATG)n 981 + +chr21 9838353 9838532 (GAATG)n 738 + +chr21 9838572 9838756 (GAATG)n 751 + +chr21 9838787 9838957 (GAATG)n 509 + +chr21 9839005 9839182 (GAATG)n 584 + +chr21 9839215 9839666 (GAATG)n 777 + +chr21 9839677 9839857 (GAATG)n 573 + +chr21 9839882 9840062 (GAATG)n 830 + +chr21 9840109 9840572 (GAATG)n 765 + +chr21 9840598 9841028 (GAATG)n 807 + +chr21 9841042 9841763 (GAATG)n 1467 + +chr21 9841786 9842329 (GAATG)n 1233 + +chr21 9842357 9842533 (GAATG)n 984 + +chr21 9842556 9842735 (GAATG)n 774 + +chr21 9842761 9843791 (GAATG)n 899 + +chr21 9843840 9845003 (GAATG)n 969 + +chr21 9845039 9845218 (GAATG)n 576 + +chr21 9845256 9845624 (GAATG)n 771 + +chr21 9845635 9845814 (GAATG)n 870 + +chr21 9845825 9845897 (GAATG)n 248 + +chr21 9845914 9846241 (GAATG)n 767 + +chr21 9846254 9846430 (GAATG)n 774 + +chr21 9846463 9846894 (GAATG)n 713 + +chr21 9846912 9847693 (GAATG)n 832 + +chr21 9847709 9848307 (GAATG)n 863 + +chr21 9848314 9848348 (TAATG)n 198 + +chr21 9848358 9848717 (GAATG)n 914 + +chr21 9848778 9849142 (GAATG)n 1083 + +chr21 9849182 9849542 (GAATG)n 945 + +chr21 9849563 9849739 (GAATG)n 802 + +chr21 9849762 9849941 (GAATG)n 785 + +chr21 9849970 9850694 (GAATG)n 879 + +chr21 9850706 9850810 (GAATG)n 290 + +chr21 9850833 9851402 (GAATG)n 879 + +chr21 9851424 9852045 L1PA2 5360 - +chr21 9852045 9852343 (GAATG)n 945 + +chr21 9852358 9852539 (GAATG)n 644 + +chr21 9852551 9853020 (GAATG)n 924 + +chr21 9853037 9854217 (GAATG)n 903 + +chr21 9854239 9854783 (GAATG)n 913 + +chr21 9854794 9855257 (GAATG)n 714 + +chr21 9855298 9855693 (GAATG)n 820 + +chr21 9855714 9855892 (GAATG)n 1004 + +chr21 9855952 9856916 (GAATG)n 1062 + +chr21 9856936 9858610 (GAATG)n 963 + +chr21 9858625 9858805 (GAATG)n 966 + +chr21 9858844 9859012 (GAATG)n 589 + +chr21 9859023 9859978 (GAATG)n 1062 + +chr21 9860003 9860437 (GAATG)n 1053 + +chr21 9860457 9861178 (GAATG)n 1002 + +chr21 9861231 9861411 (GAATG)n 802 + +chr21 9861461 9862055 (GAATG)n 856 + +chr21 9862092 9862211 (GAATG)n 249 + +chr21 9862222 9862401 (GAATG)n 615 + +chr21 9862415 9862784 (GAATG)n 797 + +chr21 9862812 9863066 (GAATG)n 792 + +chr21 9863077 9863365 (GAATG)n 773 + +chr21 9863376 9863924 (GAATG)n 1023 + +chr21 9863947 9864768 (GAATG)n 945 + +chr21 9864813 9865422 (GAATG)n 1059 + +chr21 9865433 9866318 (GAATG)n 1158 + +chr21 9866346 9867070 (GAATG)n 978 + +chr21 9867085 9869711 (GAATG)n 1014 + +chr21 9869742 9869927 (GAATG)n 740 + +chr21 9869938 9870116 (GAATG)n 620 + +chr21 9870127 9870306 (GAATG)n 987 + +chr21 9870327 9870806 (GAATG)n 900 + +chr21 9870823 9870994 (GAATG)n 774 + +chr21 9871023 9872721 (GAATG)n 1143 + +chr21 9872749 9872924 (GAATG)n 531 + +chr21 9872943 9874085 (GAATG)n 1079 + +chr21 9874128 9874663 (GAATG)n 936 + +chr21 9874683 9874861 (GAATG)n 1026 + +chr21 9874878 9875057 (GAATG)n 684 + +chr21 9875069 9875208 (TAATG)n 625 + +chr21 9875243 9875428 (GAATG)n 713 + +chr21 9875443 9875623 (GAATG)n 1275 + +chr21 9875638 9875818 (GAATG)n 852 + +chr21 9875848 9876028 (GAATG)n 810 + +chr21 9876039 9876087 (GAATG)n 234 + +chr21 9876099 9876892 (GAATG)n 951 + +chr21 9876925 9877232 (GAATG)n 680 + +chr21 9877243 9877711 (GAATG)n 939 + +chr21 9877724 9877882 (GAATG)n 804 + +chr21 9877919 9878093 (GAATG)n 1123 + +chr21 9878123 9879079 (GAATG)n 1124 + +chr21 9879100 9879462 (GAATG)n 716 + +chr21 9879474 9879520 (GAATG)n 240 + +chr21 9879533 9879897 (GAATG)n 644 + +chr21 9879912 9880135 (GAATG)n 869 + +chr21 9880150 9880607 (GAATG)n 1008 + +chr21 9880655 9880831 (GAATG)n 575 + +chr21 9880855 9881472 (GAATG)n 969 + +chr21 9881499 9881738 (GAATG)n 870 + +chr21 9881749 9882394 (GAATG)n 819 + +chr21 9882409 9882589 (GAATG)n 960 + +chr21 9883029 9883138 L1MCb 324 + +chr21 9883398 9883435 (TG)n 333 + +chr21 9885154 9885513 THE1B 2222 - +chr21 9885540 9885671 L1MC 375 - +chr21 9885669 9885832 L1MC1 655 - +chr21 9889202 9889265 (TG)n 207 + +chr21 9889475 9889670 MER4A1 2503 - +chr21 9889670 9889963 AluSx 2156 + +chr21 9889963 9890213 MER4A1 2503 - +chr21 9890419 9890705 AluSq 1968 - +chr21 9890709 9891010 AluSc 2209 - +chr21 9891079 9891401 L1MCb 611 + +chr21 9891505 9891563 AT_rich 23 + +chr21 9891576 9891702 L1MCb 233 + +chr21 9891728 9892366 L1MA5 1915 + +chr21 9892345 9892803 L1MA5 2141 + +chr21 9893076 9893104 (TG)n 231 + +chr21 9895261 9895577 MER65A 1425 + +chr21 9895577 9895746 MER89-int 1143 - +chr21 9895746 9896052 AluSp 2111 - +chr21 9896052 9896599 MER89-int 1143 - +chr21 9896786 9896995 MER89-int 505 - +chr21 9897105 9903238 L1PA5 25934 - +chr21 9904001 9905118 L1MA5 3701 + +chr21 9905432 9906014 L1MCa 443 - +chr21 9907854 9908091 HERVL 520 - +chr21 9909375 9909722 L2 489 + +chr21 9910156 9910185 AT_rich 22 + +chr21 9910476 9910618 GA-rich 315 + +chr21 9910648 9912163 L1MB4 2915 - +chr21 9912216 9912640 MLT1C 1824 - +chr21 9912750 9913466 L1M4b 609 - +chr21 9913466 9913749 AluY 2156 - +chr21 9913749 9914124 L1M4b 931 - +chr21 9914124 9914574 L1MB5 1072 + +chr21 9914589 9914656 L1PREC2 238 + +chr21 9914843 9914991 L1MD 304 + +chr21 9915181 9915330 L1MCc 302 + +chr21 9915414 9915694 MLT1A0 1356 + +chr21 9915934 9916074 L1MCc 364 + +chr21 9916131 9916559 L1MCc 841 + +chr21 9916619 9916913 CT-rich 500 + +chr21 9916976 9917150 CT-rich 531 + +chr21 9917248 9917382 MLT1D 292 + +chr21 9918739 9919035 AluSx 2120 + +chr21 9919655 9919726 L2 216 - +chr21 9921306 9921369 MIRb 193 - +chr21 9922373 9922666 AluSg 2119 - +chr21 9922666 9926422 L1PA16 16024 + +chr21 9927575 9927885 AluJb 1764 + +chr21 9928614 9928678 (TA)n 201 + +chr21 9929258 9929378 MER85 843 - +chr21 9931102 9931696 MER54A 2853 + +chr21 9931696 9931817 FRAM 931 + +chr21 9932465 9932755 AluSx 1989 - +chr21 9932807 9933105 AluSc 2273 - +chr21 9933169 9933190 AT_rich 21 + +chr21 9933889 9934201 AluSp 2357 + +chr21 9934224 9934472 AluJo 1202 + +chr21 9934494 9934528 (CTAA)n 285 + +chr21 9934776 9934888 MIRb 359 - +chr21 9935682 9935869 MER5A 480 + +chr21 9936613 9936925 AluSx 2295 + +chr21 9937153 9937249 L3b 275 - +chr21 9938995 9939272 AluSx 2012 + +chr21 9939275 9939300 (CAAAA)n 225 + +chr21 9940346 9940373 (TTTTG)n 243 + +chr21 9940634 9940759 MIR 401 + +chr21 9940759 9941166 L1MC5 566 + +chr21 9941341 9941427 MIR 205 + +chr21 9941494 9941522 (CA)n 252 + +chr21 9942142 9942166 (TTTG)n 183 + +chr21 9942169 9942448 AluSx 1930 - +chr21 9942508 9942699 MIR3 482 - +chr21 9942802 9942913 Charlie9 382 - +chr21 9943444 9943603 MER96B 622 - +chr21 9943950 9944046 AluSg/x 580 - +chr21 9944161 9944385 L1M5 303 + +chr21 9944381 9944789 L1PA15-16 2435 + +chr21 9944796 9945948 L1PA15-16 6395 + +chr21 9945918 9946178 L1P4 1056 + +chr21 9946179 9946476 AluSx 2322 + +chr21 9946478 9946781 AluSq 2443 + +chr21 9946781 9947093 L1PA16 1780 + +chr21 9947167 9947496 L1M5 834 + +chr21 9947590 9947693 L1MEe 302 + +chr21 9947753 9949068 L1MEe 6375 + +chr21 9949068 9949379 AluSx 1960 - +chr21 9949379 9949412 L1MEe 6375 + +chr21 9949412 9949448 (CA)n 324 + +chr21 9949448 9949683 L1MEe 6375 + +chr21 9949683 9949990 AluJb 1868 + +chr21 9949990 9951295 L1MEe 6375 + +chr21 9951295 9951595 AluSx 2059 + +chr21 9951595 9951635 L1M5 992 + +chr21 9951676 9951968 L1M5 574 + +chr21 9951997 9952099 MER7D 229 + +chr21 9952113 9952295 L1M5 352 + +chr21 9952295 9952592 AluJb 1954 + +chr21 9952592 9952724 L1M5 352 + +chr21 9953020 9953097 MADE2 345 - 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+chr21 46822372 46822671 AluSc 2451 + +chr21 46822671 46827099 L1PA10 24103 - +chr21 46827140 46827878 L1M4b 6661 + +chr21 46827878 46828261 MSTD 1585 + +chr21 46828261 46828988 L1M4b 6661 + +chr21 46828988 46829029 (TA)n 369 + +chr21 46829029 46829333 AluY 2455 - +chr21 46829333 46829612 L1M4b 6661 + +chr21 46829614 46829700 LTR28 412 + +chr21 46829703 46829888 L1PB1 1209 + +chr21 46829888 46831908 L1PB1 22743 + +chr21 46831908 46832185 AluY 2153 + +chr21 46832185 46835577 L1PB1 22743 + +chr21 46835577 46835960 THE1B 1806 + +chr21 46835960 46837527 THE1B-int 11832 + +chr21 46837527 46837887 THE1B 2082 + +chr21 46837888 46838054 L1PB1 1110 + +chr21 46838087 46838351 LTR28 2371 + +chr21 46838351 46838643 AluY 2247 + +chr21 46838643 46838999 LTR28 2371 + +chr21 46839049 46839219 L1M4 433 + +chr21 46842067 46842196 MER45A 351 - +chr21 46842525 46842568 MLT1L 239 + +chr21 46842695 46842955 AluSg 2037 - +chr21 46843586 46843636 L1M2 232 + +chr21 46844600 46844908 AluJb 1786 + +chr21 46845134 46845217 MIRb 298 - +chr21 46847006 46847122 LTR33 274 + +chr21 46847189 46847363 L1M5 346 + +chr21 46847406 46847642 L1M5 343 + +chr21 46850078 46850140 MIR3 213 - +chr21 46851145 46851257 MIRb 369 + +chr21 46851559 46851931 ERVL-E 1011 + +chr21 46852166 46852392 ERVL-E 2076 + +chr21 46852392 46852943 MER41D 3317 - +chr21 46852943 46853568 ERVL-E 2076 + +chr21 46853570 46854379 ERVL-E 2847 + +chr21 46854749 46855204 LTR40c 681 - +chr21 46855352 46855473 LTR41 470 + +chr21 46855558 46855867 AluY 2540 + +chr21 46855946 46857278 L1MCa 5613 - +chr21 46857273 46857934 L1PA13 5918 - +chr21 46857934 46858275 AluSx 1988 - +chr21 46858275 46858774 L1PA13 5918 - +chr21 46858786 46860165 L1PREC2 14305 - +chr21 46860165 46860473 AluSx 1973 - +chr21 46860473 46861221 L1PREC2 14305 - +chr21 46861234 46861395 L1MCa 8427 - +chr21 46861395 46861766 THE1C 2800 - +chr21 46861766 46861799 L1MCa 8427 - +chr21 46861799 46862107 Tigger3b 5383 + +chr21 46862107 46862175 (TCTA)n 539 + +chr21 46862175 46862615 Tigger3b 5383 + +chr21 46862615 46862917 AluSx 2125 - +chr21 46862917 46863082 Tigger3b 5383 + +chr21 46863082 46863102 (TAAA)n 180 + +chr21 46863102 46863624 Tigger3b 5383 + +chr21 46863624 46865119 L1MCa 8427 - +chr21 46867255 46867547 AluSx 1993 + +chr21 46867729 46868002 AluSq 1905 + +chr21 46868002 46868029 AT_rich 27 + +chr21 46869218 46869330 MIR 279 - +chr21 46869393 46869686 AluSx 1829 - +chr21 46869686 46869777 MLT1G1 324 - +chr21 46869771 46870175 MLT1G1-int 734 - +chr21 46870189 46870298 MLT1F-int 508 + +chr21 46870299 46870846 MLT1G1-int 1143 - +chr21 46870861 46871020 MLT1H-int 281 - +chr21 46871026 46871493 MLT1G 703 - +chr21 46871541 46871918 THE1C 2596 - +chr21 46871919 46872007 MLT1B 1669 + +chr21 46872007 46872430 LTR47A 2432 - +chr21 46872430 46872737 MLT1B 1669 + +chr21 46872785 46873070 MLT1E 904 - +chr21 46873095 46873454 LTR52 646 + +chr21 46873520 46874124 L1MEc 858 - +chr21 46874124 46874428 AluSx 1964 + +chr21 46874428 46874507 L1MEc 858 - +chr21 46874507 46874602 L1PA7 709 - +chr21 46874602 46874919 L1MEc 295 - +chr21 46874934 46875153 L1MEc 313 - +chr21 46875147 46875975 L1PA7 6504 - +chr21 46875951 46876130 L1P2 946 - +chr21 46876132 46877492 MER4-int 9929 - +chr21 46877492 46877787 AluSx 1871 + +chr21 46877787 46878473 MER4-int 9929 - +chr21 46878473 46878547 L4 180 - +chr21 46878547 46878778 MER4-int 9929 - +chr21 46878781 46879238 MER4A1 3169 - +chr21 46879243 46879427 MER4B 623 - +chr21 46879943 46879972 GC_rich 22 + +chr21 46881993 46882135 L1MCa 337 + +chr21 46882163 46882318 FAM 866 + +chr21 46882338 46882630 L1ME3B 441 - +chr21 46882709 46883022 L1M5 489 - +chr21 46883100 46884029 L1MEc 2905 - +chr21 46884029 46884067 (TG)n 309 + +chr21 46884067 46884748 L1MEc 2905 - +chr21 46884778 46885039 AluY 1999 - +chr21 46885048 46885259 L1M4 307 - +chr21 46885340 46885480 AluJb 878 + +chr21 46885502 46885745 L1MC4a 301 + +chr21 46885745 46886054 AluSx 1935 + +chr21 46886059 46886096 (TG)n 270 + +chr21 46886242 46886708 L1ME4a 405 + +chr21 46886812 46886962 L1ME4a 361 + +chr21 46887080 46887388 AluSx 1967 + +chr21 46888920 46889201 MER58B 1178 - +chr21 46889293 46889629 AluJo 1519 + +chr21 46889638 46889821 AluJo 850 + +chr21 46889914 46890044 L1ME3B 405 + +chr21 46890044 46890353 AluSx 1946 - +chr21 46890353 46890614 L1ME3B 405 + +chr21 46890829 46891136 L1MC4a 413 - +chr21 46891141 46891421 MLT1A1 693 - +chr21 46891477 46891642 L1MC4_3endX 343 - +chr21 46891836 46892003 FRAM 650 - +chr21 46892029 46892086 AT_rich 22 + +chr21 46892396 46892604 L1MC4a 314 - +chr21 46892583 46892681 L1MD 293 - +chr21 46896438 46896576 L1PREC2 277 + +chr21 46896932 46897040 L1ME4a 288 + +chr21 46898261 46898291 (T)n 195 + +chr21 46898475 46898726 L1ME4a 442 + +chr21 46898714 46898903 L1MD2 776 + +chr21 46898903 46899208 MER2 1135 + +chr21 46899304 46899922 L1MD2 2612 + +chr21 46899916 46900310 L1MD2 1306 + +chr21 46900317 46900724 MSTB1 2258 + +chr21 46900724 46902105 L1MD2 2718 + +chr21 46902161 46902336 L1ME4a 384 + +chr21 46902470 46902579 MER45B 546 - +chr21 46903800 46903973 L1M5 344 + +chr21 46904289 46904311 AT_rich 22 + +chr21 46906284 46906449 G-rich 373 + +chr21 46909243 46909287 L2 195 + +chr21 46909413 46909464 AT_rich 23 + +chr21 46909464 46909768 AluJo 2015 + +chr21 46909769 46910593 L1ME3A 1283 - +chr21 46910643 46910947 AluSx 2427 - +chr21 46911036 46911163 AluJo 773 + +chr21 46911163 46911432 AluSx 2091 + +chr21 46913108 46913727 L1PA3 5539 - +chr21 46915754 46916276 MLT1E2 1609 - +chr21 46916330 46916418 L1M5 226 - +chr21 46916433 46916857 L1M5 1626 - +chr21 46916857 46917170 AluJo 1400 + +chr21 46917170 46917283 L1M5 1626 - +chr21 46917286 46917758 L1MA4A 2227 + +chr21 46917764 46917862 L1MA4A 435 + +chr21 46917957 46918166 MIR 320 - +chr21 46918500 46918536 AT_rich 22 + +chr21 46918925 46919030 GA-rich 252 + +chr21 46919402 46919654 L2 390 + +chr21 46919654 46919928 AluSx 1723 - +chr21 46919928 46920171 L2 390 + +chr21 46920752 46922048 L1PA7 7374 - +chr21 46922123 46922411 L1ME1 883 + +chr21 46922411 46922704 AluJb 1385 - +chr21 46922718 46922935 L1ME1 699 + +chr21 46923377 46923802 MLT1K 323 - +chr21 46924116 46924575 HAL1 655 + +chr21 46924661 46924875 MER74A 443 + +chr21 46925595 46925624 AT_rich 22 + +chr21 46926764 46927048 MLT1I 641 - +chr21 46927048 46927090 (A)n 378 + +chr21 46927155 46927194 MLT1I 248 - +chr21 46927433 46927614 (TTAGGG)n 234 + +chr21 46928301 46928745 MER4A1 2938 - +chr21 46929613 46930969 L1MC3 5007 - +chr21 46930969 46931413 MSTB1 1749 - +chr21 46931413 46931818 L1MC3 5007 - +chr21 46931945 46932055 MER34B-int 303 - +chr21 46932058 46932281 AluJb 1504 - +chr21 46932282 46932323 AluJb 228 - +chr21 46932323 46932751 MER34B-int 2060 - +chr21 46932771 46933151 LTR10C 1336 - +chr21 46933171 46933204 (CA)n 297 + +chr21 46933260 46934052 MER34B-int 3116 - +chr21 46934052 46934352 AluY 2333 - +chr21 46934352 46934522 MER34B-int 3116 - +chr21 46934536 46935047 MER34B-int 1297 - +chr21 46935651 46936098 MER34B-int 1588 - +chr21 46936101 46936169 MLT2B3 330 + +chr21 46936194 46936262 MLT2B3 406 + +chr21 46936287 46936355 MLT2B3 375 + +chr21 46936380 46936448 MLT2B3 330 + +chr21 46936473 46936541 MLT2B3 346 + +chr21 46936566 46936632 MLT2B3 335 + +chr21 46936657 46936725 MLT2B5 417 + +chr21 46936750 46936977 MLT2B3 2194 + +chr21 46936977 46937339 THE1C 2217 + +chr21 46937339 46937689 MLT2B5 1691 + +chr21 46937696 46938061 MER34B-int 678 - +chr21 46938036 46938374 MER34B-int 910 - +chr21 46938415 46938527 MER34B-int 268 - +chr21 46938776 46938841 MER72 3923 - +chr21 46938841 46939137 AluSq 2287 - +chr21 46939137 46939777 MER72 3923 - +chr21 46939986 46940174 L1MC 565 - +chr21 46940179 46940735 MER34C_ 2769 - +chr21 46940746 46941357 L1MC 1506 - +chr21 46941373 46941479 LTR60 529 + +chr21 46941590 46941894 AluYb8 2829 + +chr21 46941894 46942298 LTR60 958 + +chr21 46942142 46944181 TAR1 16459 + +chr21 46944181 46944323 (TTAGGG)n 1057 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/genomes/human.hg18.genome Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,50 @@ +chr1 247249719 +chr1_random 1663265 +chr10 135374737 +chr10_random 113275 +chr11 134452384 +chr11_random 215294 +chr12 132349534 +chr13 114142980 +chr13_random 186858 +chr14 106368585 +chr15 100338915 +chr15_random 784346 +chr16 88827254 +chr16_random 105485 +chr17 78774742 +chr17_random 2617613 +chr18 76117153 +chr18_random 4262 +chr19 63811651 +chr19_random 301858 +chr2 242951149 +chr2_random 185571 +chr20 62435964 +chr21 46944323 +chr21_random 1679693 +chr22 49691432 +chr22_random 257318 +chr22_h2_hap1 63661 +chr3 199501827 +chr3_random 749256 +chr4 191273063 +chr4_random 842648 +chr5 180857866 +chr5_random 143687 +chr5_h2_hap1 1794870 +chr6 170899992 +chr6_random 1875562 +chr6_cox_hap1 4731698 +chr6_qbl_hap2 4565931 +chr7 158821424 +chr7_random 549659 +chr8 146274826 +chr8_random 943810 +chr9 140273252 +chr9_random 1146434 +chrM 16571 +chrX 154913754 +chrX_random 1719168 +chrY 57772954 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/genomes/human.hg19.genome Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,94 @@ +chr1 249250621 +chr2 243199373 +chr3 198022430 +chr4 191154276 +chr5 180915260 +chr6 171115067 +chr7 159138663 +chrX 155270560 +chr8 146364022 +chr9 141213431 +chr10 135534747 +chr11 135006516 +chr12 133851895 +chr13 115169878 +chr14 107349540 +chr15 102531392 +chr16 90354753 +chr17 81195210 +chr18 78077248 +chr20 63025520 +chrY 59373566 +chr19 59128983 +chr22 51304566 +chr21 48129895 +chr6_ssto_hap7 4928567 +chr6_mcf_hap5 4833398 +chr6_cox_hap2 4795371 +chr6_mann_hap4 4683263 +chr6_apd_hap1 4622290 +chr6_qbl_hap6 4611984 +chr6_dbb_hap3 4610396 +chr17_ctg5_hap1 1680828 +chr4_ctg9_hap1 590426 +chr1_gl000192_random 547496 +chrUn_gl000225 211173 +chr4_gl000194_random 191469 +chr4_gl000193_random 189789 +chr9_gl000200_random 187035 +chrUn_gl000222 186861 +chrUn_gl000212 186858 +chr7_gl000195_random 182896 +chrUn_gl000223 180455 +chrUn_gl000224 179693 +chrUn_gl000219 179198 +chr17_gl000205_random 174588 +chrUn_gl000215 172545 +chrUn_gl000216 172294 +chrUn_gl000217 172149 +chr9_gl000199_random 169874 +chrUn_gl000211 166566 +chrUn_gl000213 164239 +chrUn_gl000220 161802 +chrUn_gl000218 161147 +chr19_gl000209_random 159169 +chrUn_gl000221 155397 +chrUn_gl000214 137718 +chrUn_gl000228 129120 +chrUn_gl000227 128374 +chr1_gl000191_random 106433 +chr19_gl000208_random 92689 +chr9_gl000198_random 90085 +chr17_gl000204_random 81310 +chrUn_gl000233 45941 +chrUn_gl000237 45867 +chrUn_gl000230 43691 +chrUn_gl000242 43523 +chrUn_gl000243 43341 +chrUn_gl000241 42152 +chrUn_gl000236 41934 +chrUn_gl000240 41933 +chr17_gl000206_random 41001 +chrUn_gl000232 40652 +chrUn_gl000234 40531 +chr11_gl000202_random 40103 +chrUn_gl000238 39939 +chrUn_gl000244 39929 +chrUn_gl000248 39786 +chr8_gl000196_random 38914 +chrUn_gl000249 38502 +chrUn_gl000246 38154 +chr17_gl000203_random 37498 +chr8_gl000197_random 37175 +chrUn_gl000245 36651 +chrUn_gl000247 36422 +chr9_gl000201_random 36148 +chrUn_gl000235 34474 +chrUn_gl000239 33824 +chr21_gl000210_random 27682 +chrUn_gl000231 27386 +chrUn_gl000229 19913 +chrM 16571 +chrUn_gl000226 15008 +chr18_gl000207_random 4262 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/genomes/mouse.mm8.genome Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,35 @@ +chr1 197069962 +chr2 181976762 +chr3 159872112 +chr4 155029701 +chr5 152003063 +chr6 149525685 +chr7 145134094 +chr8 132085098 +chr9 124000669 +chrM 16299 +chrX 165556469 +chrY 16029404 +chr10 129959148 +chr11 121798632 +chr12 120463159 +chr13 120614378 +chr14 123978870 +chr15 103492577 +chr16 98252459 +chr17 95177420 +chr18 90736837 +chr19 61321190 +chr1_random 172274 +chr5_random 2921247 +chr7_random 243910 +chr8_random 206961 +chr9_random 17232 +chrX_random 39696 +chrY_random 14577732 +chr10_random 10781 +chr13_random 436191 +chr15_random 105932 +chr17_random 89091 +chrUn_random 1540053 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/genomes/mouse.mm9.genome Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,36 @@ +chr1 197195432 +chr2 181748087 +chr3 159599783 +chr4 155630120 +chr5 152537259 +chr6 149517037 +chr7 152524553 +chr8 131738871 +chr9 124076172 +chr10 129993255 +chr11 121843856 +chr12 121257530 +chr13 120284312 +chr14 125194864 +chr15 103494974 +chr16 98319150 +chr17 95272651 +chr18 90772031 +chr19 61342430 +chrX 166650296 +chrY 15902555 +chrM 16299 +chr13_random 400311 +chr16_random 3994 +chr17_random 628739 +chr1_random 1231697 +chr3_random 41899 +chr4_random 160594 +chr5_random 357350 +chr7_random 362490 +chr8_random 849593 +chr9_random 449403 +chrUn_random 5900358 +chrX_random 1785075 +chrY_random 58682461 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,48 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= multiCovMain.cpp multiCovBam.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= multiCovBam + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/annotateBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,43 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= annotateMain.cpp annotateBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= annotateBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/annotateBed/annotateBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,209 @@ +/***************************************************************************** + annotateBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "annotateBed.h" + +// build +BedAnnotate::BedAnnotate(const string &mainFile, const vector<string> &annoFileNames, + const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool reportBoth) : + + _mainFile(mainFile), + _annoFileNames(annoFileNames), + _annoTitles(annoTitles), + _sameStrand(sameStrand), + _diffStrand(diffStrand), + _reportCounts(reportCounts), + _reportBoth(reportBoth) +{ + _bed = new BedFile(_mainFile); +} + + +// destroy and delete the open file pointers +BedAnnotate::~BedAnnotate(void) { + delete _bed; + CloseAnnoFiles(); +} + + +void BedAnnotate::OpenAnnoFiles() { + for (size_t i=0; i < _annoFileNames.size(); ++i) { + BedFile *file = new BedFile(_annoFileNames[i]); + file->Open(); + _annoFiles.push_back(file); + } +} + + +void BedAnnotate::CloseAnnoFiles() { + for (size_t i=0; i < _annoFiles.size(); ++i) { + BedFile *file = _annoFiles[i]; + delete file; + _annoFiles[i] = NULL; + } +} + + +void BedAnnotate::PrintHeader() { + // print a hash to indicate header and then write a tab + // for each field in the main file. + printf("#"); + for (size_t i = 0; i < _bed->bedType; ++i) + printf("\t"); + + // now print the label for each file. + if (_reportBoth == false) { + for (size_t i = 0; i < _annoTitles.size(); ++i) + printf("%s\t", _annoTitles[i].c_str()); + printf("\n"); + } + else { + for (size_t i = 0; i < _annoTitles.size(); ++i) + printf("%s_cnt\t%s_pct", _annoTitles[i].c_str(), _annoTitles[i].c_str()); + printf("\n"); + } +} + + +void BedAnnotate::InitializeMainFile() { + // process each chromosome + masterBedCovListMap::iterator chromItr = _bed->bedCovListMap.begin(); + masterBedCovListMap::iterator chromEnd = _bed->bedCovListMap.end(); + for (; chromItr != chromEnd; ++chromItr) { + // for each chrom, process each bin + binsToBedCovLists::iterator binItr = chromItr->second.begin(); + binsToBedCovLists::iterator binEnd = chromItr->second.end(); + for (; binItr != binEnd; ++binItr) { + // initialize BEDCOVLIST in this chrom/bin + vector<BEDCOVLIST>::iterator bedItr = binItr->second.begin(); + vector<BEDCOVLIST>::iterator bedEnd = binItr->second.end(); + for (; bedItr != bedEnd; ++bedItr) { + // initialize the depthMaps, counts, etc. for each anno file. + for (size_t i = 0; i < _annoFiles.size(); ++i) { + map<unsigned int, DEPTH> dummy; + bedItr->depthMapList.push_back(dummy); + bedItr->counts.push_back(0); + bedItr->minOverlapStarts.push_back(INT_MAX); + } + } + } + } +} + + +void BedAnnotate::AnnotateBed() { + + // load the "main" bed file into a map so + // that we can easily compare each annoFile to it for overlaps + _bed->loadBedCovListFileIntoMap(); + // open the annotations files for processing; + OpenAnnoFiles(); + // initialize counters, depths, etc. for the main file + InitializeMainFile(); + + // annotate the main file with the coverage from the annotation files. + for (size_t annoIndex = 0; annoIndex < _annoFiles.size(); ++annoIndex) { + // grab the current annotation file. + BedFile *anno = _annoFiles[annoIndex]; + int lineNum = 0; + BED a, nullBed; + BedLineStatus bedStatus; + + // process each entry in the current anno file + while ((bedStatus = anno->GetNextBed(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + _bed->countListHits(a, annoIndex, _sameStrand, _diffStrand); + a = nullBed; + } + } + } + + // report the annotations of the main file from the anno file. + ReportAnnotations(); + // close the annotations files; + CloseAnnoFiles(); +} + + +void BedAnnotate::ReportAnnotations() { + + if (_annoTitles.size() > 0) { + PrintHeader(); + } + + // process each chromosome + masterBedCovListMap::const_iterator chromItr = _bed->bedCovListMap.begin(); + masterBedCovListMap::const_iterator chromEnd = _bed->bedCovListMap.end(); + for (; chromItr != chromEnd; ++chromItr) { + // for each chrom, process each bin + binsToBedCovLists::const_iterator binItr = chromItr->second.begin(); + binsToBedCovLists::const_iterator binEnd = chromItr->second.end(); + for (; binItr != binEnd; ++binItr) { + // for each chrom & bin, compute and report + // the observed coverage for each feature + vector<BEDCOVLIST>::const_iterator bedItr = binItr->second.begin(); + vector<BEDCOVLIST>::const_iterator bedEnd = binItr->second.end(); + for (; bedItr != bedEnd; ++bedItr) { + // print the main BED entry. + _bed->reportBedTab(*bedItr); + + // now report the coverage from each annotation file. + for (size_t i = 0; i < _annoFiles.size(); ++i) { + unsigned int totalLength = 0; + int zeroDepthCount = 0; // number of bases with zero depth + int depth = 0; // tracks the depth at the current base + + // the start is either the first base in the feature OR + // the leftmost position of an overlapping feature. e.g. (s = start): + // A ---------- + // B s ------------ + int start = min(bedItr->minOverlapStarts[i], bedItr->start); + + map<unsigned int, DEPTH>::const_iterator depthItr; + map<unsigned int, DEPTH>::const_iterator depthEnd; + + // compute the coverage observed at each base in the feature marching from start to end. + for (CHRPOS pos = start+1; pos <= bedItr->end; pos++) { + // map pointer grabbing the starts and ends observed at this position + depthItr = bedItr->depthMapList[i].find(pos); + depthEnd = bedItr->depthMapList[i].end(); + + // increment coverage if starts observed at this position. + if (depthItr != depthEnd) + depth += depthItr->second.starts; + // update zero depth + if ((pos > bedItr->start) && (pos <= bedItr->end) && (depth == 0)) + zeroDepthCount++; + // decrement coverage if ends observed at this position. + if (depthItr != depthEnd) + depth = depth - depthItr->second.ends; + } + // Summarize the coverage for the current interval, + CHRPOS length = bedItr->end - bedItr->start; + totalLength += length; + int nonZeroBases = (length - zeroDepthCount); + float fractCovered = (float) nonZeroBases / length; + if (_reportCounts == false && _reportBoth == false) + printf("%f\t", fractCovered); + else if (_reportCounts == true && _reportBoth == false) + printf("%d\t", bedItr->counts[i]); + else if (_reportCounts == false && _reportBoth == true) + printf("%d\t%f\t", bedItr->counts[i], fractCovered); + } + // print newline for next feature. + printf("\n"); + } + } + } +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/annotateBed/annotateBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,71 @@ +/***************************************************************************** + annotateBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef ANNOTATEBED_H +#define ANNOTATEBED_H + +#include "bedFile.h" +#include <vector> +#include <algorithm> +#include <iostream> +#include <iomanip> +#include <fstream> +#include <stdlib.h> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class BedAnnotate { + +public: + + // constructor + BedAnnotate(const string &mainFile, const vector<string> &annoFileNames, + const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool reportBoth); + + // destructor + ~BedAnnotate(void); + + // annotate the master file with all of the annotation files. + void AnnotateBed(); + +private: + + // input files. + string _mainFile; + vector<string> _annoFileNames; + vector<string> _annoTitles; + + // instance of a bed file class. + BedFile *_bed; + vector<BedFile*> _annoFiles; + + // do we care about strandedness when counting coverage? + bool _sameStrand; + bool _diffStrand; + + bool _reportCounts; + bool _reportBoth; + + // private function for reporting coverage information + void ReportAnnotations(); + + void OpenAnnoFiles(); + + void CloseAnnoFiles(); + + void PrintHeader(); + + void InitializeMainFile(); +}; +#endif /* ANNOTATEBED_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/annotateBed/annotateMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,170 @@ +/***************************************************************************** + annotateMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "annotateBed.h" +#include "version.h" + +using namespace std; + +// define the version +#define PROGRAM_NAME "annotateBed" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input file + string mainFile; + + // parm flags + bool sameStrand = false; + bool diffStrand = false; + bool haveBed = false; + bool haveFiles = false; + bool haveTitles = false; + bool reportCounts = false; + bool reportBoth = false; + + // list of annotation files / names + vector<string> inputFiles; + vector<string> inputTitles; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + haveBed = true; + mainFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-files", 6, parameterLength)) { + if ((i+1) < argc) { + haveFiles = true; + i = i+1; + string file = argv[i]; + while (file[0] != '-' && i < argc) { + inputFiles.push_back(file); + i++; + if (i < argc) + file = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-names", 6, parameterLength)) { + if ((i+1) < argc) { + haveTitles = true; + i = i+1; + string title = argv[i]; + while (title[0] != '-' && i < argc) { + inputTitles.push_back(title); + i++; + if (i < argc) + title = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-counts", 7, parameterLength)) { + reportCounts = true; + } + else if(PARAMETER_CHECK("-both", 5, parameterLength)) { + reportBoth = true; + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + sameStrand = true; + } + else if (PARAMETER_CHECK("-S", 2, parameterLength)) { + diffStrand = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed || !haveFiles) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i and -files files. " << endl << "*****" << endl; + showHelp = true; + } + if (sameStrand && diffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedAnnotate *ba = new BedAnnotate(mainFile, inputFiles, inputTitles, sameStrand, diffStrand, reportCounts, reportBoth); + ba->AnnotateBed(); + delete ba; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Annotates the depth & breadth of coverage of features from multiple files" << endl; + cerr << "\t on the intervals in -i." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -files FILE1 FILE2 .. FILEn" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-names\t" << "A list of names (one / file) to describe each file in -i." << endl; + cerr << "\t\tThese names will be printed as a header line." << endl << endl; + + cerr << "\t-counts\t" << "Report the count of features in each file that overlap -i." << endl; + cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl; + + cerr << "\t-both\t" << "Report the counts followed by the % coverage." << endl; + cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl; + + cerr << "\t-s\t" << "Require same strandedness. That is, only counts overlaps" << endl; + cerr << "\t\ton the _same_ strand." << endl; + cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl; + + cerr << "\t-S\t" << "Require different strandedness. That is, only count overlaps" << endl; + cerr << "\t\ton the _opposite_ strand." << endl; + cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl; + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bamToBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,47 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary + + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= bamToBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=BamAncillary.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= bamToBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamAncillary/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bamToBed/bamToBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,564 @@ +/***************************************************************************** + bamToBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "version.h" +#include "api/BamReader.h" +#include "api/BamAux.h" +#include "BamAncillary.h" +#include "bedFile.h" +using namespace BamTools; + +#include <vector> +#include <algorithm> // for swap() +#include <iostream> +#include <fstream> +#include <stdlib.h> + +using namespace std; + + +// define our program name +#define PROGRAM_NAME "bamToBed" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + + +// function declarations +void ShowHelp(void); + +void ConvertBamToBed(const string &bamFile, const bool &useEditDistance, const string &bamTag, + const bool &writeBed12, const bool &obeySplits, const string &color, const bool &useCigar); +void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance); + +void PrintBed(const BamAlignment &bam, const RefVector &refs, bool useEditDistance, const string &bamTag, bool obeySplits, bool useCigar); +void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDistance, const string &bamTag, string color = "255,0,0"); +void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2, + const RefVector &refs, bool useEditDistance); + +void ParseCigarBed12(const vector<CigarOp> &cigar, vector<int> &blockStarts, + vector<int> &blockEnds, int &alignmentEnd); +string BuildCigarString(const vector<CigarOp> &cigar); + +bool IsCorrectMappingForBEDPE (const BamAlignment &bam); + + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bamFile = "stdin"; + string color = "255,0,0"; + string tag = ""; + + bool haveBam = true; + bool haveColor = false; + bool haveOtherTag = false; + bool writeBedPE = false; + bool writeBed12 = false; + bool useEditDistance = false; + bool useAlignmentScore = false; + bool useCigar = false; + bool obeySplits = false; + + // check to see if we should print out some help + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bamFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) { + writeBedPE = true; + } + else if(PARAMETER_CHECK("-bed12", 6, parameterLength)) { + writeBed12 = true; + } + else if(PARAMETER_CHECK("-split", 6, parameterLength)) { + obeySplits = true; + } + else if(PARAMETER_CHECK("-ed", 3, parameterLength)) { + useEditDistance = true; + } + else if(PARAMETER_CHECK("-cigar", 6, parameterLength)) { + useCigar = true; + } + else if(PARAMETER_CHECK("-as", 3, parameterLength)) { + useAlignmentScore = true; + } + else if(PARAMETER_CHECK("-color", 6, parameterLength)) { + if ((i+1) < argc) { + haveColor = true; + color = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-tag", 4, parameterLength)) { + if ((i+1) < argc) { + haveOtherTag = true; + tag = argv[i + 1]; + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have an input files + if (haveBam == false) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i (BAM) file. " << endl << "*****" << endl; + showHelp = true; + } + if (haveColor == true && writeBed12 == false) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot use color without BED12. " << endl << "*****" << endl; + showHelp = true; + } + if (useEditDistance == true && obeySplits == true) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot use -ed with -splits. Edit distances cannot be computed for each \'chunk\'." << endl << "*****" << endl; + showHelp = true; + } + if (useEditDistance == true && useCigar == true) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot use -cigar with -splits. Not yet supported." << endl << "*****" << endl; + showHelp = true; + } + if (useEditDistance == true && haveOtherTag == true) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot use -ed with -tag. Choose one or the other." << endl << "*****" << endl; + showHelp = true; + } + if (writeBedPE == true && haveOtherTag == true) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot use -tag with -bedpe." << endl << "*****" << endl; + showHelp = true; + } + // if there are no problems, let's convert BAM to BED or BEDPE + if (!showHelp) { + if (writeBedPE == false) + ConvertBamToBed(bamFile, useEditDistance, tag, writeBed12, obeySplits, color, useCigar); // BED or "blocked BED" + else + ConvertBamToBedpe(bamFile, useEditDistance); // BEDPE + } + else { + ShowHelp(); + } +} + + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Converts BAM alignments to BED6 or BEDPE format." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bam> " << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-bedpe\t" << "Write BEDPE format." << endl; + cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl; + + cerr << "\t-bed12\t" << "Write \"blocked\" BED format (aka \"BED12\")." << endl << endl; + cerr << "\t\thttp://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1" << endl << endl; + + cerr << "\t-split\t" << "Report \"split\" BAM alignments as separate BED entries." << endl << endl; + + cerr << "\t-ed\t" << "Use BAM edit distance (NM tag) for BED score." << endl; + cerr << "\t\t- Default for BED is to use mapping quality." << endl; + cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl; + cerr << "\t\t the two mapping qualities for the pair." << endl; + cerr << "\t\t- When -ed is used with -bedpe, the total edit" << endl; + cerr << "\t\t distance from the two mates is reported." << endl << endl; + + cerr << "\t-tag\t" << "Use other NUMERIC BAM alignment tag for BED score." << endl; + cerr << "\t\t- Default for BED is to use mapping quality." << endl; + cerr << "\t\t Disallowed with BEDPE output." << endl << endl; + + cerr << "\t-color\t" << "An R,G,B string for the color used with BED12 format." << endl; + cerr << "\t\tDefault is (255,0,0)." << endl << endl; + + cerr << "\t-cigar\t" << "Add the CIGAR string to the BED entry as a 7th column." << endl << endl; + + + // end the program here + exit(1); +} + + +void ConvertBamToBed(const string &bamFile, const bool &useEditDistance, const string &bamTag, + const bool &writeBed12, const bool &obeySplits, const string &color, const bool &useCigar) { + // open the BAM file + BamReader reader; + reader.Open(bamFile); + + // get header & reference information + string header = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // rip through the BAM file and convert each mapped entry to BED + BamAlignment bam; + while (reader.GetNextAlignment(bam)) { + if (bam.IsMapped() == true) { + if (writeBed12 == false) // BED + PrintBed(bam, refs, useEditDistance, bamTag, obeySplits, useCigar); + else //"blocked" BED + PrintBed12(bam, refs, useEditDistance, bamTag, color); + } + } + reader.Close(); +} + + +/* + Assumptions: + 1. The BAM file is grouped/sorted by query name, + not alignment position +*/ +void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance) { + // open the BAM file + BamReader reader; + reader.Open(bamFile); + + // get header & reference information + string header = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // rip through the BAM file and convert each mapped entry to BEDPE + BamAlignment bam1, bam2; + while (reader.GetNextAlignment(bam1)) { + // the alignment must be paired + if (bam1.IsPaired() == true) { + // grab the second alignment for the pair. + reader.GetNextAlignment(bam2); + + // require that the alignments are from the same query + if (bam1.Name == bam2.Name) { + PrintBedPE(bam1, bam2, refs, useEditDistance); + } + else { + cerr << "*****ERROR: -bedpe requires BAM to be sorted/grouped by query name. " << endl; + exit(1); + } + } + } + reader.Close(); +} + + +void ParseCigarBed12(const vector<CigarOp> &cigar, vector<int> &blockStarts, vector<int> &blockLengths, unsigned int &alignmentEnd) { + + int currPosition = 0; + int blockLength = 0; + + // Rip through the CIGAR ops and figure out if there is more + // than one block for this alignment + vector<CigarOp>::const_iterator cigItr = cigar.begin(); + vector<CigarOp>::const_iterator cigEnd = cigar.end(); + for (; cigItr != cigEnd; ++cigItr) { + switch (cigItr->Type) { + case ('M') : + blockLength += cigItr->Length; + currPosition += cigItr->Length; + case ('I') : break; + case ('S') : break; + case ('D') : break; + blockLength += cigItr->Length; + currPosition += cigItr->Length; + case ('P') : break; + case ('N') : + blockStarts.push_back(currPosition + cigItr->Length); + blockLengths.push_back(blockLength); + currPosition += cigItr->Length; + blockLength = 0; + case ('H') : break; // for 'H' - do nothing, move to next op + default : + printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here + exit(1); + } + } + // add the kast block and set the + // alignment end (i.e., relative to the start) + blockLengths.push_back(blockLength); + alignmentEnd = currPosition; +} + + +string BuildCigarString(const vector<CigarOp> &cigar) { + + stringstream cigarString; + + for (size_t i = 0; i < cigar.size(); ++i) { + //cerr << cigar[i].Type << " " << cigar[i].Length << endl; + switch (cigar[i].Type) { + case ('M') : + case ('I') : + case ('D') : + case ('N') : + case ('S') : + case ('H') : + case ('P') : + cigarString << cigar[i].Length << cigar[i].Type; + } + } + return cigarString.str(); +} + + +void PrintBed(const BamAlignment &bam, const RefVector &refs, bool useEditDistance, const string &bamTag, bool obeySplits, bool useCigar) { + + // set the strand + string strand = "+"; + if (bam.IsReverseStrand() == true) strand = "-"; + + // set the name of the feature based on the sequence + string name = bam.Name; + if (bam.IsFirstMate() == true) name += "/1"; + if (bam.IsSecondMate() == true) name += "/2"; + + // get the unpadded (parm = false) end position based on the CIGAR + unsigned int alignmentEnd = bam.GetEndPosition(false, false); + + // report the entire BAM footprint as a single BED entry + if (obeySplits == false) { + // report the alignment in BED6 format. + if (useEditDistance == false && bamTag == "") { + printf("%s\t%d\t%d\t\%s\t%d\t%s", refs.at(bam.RefID).RefName.c_str(), bam.Position, + alignmentEnd, name.c_str(), bam.MapQuality, strand.c_str()); + } + else if (useEditDistance == true && bamTag == "") { + uint32_t editDistance; + if (bam.GetTag("NM", editDistance)) { + printf("%s\t%d\t%d\t\%s\t%u\t%s", refs.at(bam.RefID).RefName.c_str(), bam.Position, + alignmentEnd, name.c_str(), editDistance, strand.c_str()); + } + else { + cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n"; + exit(1); + } + } + else if (useEditDistance == false && bamTag != "") { + int32_t tagValue; + if (bam.GetTag(bamTag, tagValue)) { + printf("%s\t%d\t%d\t\%s\t%d\t%s", refs.at(bam.RefID).RefName.c_str(), bam.Position, + alignmentEnd, name.c_str(), tagValue, strand.c_str()); + } + else { + cerr << "The requested tag (" << bamTag << ") was not found in the BAM file. Exiting\n"; + exit(1); + } + } + + // does the user want CIGAR as well? + if (useCigar == false) { + printf("\n"); + } + else { + string cigar = BuildCigarString(bam.CigarData); + printf("\t%s\n", cigar.c_str()); + } + } + // Report each chunk of the BAM alignment as a discrete BED entry + // For example 10M100N10M would be reported as two seprate BED entries of length 10 + else { + vector<BED> bedBlocks; + // Load the alignment blocks in bam into the bedBlocks vector. + // Don't trigger a new block when a "D" (deletion) CIGAR op is found. + getBamBlocks(bam, refs, bedBlocks, false); + + vector<BED>::const_iterator bedItr = bedBlocks.begin(); + vector<BED>::const_iterator bedEnd = bedBlocks.end(); + for (; bedItr != bedEnd; ++bedItr) { + printf("%s\t%d\t%d\t\%s\t%d\t%s\n", refs.at(bam.RefID).RefName.c_str(), bedItr->start, + bedItr->end, name.c_str(), bam.MapQuality, strand.c_str()); + } + } +} + + +void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDistance, const string &bamTag, string color) { + + // set the strand + string strand = "+"; + if (bam.IsReverseStrand()) strand = "-"; + + // set the name of the feature based on the sequence + string name = bam.Name; + if (bam.IsFirstMate()) name += "/1"; + if (bam.IsSecondMate()) name += "/2"; + + // parse the CIGAR string and figure out the alignment blocks + unsigned int alignmentEnd; + vector<int> blockLengths; + vector<int> blockStarts; + blockStarts.push_back(0); + + // extract the block starts and lengths from the CIGAR string + ParseCigarBed12(bam.CigarData, blockStarts, blockLengths, alignmentEnd); + alignmentEnd += bam.Position; + + // write BED6 portion + if (useEditDistance == false && bamTag == "") { + printf("%s\t%d\t%d\t\%s\t%d\t%s\t", refs.at(bam.RefID).RefName.c_str(), bam.Position, + alignmentEnd, name.c_str(), bam.MapQuality, strand.c_str()); + } + else if (useEditDistance == true && bamTag != "") { + uint32_t editDistance; + if (bam.GetTag("NM", editDistance)) { + printf("%s\t%d\t%d\t\%s\t%u\t%s\t", refs.at(bam.RefID).RefName.c_str(), bam.Position, + alignmentEnd, name.c_str(), editDistance, strand.c_str()); + } + else { + cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n"; + exit(1); + } + } + else if (useEditDistance == false && bamTag != "") { + int32_t tagValue; + if (bam.GetTag(bamTag, tagValue)) { + printf("%s\t%d\t%d\t\%s\t%d\t%s\t", refs.at(bam.RefID).RefName.c_str(), bam.Position, + alignmentEnd, name.c_str(), tagValue, strand.c_str()); + } + else { + cerr << "The requested tag (" << bamTag << ") was not found in the BAM file. Exiting\n"; + exit(1); + } + } + + // write the colors, etc. + printf("%d\t%d\t%s\t%d\t", bam.Position, alignmentEnd, color.c_str(), (int) blockStarts.size()); + + // now write the lengths portion + unsigned int b; + for (b = 0; b < blockLengths.size() - 1; ++b) { + printf("%d,", blockLengths[b]); + } + printf("%d\t", blockLengths[b]); + + // now write the starts portion + for (b = 0; b < blockStarts.size() - 1; ++b) { + printf("%d,", blockStarts[b]); + } + printf("%d\n", blockStarts[b]); +} + + +void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2, const RefVector &refs, bool useEditDistance) { + + // initialize BEDPE variables + string chrom1, chrom2, strand1, strand2; + int start1, start2, end1, end2; + uint32_t editDistance1, editDistance2; + start1 = start2 = end1 = end2 = -1; + chrom1 = chrom2 = strand1 = strand2 = "."; + editDistance1 = editDistance2 = 0; + uint16_t minMapQuality = 0; + + // extract relevant info for end 1 + if (bam1.IsMapped()) { + chrom1 = refs.at(bam1.RefID).RefName; + start1 = bam1.Position; + end1 = bam1.GetEndPosition(false); + strand1 = "+"; + if (bam1.IsReverseStrand()) strand1 = "-"; + + // extract the edit distance from the NM tag + // if possible. otherwise, complain. + if (useEditDistance == true && bam1.GetTag("NM", editDistance1) == false) { + cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n"; + exit(1); + } + } + + // extract relevant info for end 2 + if (bam2.IsMapped()) { + chrom2 = refs.at(bam2.RefID).RefName; + start2 = bam2.Position; + end2 = bam2.GetEndPosition(false); + strand2 = "+"; + if (bam2.IsReverseStrand()) strand2 = "-"; + + // extract the edit distance from the NM tag + // if possible. otherwise, complain. + if (useEditDistance == true && bam2.GetTag("NM", editDistance2) == false) { + cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n"; + exit(1); + } + } + + // swap the ends if necessary + if ( chrom1 > chrom2 || ((chrom1 == chrom2) && (start1 > start2)) ) { + swap(chrom1, chrom2); + swap(start1, start2); + swap(end1, end2); + swap(strand1, strand2); + } + + // report BEDPE using min mapQuality + if (useEditDistance == false) { + // compute the minimum mapping quality b/w the two ends of the pair. + if (bam1.IsMapped() == true && bam2.IsMapped() == true) + minMapQuality = min(bam1.MapQuality, bam2.MapQuality); + + printf("%s\t%d\t%d\t\%s\t%d\t%d\t%s\t%d\t%s\t%s\n", + chrom1.c_str(), start1, end1, chrom2.c_str(), start2, end2, + bam1.Name.c_str(), minMapQuality, strand1.c_str(), strand2.c_str()); + } + // report BEDPE using total edit distance + else { + uint16_t totalEditDistance = 0; + if (bam1.IsMapped() == true && bam2.IsMapped() == true) + totalEditDistance = editDistance1 + editDistance2; + else if (bam1.IsMapped() == true) + totalEditDistance = editDistance1; + else if (bam2.IsMapped() == true) + totalEditDistance = editDistance2; + + printf("%s\t%d\t%d\t\%s\t%d\t%d\t%s\t%d\t%s\t%s\n", + chrom1.c_str(), start1, end1, chrom2.c_str(), start2, end2, + bam1.Name.c_str(), totalEditDistance, strand1.c_str(), strand2.c_str()); + } +} + + +// deprecated. +bool IsCorrectMappingForBEDPE (const BamAlignment &bam) { + + if ( (bam.RefID == bam.MateRefID) && (bam.InsertSize > 0) ) { + return true; + } + else if ( (bam.RefID == bam.MateRefID) && (bam.InsertSize == 0) && bam.IsFirstMate() ) { + return true; + } + else if ( (bam.RefID != bam.MateRefID) && bam.IsFirstMate() ) { + return true; + } + else return false; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bed12ToBed6/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,44 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= bed12ToBed6.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= bed12ToBed6 + + +all: $(PROGRAM) + +.PHONY: all + + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bed12ToBed6/bed12ToBed6.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,168 @@ +/***************************************************************************** + bed12ToBed6.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "bedFile.h" +#include "version.h" + +#include <vector> +#include <iostream> +#include <fstream> +#include <stdlib.h> + +using namespace std; + + +// define our program name +#define PROGRAM_NAME "bed12ToBed6" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + + +// function declarations +void ShowHelp(void); +void DetermineBedInput(BedFile *bed); +void ProcessBed(istream &bedInput, BedFile *bed); + + +bool addBlockNums = false; + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + bool haveBed = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-n", 2, parameterLength)) { + addBlockNums = true; + i++; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have an input files + if (!haveBed ) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedFile *bed = new BedFile(bedFile); + DetermineBedInput(bed); + } + else { + ShowHelp(); + } +} + + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Splits BED12 features into discrete BED6 features." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed12>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-n\t" << "Force the score to be the (1-based) block number from the BED12." << endl << endl; + + + // end the program here + exit(1); +} + + +void DetermineBedInput(BedFile *bed) { + + // dealing with a proper file + if (bed->bedFile != "stdin") { + + ifstream bedStream(bed->bedFile.c_str(), ios::in); + if ( !bedStream ) { + cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + ProcessBed(bedStream, bed); + } + // reading from stdin + else { + ProcessBed(cin, bed); + } +} + + +void ProcessBed(istream &bedInput, BedFile *bed) { + + // process each BED entry and convert to BAM + BED bedEntry, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + // open the BED file for reading. + bed->Open(); + while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + + bedVector bedBlocks; // vec to store the discrete BED "blocks" from a + splitBedIntoBlocks(bedEntry, lineNum, bedBlocks); + + for (int i = 0; i < (int) bedBlocks.size(); ++i) { + if (addBlockNums == false) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(), + bedBlocks[i].score.c_str(), bedBlocks[i].strand.c_str()); + } + else { + if (bedBlocks[i].strand == "+") + printf ("%s\t%d\t%d\t%s\t%d\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(), + i+1, bedBlocks[i].strand.c_str()); + else + printf ("%s\t%d\t%d\t%s\t%d\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(), + (int) ((bedBlocks.size()+1)-i), bedBlocks[i].strand.c_str()); + } + } + bedEntry = nullBed; + } + } + // close up + bed->Close(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bedToBam/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,53 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= bedToBam.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= bedToBam + + +all: $(PROGRAM) + +.PHONY: all + + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bedToBam/bedToBam.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,357 @@ +/***************************************************************************** + bedToBam.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "bedFile.h" +#include "genomeFile.h" +#include "version.h" + + +#include "api/BamReader.h" +#include "api/BamAux.h" +#include "api/BamWriter.h" +using namespace BamTools; + +#include <vector> +#include <iostream> +#include <fstream> +#include <stdlib.h> + +using namespace std; + + +// define our program name +#define PROGRAM_NAME "bedToBam" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + + +// function declarations +void ShowHelp(void); +void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED12, int mapQual, bool uncompressedBam); +void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int> &chromToId, bool isBED12, int mapQual, int lineNum); +void MakeBamHeader(const string &genomeFile, RefVector &refs, string &header, map<string, int> &chromToInt); +int reg2bin(int beg, int end); + + + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + string genomeFile; + + unsigned int mapQual = 255; + + bool haveBed = true; + bool haveGenome = false; + bool haveMapQual = false; + bool isBED12 = false; + bool uncompressedBam = false; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-mapq", 5, parameterLength)) { + haveMapQual = true; + if ((i+1) < argc) { + mapQual = atoi(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-bed12", 6, parameterLength)) { + isBED12 = true; + } + else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) { + uncompressedBam = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have an input files + if (!haveBed ) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl; + showHelp = true; + } + if (!haveGenome ) { + cerr << endl << "*****" << endl << "*****ERROR: Need -g (genome) file. " << endl << "*****" << endl; + showHelp = true; + } + if (mapQual < 0 || mapQual > 255) { + cerr << endl << "*****" << endl << "*****ERROR: MAPQ must be in range [0,255]. " << endl << "*****" << endl; + showHelp = true; + } + + + if (!showHelp) { + BedFile *bed = new BedFile(bedFile); + GenomeFile *genome = new GenomeFile(genomeFile); + + ProcessBed(cin, bed, genome, isBED12, mapQual, uncompressedBam); + } + else { + ShowHelp(); + } +} + + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Converts feature records to BAM format." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-mapq\t" << "Set the mappinq quality for the BAM records." << endl; + cerr << "\t\t(INT) Default: 255" << endl << endl; + + cerr << "\t-bed12\t" << "The BED file is in BED12 format. The BAM CIGAR" << endl; + cerr << "\t\tstring will reflect BED \"blocks\"." << endl << endl; + + cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) BED files must be at least BED4 to be amenable to BAM (needs name field)." << endl << endl; + + + // end the program here + exit(1); +} + + +void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED12, int mapQual, bool uncompressedBam) { + + BamWriter *writer = new BamWriter(); + + // build a BAM header from the genomeFile + RefVector refs; + string bamHeader; + map<string, int, std::less<string> > chromToId; + MakeBamHeader(genome->getGenomeFileName(), refs, bamHeader, chromToId); + + // set compression mode + BamWriter::CompressionMode compressionMode = BamWriter::Compressed; + if ( uncompressedBam ) compressionMode = BamWriter::Uncompressed; + writer->SetCompressionMode(compressionMode); + // open a BAM and add the reference headers to the BAM file + writer->Open("stdout", bamHeader, refs); + + + // process each BED entry and convert to BAM + BED bedEntry, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + // open the BED file for reading. + bed->Open(); + while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + BamAlignment bamEntry; + if (bed->bedType >= 4) { + ConvertBedToBam(bedEntry, bamEntry, chromToId, isBED12, mapQual, lineNum); + writer->SaveAlignment(bamEntry); + } + else { + cerr << "Error: BED entry without name found at line: " << lineNum << ". Exiting!" << endl; + exit (1); + } + bedEntry = nullBed; + } + } + //close up + bed->Close(); + writer->Close(); +} + + +void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int, std::less<string> > &chromToId, + bool isBED12, int mapQual, int lineNum) { + + bam.Name = bed.name; + bam.Position = bed.start; + bam.Bin = reg2bin(bed.start, bed.end); + + // hard-code the sequence and qualities. + int bedLength = bed.end - bed.start; + + // set dummy seq and qual strings. the input is BED, + // so the sequence is inherently the same as it's + // reference genome. + // Thanks to James M. Ward for pointing this out. + bam.QueryBases = ""; + bam.Qualities = ""; + + // chrom and map quality + bam.RefID = chromToId[bed.chrom]; + bam.MapQuality = mapQual; + + // set the BAM FLAG + bam.AlignmentFlag = 0; + if (bed.strand == "-") + bam.SetIsReverseStrand(true); + + bam.MatePosition = -1; + bam.InsertSize = 0; + bam.MateRefID = -1; + + bam.CigarData.clear(); + + if (isBED12 == false) { + CigarOp cOp; + cOp.Type = 'M'; + cOp.Length = bedLength; + bam.CigarData.push_back(cOp); + } + // we're being told that the input is BED12. + else{ + + // does it smell like BED12? if so, process it. + if (bed.otherFields.size() == 6) { + + // extract the relevant BED fields to convert BED12 to BAM + // namely: blockCount, blockStarts, blockEnds + unsigned int blockCount = atoi(bed.otherFields[3].c_str()); + + vector<int> blockSizes, blockStarts; + Tokenize(bed.otherFields[4], blockSizes, ","); + Tokenize(bed.otherFields[5], blockStarts, ","); + + // make sure this is a well-formed BED12 entry. + if (blockSizes.size() != blockCount) { + cerr << "Error: Number of BED blocks does not match blockCount at line: " << lineNum << ". Exiting!" << endl; + exit (1); + } + else { + // does the first block start after the bed.start? + // if so, we need to do some "splicing" + if (blockStarts[0] > 0) { + CigarOp cOp; + cOp.Length = blockStarts[0]; + cOp.Type = 'N'; + bam.CigarData.push_back(cOp); + } + // handle the "middle" blocks + for (unsigned int i = 0; i < blockCount - 1; ++i) { + CigarOp cOp; + cOp.Length = blockSizes[i]; + cOp.Type = 'M'; + bam.CigarData.push_back(cOp); + + if (blockStarts[i+1] > (blockStarts[i] + blockSizes[i])) { + CigarOp cOp; + cOp.Length = (blockStarts[i+1] - (blockStarts[i] + blockSizes[i])); + cOp.Type = 'N'; + bam.CigarData.push_back(cOp); + } + } + // handle the last block. + CigarOp cOp; + cOp.Length = blockSizes[blockCount - 1]; + cOp.Type = 'M'; + bam.CigarData.push_back(cOp); + } + } + // it doesn't smell like BED12. complain. + else { + cerr << "You've indicated that the input file is in BED12 format, yet the relevant fields cannot be found. Exiting." << endl << endl; + exit(1); + } + } +} + + +void MakeBamHeader(const string &genomeFile, RefVector &refs, string &header, + map<string, int, std::less<string> > &chromToId) { + + // make a genome map of the genome file. + GenomeFile genome(genomeFile); + + header += "@HD\tVN:1.0\tSO:unsorted\n"; + header += "@PG\tID:BEDTools_bedToBam\tVN:V"; + header += VERSION; + header += "\n"; + + int chromId = 0; + vector<string> chromList = genome.getChromList(); + sort(chromList.begin(), chromList.end()); + + // create a BAM header (@SQ) entry for each chrom in the BEDTools genome file. + vector<string>::const_iterator genomeItr = chromList.begin(); + vector<string>::const_iterator genomeEnd = chromList.end(); + for (; genomeItr != genomeEnd; ++genomeItr) { + chromToId[*genomeItr] = chromId; + chromId++; + + // add to the header text + int size = genome.getChromSize(*genomeItr); + string chromLine = "@SQ\tSN:" + *genomeItr + "\tAS:" + genomeFile + "\tLN:" + ToString(size) + "\n"; + header += chromLine; + + // create a chrom entry and add it to + // the RefVector + RefData chrom; + chrom.RefName = *genomeItr; + chrom.RefLength = size; + refs.push_back(chrom); + } +} + + +/* Taken directly from the SAMTools spec +calculate bin given an alignment in [beg,end) (zero-based, half-close, half-open) */ +int reg2bin(int beg, int end) { + --end; + if (beg>>14 == end>>14) return ((1<<15)-1)/7 + (beg>>14); + if (beg>>17 == end>>17) return ((1<<12)-1)/7 + (beg>>17); + if (beg>>20 == end>>20) return ((1<<9)-1)/7 + (beg>>20); + if (beg>>23 == end>>23) return ((1<<6)-1)/7 + (beg>>23); + if (beg>>26 == end>>26) return ((1<<3)-1)/7 + (beg>>26); + return 0; +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bedToIgv/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,51 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= bedToIgv.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= bedToIgv + + +all: $(PROGRAM) + +.PHONY: all + + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/bedToIgv/bedToIgv.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,269 @@ +/***************************************************************************** + bedToIgv.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "bedFile.h" +#include "genomeFile.h" +#include "version.h" + +#include <vector> +#include <iostream> +#include <fstream> +#include <stdlib.h> + +using namespace std; + +// define our program name +#define PROGRAM_NAME "bedToIgv" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +void DetermineBedInput(BedFile *bed, string path, string sortType, string session, + bool collapse, bool useNames, string imageType, int slop); +void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session, + bool collapse, bool useNames, string imageType, int slop); + + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + string imagePath = "./"; + string sortType = "none"; + string session = "none"; + int slop = 0; + string imageType = "png"; + + bool haveBed = true; + bool collapse = false; + bool useNames = false; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-path", 5, parameterLength)) { + if ((i+1) < argc) { + imagePath = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-sort", 5, parameterLength)) { + if ((i+1) < argc) { + sortType = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-sess", 5, parameterLength)) { + if ((i+1) < argc) { + session = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-clps", 5, parameterLength)) { + collapse = true; + } + else if(PARAMETER_CHECK("-name", 5, parameterLength)) { + useNames = true; + } + else if(PARAMETER_CHECK("-slop", 5, parameterLength)) { + if ((i+1) < argc) { + slop = atoi(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-img", 4, parameterLength)) { + if ((i+1) < argc) { + imageType = argv[i + 1]; + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have an input files + if (!haveBed ) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl; + showHelp = true; + } + if (sortType != "none") { + if ((sortType != "base") && (sortType != "position") && (sortType != "strand") && + (sortType != "quality") && (sortType != "sample") && (sortType != "readGroup")) { + cerr << endl << "*****" << endl << "*****ERROR: Invalid sort option. " << endl << "*****" << endl; + showHelp = true; + } + } + if (slop < 0) { + cerr << endl << "*****" << endl << "*****ERROR: Slop must be >= 0. " << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedFile *bed = new BedFile(bedFile); + DetermineBedInput(bed, imagePath, sortType, session, collapse, useNames, imageType, slop); + } + else { + ShowHelp(); + } +} + + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Creates a batch script to create IGV images " << endl; + cerr << " at each interval defined in a BED/GFF/VCF file." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-path\t" << "The full path to which the IGV snapshots should be written." << endl; + cerr << "\t\t(STRING) Default: ./" << endl << endl; + + cerr << "\t-sess\t" << "The full path to an existing IGV session file to be " << endl; + cerr << "\t\tloaded prior to taking snapshots." << endl << endl; + cerr << "\t\t(STRING) Default is for no session to be loaded." << endl << endl; + + cerr << "\t-sort\t" << "The type of BAM sorting you would like to apply to each image. " << endl; + cerr << "\t\tOptions: base, position, strand, quality, sample, and readGroup" << endl; + cerr << "\t\tDefault is to apply no sorting at all." << endl << endl; + + cerr << "\t-clps\t" << "Collapse the aligned reads prior to taking a snapshot. " << endl; + cerr << "\t\tDefault is to no collapse." << endl << endl; + + cerr << "\t-name\t" << "Use the \"name\" field (column 4) for each image's filename. " << endl; + cerr << "\t\tDefault is to use the \"chr:start-pos.ext\"." << endl << endl; + + cerr << "\t-slop\t" << "Number of flanking base pairs on the left & right of the image." << endl; + cerr << "\t\t- (INT) Default = 0." << endl << endl; + + cerr << "\t-img\t" << "The type of image to be created. " << endl; + cerr << "\t\tOptions: png, eps, svg" << endl; + cerr << "\t\tDefault is png." << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) The resulting script is meant to be run from within the IGV GUI version 1.5 or later." << endl; + cerr << "\t(2) Unless you use the -sess option, it is assumed that prior to running the script, " << endl; + cerr << "\t\tyou have loaded the proper genome, tracks and data files." << endl << endl; + + + // end the program here + exit(1); +} + + +void DetermineBedInput(BedFile *bed, string path, string sortType, string session, + bool collapse, bool useNames, string imageType, int slop) { + + // dealing with a proper file + if (bed->bedFile != "stdin") { + + ifstream bedStream(bed->bedFile.c_str(), ios::in); + if ( !bedStream ) { + cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + ProcessBed(bedStream, bed, path, sortType, session, collapse, useNames, imageType, slop); + } + // reading from stdin + else { + ProcessBed(cin, bed, path, sortType, session, collapse, useNames, imageType, slop); + } +} + + +void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session, + bool collapse, bool useNames, string imageType, int slop) { + + // set the image path + cout << "snapshotDirectory " << path << endl; + + // should we load a session + if (session != "none") + cout << "load " << session << endl; + + + BED bedEntry, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + + bed->Open(); + // process each BED entry and convert to an IGV request + while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + + string filename = bedEntry.chrom + "_" + ToString(bedEntry.start) + "_" + ToString(bedEntry.end); + string locus = bedEntry.chrom + ":" + ToString(bedEntry.start - slop) + "-" + ToString(bedEntry.end + slop); + + if (useNames == true) { + if (bedEntry.name.empty() == false) + filename = filename + "_" + bedEntry.name; + else { + cerr << "Error: You requested that filenames be based upon the name field. However, it appears to be empty. Exiting!" << endl; + exit (1); + } + } + if (slop > 0) { + filename = filename + "_" + "slop" + ToString(slop); + } + // goto + cout << "goto " << locus << endl; + + // sort + if (sortType != "none") + cout << "sort " << sortType << endl; + + // collapse + if (collapse == true) + cout << "collapse" << endl; + + // snapshot + cout << "snapshot " << filename << "." << imageType << endl; + + // reset + bedEntry = nullBed; + } + } + // close up + bed->Close(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/closestBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,41 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= closestMain.cpp closestBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= closestBed + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/closestBed/closestBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,234 @@ +/***************************************************************************** + closestBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "closestBed.h" + +const int MAXSLOP = 256000000; // 2*MAXSLOP = 512 megabases. + // We don't want to keep looking if we + // can't find a nearby feature within 512 Mb. +const int SLOPGROWTH = 2048000; + + +/* + Constructor +*/ +BedClosest::BedClosest(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand, + string &tieMode, bool reportDistance, bool signDistance, string &_strandedDistMode, + bool ignoreOverlaps) + : _bedAFile(bedAFile) + , _bedBFile(bedBFile) + , _tieMode(tieMode) + , _sameStrand(sameStrand) + , _diffStrand(diffStrand) + , _reportDistance(reportDistance) + , _signDistance(signDistance) + , _strandedDistMode(_strandedDistMode) + , _ignoreOverlaps(ignoreOverlaps) +{ + _bedA = new BedFile(_bedAFile); + _bedB = new BedFile(_bedBFile); + FindClosestBed(); +} + + +/* + Destructor +*/ +BedClosest::~BedClosest(void) { +} + + +void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) { + + int slop = 0; // start out just looking for overlaps + // within the current bin (~128Kb) + + // update the current feature's start and end + + CHRPOS aFudgeStart = 0; + CHRPOS aFudgeEnd; + int numOverlaps = 0; + vector<BED> closestB; + CHRPOS minDistance = INT_MAX; + int32_t curDistance = INT_MAX; + vector<int32_t> distances; + + // is there at least one feature in B on the same chrom + // as the current A feature? + if(_bedB->bedMap.find(a.chrom) != _bedB->bedMap.end()) { + + while ((numOverlaps == 0) && (slop <= MAXSLOP)) { + + // add some slop (starting at 0 bases) to a in hopes + // of finding a hit in B + if ((static_cast<int>(a.start) - slop) > 0) + aFudgeStart = a.start - slop; + else + aFudgeStart = 0; + + if ((static_cast<int>(a.start) + slop) < (2 * MAXSLOP)) + aFudgeEnd = a.end + slop; + else + aFudgeEnd = 2 * MAXSLOP; + + // THE HEAVY LIFTING + // search for hits with the current slop added + _bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, _sameStrand, _diffStrand); + + vector<BED>::const_iterator h = hits.begin(); + vector<BED>::const_iterator hitsEnd = hits.end(); + for (; h != hitsEnd; ++h) { + + // do the actual features overlap? + int s = max(a.start, h->start); + int e = min(a.end, h->end); + int overlapBases = (e - s); // the number of overlapping bases b/w a and b + + // make sure we allow overlapping features. + if ((overlapBases > 0) && (_ignoreOverlaps == true)) + continue; + else + numOverlaps++; + + // there is overlap. make sure we allow overlapping features () + if (overlapBases > 0) { + closestB.push_back(*h); + distances.push_back(0); + } + // the hit is to the "left" of A + else if (h->end <= a.start) { + curDistance = a.start - h->end; + if (_signDistance) { + if ((_strandedDistMode == "ref") + || (_strandedDistMode == "a" && a.strand != "-") + || (_strandedDistMode == "b" && h->strand == "-")) { + curDistance = -curDistance; + } + } + + if (abs(curDistance) < minDistance) { + minDistance = abs(curDistance); + + closestB.clear(); + closestB.push_back(*h); + distances.clear(); + distances.push_back(curDistance); + } + else if (abs(curDistance) == minDistance) { + minDistance = abs(curDistance); + closestB.push_back(*h); + distances.push_back(curDistance); + } + } + // the hit is to the "right" of A + else if (h->start >= a.end) { + curDistance = h->start - a.end; + if (_signDistance) { + if ((_strandedDistMode == "a" && a.strand == "-") + || (_strandedDistMode == "b" && h->strand != "-")) { + curDistance = -curDistance; + } + } + if (abs(curDistance) < minDistance) { + minDistance = abs(curDistance); + closestB.clear(); + closestB.push_back(*h); + distances.clear(); + distances.push_back(curDistance); + } + else if (abs(curDistance) == minDistance) { + minDistance = abs(curDistance); + closestB.push_back(*h); + distances.push_back(curDistance); + } + } + } + // if no overlaps were found, we'll widen the range + // by SLOPGROWTH in each direction and search again. + slop += SLOPGROWTH; + } + } + // there is no feature in B on the same chromosome as A + else { + _bedA->reportBedTab(a); + if (_reportDistance == true) { + _bedB->reportNullBedTab(); + cout << -1 << endl; + } + else + _bedB->reportNullBedNewLine(); + } + + // report the closest feature(s) in B to the current A feature. + // obey the user's reporting request (_tieMode) + if (numOverlaps > 0) { + if (closestB.size() == 1 || _tieMode == "first") { + _bedA->reportBedTab(a); + if (_reportDistance == true) { + _bedB->reportBedTab(closestB[0]); + cout << distances[0] << endl; + } + else + _bedB->reportBedNewLine(closestB[0]); + } + else { + if (_tieMode == "all") { + size_t i = 0; + for (vector<BED>::iterator b = closestB.begin(); b != closestB.end(); ++b) { + _bedA->reportBedTab(a); + if (_reportDistance == true) { + _bedB->reportBedTab(*b); + cout << distances[i++] <<endl; + } + else + _bedB->reportBedNewLine(*b); + } + } + else if (_tieMode == "last") { + _bedA->reportBedTab(a); + if (_reportDistance == true) { + _bedB->reportBedTab(closestB[closestB.size()-1]); + cout << distances[distances.size() - 1]<<endl; + } + else + _bedB->reportBedNewLine(closestB[closestB.size()-1]); + } + } + } +} + + +void BedClosest::FindClosestBed() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedFileIntoMap(); + + BED a, nullBed; + int lineNum = 0; // current input line number + vector<BED> hits; // vector of potential hits + hits.reserve(100); + BedLineStatus bedStatus; + + _bedA->Open(); + // process each entry in A in search of the closest feature in B + while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + FindWindowOverlaps(a, hits); + hits.clear(); + a = nullBed; + } + } + _bedA->Close(); +} +// END ClosestBed +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/closestBed/closestBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,61 @@ +/***************************************************************************** + closestBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef CLOSESTBED_H +#define CLOSESTBED_H + +#include "bedFile.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class BedClosest { + +public: + + // constructor + BedClosest(string &bedAFile, string &bedBFile, + bool sameStrand, bool diffStrand, string &tieMode, + bool reportDistance, bool signDistance, string &strandedDistMode, + bool ignoreOverlaps); + + // destructor + ~BedClosest(void); + + // find the closest feature in B to A + void FindClosestBed(); + +private: + + // data + string _bedAFile; + string _bedBFile; + string _tieMode; + bool _sameStrand; + bool _diffStrand; + bool _reportDistance; + bool _signDistance; + string _strandedDistMode; + bool _ignoreOverlaps; + + BedFile *_bedA, *_bedB; + + // methods + void reportNullB(); + void FindWindowOverlaps(BED &, vector<BED> &); + +}; +#endif /* CLOSEST_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/closestBed/closestMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,202 @@ +/***************************************************************************** + closestMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "closestBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "closestBed" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + string tieMode = "all"; + string strandedDistMode = ""; + + bool haveBedA = false; + bool haveBedB = false; + bool haveTieMode = false; + bool sameStrand = false; + bool diffStrand = false; + bool ignoreOverlaps = false; + bool reportDistance = false; + bool signDistance = false; + bool haveStrandedDistMode = false; + + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if( (PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + sameStrand = true; + } + else if (PARAMETER_CHECK("-S", 2, parameterLength)) { + diffStrand = true; + } + else if (PARAMETER_CHECK("-d", 2, parameterLength)) { + reportDistance = true; + } + else if (PARAMETER_CHECK("-D", 2, parameterLength)) { + if ((i+1) < argc) { + reportDistance = true; + signDistance = true; + haveStrandedDistMode = true; + strandedDistMode = argv[i + 1]; + i++; + } + } + else if (PARAMETER_CHECK("-io", 3, parameterLength)) { + ignoreOverlaps = true; + } + else if (PARAMETER_CHECK("-t", 2, parameterLength)) { + if ((i+1) < argc) { + haveTieMode = true; + tieMode = argv[i + 1]; + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (haveTieMode && (tieMode != "all") && (tieMode != "first") + && (tieMode != "last")) { + cerr << endl << "*****" << endl << "*****ERROR: Request \"all\" or \"first\" or \"last\" for Tie Mode (-t)" << endl << "*****" << endl; + showHelp = true; + } + + if (haveStrandedDistMode && (strandedDistMode != "a") && (strandedDistMode != "b") + && (strandedDistMode != "ref")) { + cerr << endl << "*****" << endl << "*****ERROR: Request \"a\" or \"b\" or \"ref\" for Stranded Distance Mode (-D)" << endl << "*****" << endl; + showHelp = true; + } + + if (sameStrand && diffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedClosest *bc = new BedClosest(bedAFile, bedBFile, sameStrand, diffStrand, tieMode, reportDistance, signDistance, strandedDistMode, ignoreOverlaps); + delete bc; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Authors: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + cerr << "\t Erik Arner, Riken" << endl << endl; + + cerr << "Summary: For each feature in A, finds the closest " << endl; + cerr << "\t feature (upstream or downstream) in B." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-s\t" << "Require same strandedness. That is, find the closest feature in B" << endl; + cerr << "\t\tthat overlaps A on the _same_ strand." << endl; + cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + + cerr << "\t-S\t" << "Require opposite strandedness. That is, find the closest feature in B" << endl; + cerr << "\t\tthat overlaps A on the _opposite_ strand." << endl; + cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + + cerr << "\t-d\t" << "In addition to the closest feature in B, " << endl; + cerr << "\t\treport its distance to A as an extra column." << endl; + cerr << "\t\t- The reported distance for overlapping features will be 0." << endl << endl; + + cerr << "\t-D\t" << "Like -d, report the closest feature in B, and its distance to A" << endl; + cerr << "\t\tas an extra column. Unlike -d, use negative distances to report" << endl; + cerr << "\t\tupstream features. You must specify which orientation defines \"upstream\"." << endl; + cerr << "\t\tThe options are:" << endl; + cerr << "\t\t- \"ref\" Report distance with respect to the reference genome. " << endl; + cerr << "\t\t B features with a lower (start, stop) are upstream" << endl; + cerr << "\t\t- \"a\" Report distance with respect to A." << endl; + cerr << "\t\t When A is on the - strand, \"upstream\" means B has a higher (start,stop)." << endl; + cerr << "\t\t- \"b\" Report distance with respect to B." << endl; + cerr << "\t\t When B is on the - strand, \"upstream\" means A has a higher (start,stop)." << endl << endl; + + cerr << "\t-io\t" << "Ignore features in B that overlap A. That is, we want close, but " << endl; + cerr << "\t\tnot touching features only." << endl << endl; + + cerr << "\t-t\t" << "How ties for closest feature are handled. This occurs when two" << endl; + cerr << "\t\tfeatures in B have exactly the same \"closeness\" with A." << endl; + cerr << "\t\tBy default, all such features in B are reported." << endl; + cerr << "\t\tHere are all the options:" << endl; + cerr << "\t\t- \"all\" Report all ties (default)." << endl; + cerr << "\t\t- \"first\" Report the first tie that occurred in the B file." << endl; + cerr << "\t\t- \"last\" Report the last tie that occurred in the B file." << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\tReports \"none\" for chrom and \"-1\" for all other fields when a feature" << endl; + cerr << "\tis not found in B on the same chromosome as the feature in A." << endl; + cerr << "\tE.g. none\t-1\t-1" << endl << endl; + + // end the program here + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/complementBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,50 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= complementMain.cpp complementBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= complementBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/complementBed/complementBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,83 @@ +/***************************************************************************** + complementBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "complementBed.h" + +BedComplement::BedComplement(string &bedFile, string &genomeFile) { + + _bedFile = bedFile; + _genomeFile = genomeFile; + + _bed = new BedFile(bedFile); + _genome = new GenomeFile(genomeFile); + +} + + +BedComplement::~BedComplement(void) { +} + + +// +// Merge overlapping BED entries into a single entry +// +void BedComplement::ComplementBed() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + // get a list of the chroms in the user's genome + vector<string> chromList = _genome->getChromList(); + + // process each chrom in the genome + for (size_t c = 0; c < chromList.size(); ++c) { + string currChrom = chromList[c]; + + // create a "bit vector" for the chrom + CHRPOS currChromSize = _genome->getChromSize(currChrom); + vector<bool> chromMasks(currChromSize, 0); + + // mask the chrom for every feature in the BED file + bedVector::const_iterator bItr = _bed->bedMapNoBin[currChrom].begin(); + bedVector::const_iterator bEnd = _bed->bedMapNoBin[currChrom].end(); + for (; bItr != bEnd; ++bItr) { + if (bItr->end > currChromSize) { + cout << "Warninge: end of BED entry exceeds chromosome length. Please correct." << endl; + _bed->reportBedNewLine(*bItr); + exit(1); + } + + // mask all of the positions spanned by this BED entry. + for (CHRPOS b = bItr->start; b < bItr->end; b++) + chromMasks[b] = 1; + } + + // report the unmasked, that is, complemented parts of the chrom + CHRPOS i = 0; + CHRPOS start; + while (i < chromMasks.size()) { + if (chromMasks[i] == 0) { + start = i; + while ((chromMasks[i] == 0) && (i < chromMasks.size())) + i++; + + if (start > 0) + cout << currChrom << "\t" << start << "\t" << i << endl; + else + cout << currChrom << "\t" << 0 << "\t" << i << endl; + } + i++; + } + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/complementBed/complementBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,47 @@ +/***************************************************************************** + complementBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" +#include "genomeFile.h" + +#include <vector> +#include <bitset> +#include <algorithm> +#include <iostream> +#include <fstream> +#include <limits.h> +#include <stdlib.h> + +using namespace std; + + +//************************************************ +// Class methods and elements +//************************************************ +class BedComplement { + +public: + + // constructor + BedComplement(string &bedFile, string &genomeFile); + + // destructor + ~BedComplement(void); + + void ComplementBed(); + +private: + + string _bedFile; + string _genomeFile; + BedFile *_bed; + GenomeFile *_genome; +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/complementBed/complementMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,116 @@ +/***************************************************************************** + complementBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "complementBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "complementBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + string genomeFile; + + bool haveBed = true; + bool haveGenome = false; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed || !haveGenome) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file and -g Genome file. " << endl << "*****" << endl; + showHelp = true; + } + if (!showHelp) { + BedComplement *bc = new BedComplement(bedFile, genomeFile); + bc->ComplementBed(); + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Returns the base pair complement of a feature file." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl; + cerr << "\t <chromName><TAB><chromSize>" << endl << endl; + cerr << "\tFor example, Human (hg19):" << endl; + cerr << "\tchr1\t249250621" << endl; + cerr << "\tchr2\t243199373" << endl; + cerr << "\t..." << endl; + cerr << "\tchr18_gl000207_random\t4262" << endl << endl; + + cerr << "Tips: " << endl; + cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl; + cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl; + cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl; + cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl; + + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/coverageBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,51 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= coverageMain.cpp coverageBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o BamAncillary.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= coverageBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/coverageBed/coverageBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,293 @@ +/***************************************************************************** + coverageBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "coverageBed.h" + +// build +BedCoverage::BedCoverage(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand, + bool writeHistogram, bool bamInput, bool obeySplits, + bool eachBase, bool countsOnly) { + + _bedAFile = bedAFile; + _bedBFile = bedBFile; + + _bedA = new BedFile(bedAFile); + _bedB = new BedFile(bedBFile); + + _sameStrand = sameStrand; + _diffStrand = diffStrand; + _obeySplits = obeySplits; + _eachBase = eachBase; + _writeHistogram = writeHistogram; + _bamInput = bamInput; + _countsOnly = countsOnly; + + + if (_bamInput == false) + CollectCoverageBed(); + else + CollectCoverageBam(_bedA->bedFile); +} + +// destroy +BedCoverage::~BedCoverage(void) { + delete _bedA; + delete _bedB; +} + + +void BedCoverage::CollectCoverageBed() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedCovFileIntoMap(); + + int lineNum = 0; // current input line number + BED a, nullBed; + BedLineStatus bedStatus; + + _bedA->Open(); + // process each entry in A + while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + // process the BED entry as a single block + if (_obeySplits == false) + _bedB->countHits(a, _sameStrand, _diffStrand, _countsOnly); + // split the BED into discrete blocksand process each independently. + else { + bedVector bedBlocks; + splitBedIntoBlocks(a, lineNum, bedBlocks); + + // use countSplitHits to avoid over-counting each split chunk + // as distinct read coverage. + _bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly); + } + a = nullBed; + } + } + _bedA->Close(); + + // report the coverage (summary or histogram) for BED B. + if (_countsOnly == true) + ReportCounts(); + else + ReportCoverage(); +} + + +void BedCoverage::CollectCoverageBam(string bamFile) { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedCovFileIntoMap(); + + // open the BAM file + BamReader reader; + reader.Open(bamFile); + + // get header & reference information + string header = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // convert each aligned BAM entry to BED + // and compute coverage on B + BamAlignment bam; + while (reader.GetNextAlignment(bam)) { + if (bam.IsMapped()) { + // treat the BAM alignment as a single "block" + if (_obeySplits == false) { + // construct a new BED entry from the current BAM alignment. + BED a; + a.chrom = refs.at(bam.RefID).RefName; + a.start = bam.Position; + a.end = bam.GetEndPosition(false, false); + a.strand = "+"; + if (bam.IsReverseStrand()) a.strand = "-"; + + _bedB->countHits(a, _sameStrand, _diffStrand, _countsOnly); + } + // split the BAM alignment into discrete blocks and + // look for overlaps only within each block. + else { + // vec to store the discrete BED "blocks" from a + bedVector bedBlocks; + // since we are counting coverage, we do want to split blocks when a + // deletion (D) CIGAR op is encountered (hence the true for the last parm) + getBamBlocks(bam, refs, bedBlocks, true); + // use countSplitHits to avoid over-counting each split chunk + // as distinct read coverage. + _bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly); + } + } + } + // report the coverage (summary or histogram) for BED B. + if (_countsOnly == true) + ReportCounts(); + else + ReportCoverage(); + // close the BAM file + reader.Close(); +} + + +void BedCoverage::ReportCounts() { + + + // process each chromosome + masterBedCovMap::const_iterator chromItr = _bedB->bedCovMap.begin(); + masterBedCovMap::const_iterator chromEnd = _bedB->bedCovMap.end(); + for (; chromItr != chromEnd; ++chromItr) + { + // for each chrom, process each bin + binsToBedCovs::const_iterator binItr = chromItr->second.begin(); + binsToBedCovs::const_iterator binEnd = chromItr->second.end(); + for (; binItr != binEnd; ++binItr) + { + // for each chrom & bin, compute and report + // the observed coverage for each feature + vector<BEDCOV>::const_iterator bedItr = binItr->second.begin(); + vector<BEDCOV>::const_iterator bedEnd = binItr->second.end(); + for (; bedItr != bedEnd; ++bedItr) + { + _bedB->reportBedTab(*bedItr); + printf("%d\n", bedItr->count); + } + } + } +} + +void BedCoverage::ReportCoverage() { + + map<unsigned int, unsigned int> allDepthHist; + unsigned int totalLength = 0; + + // process each chromosome + masterBedCovMap::const_iterator chromItr = _bedB->bedCovMap.begin(); + masterBedCovMap::const_iterator chromEnd = _bedB->bedCovMap.end(); + for (; chromItr != chromEnd; ++chromItr) + { + // for each chrom, process each bin + binsToBedCovs::const_iterator binItr = chromItr->second.begin(); + binsToBedCovs::const_iterator binEnd = chromItr->second.end(); + for (; binItr != binEnd; ++binItr) + { + // for each chrom & bin, compute and report + // the observed coverage for each feature + vector<BEDCOV>::const_iterator bedItr = binItr->second.begin(); + vector<BEDCOV>::const_iterator bedEnd = binItr->second.end(); + for (; bedItr != bedEnd; ++bedItr) + { + int zeroDepthCount = 0; // number of bases with zero depth + int depth = 0; // tracks the depth at the current base + + // the start is either the first base in the feature OR + // the leftmost position of an overlapping feature. e.g. (s = start): + // A ---------- + // B s ------------ + int start = min(bedItr->minOverlapStart, bedItr->start); + + // track the number of bases in the feature covered by + // 0, 1, 2, ... n features in A + map<unsigned int, unsigned int> depthHist; + map<unsigned int, DEPTH>::const_iterator depthItr; + + // compute the coverage observed at each base in the feature marching from start to end. + for (CHRPOS pos = start+1; pos <= bedItr->end; pos++) + { + // map pointer grabbing the starts and ends observed at this position + depthItr = bedItr->depthMap.find(pos); + // increment coverage if starts observed at this position. + if (depthItr != bedItr->depthMap.end()) + depth += depthItr->second.starts; + // update coverage assuming the current position is within the current B feature + if ((pos > bedItr->start) && (pos <= bedItr->end)) { + if (depth == 0) zeroDepthCount++; + // update our histograms, assuming we are not reporting "per-base" coverage. + if (_eachBase == false) { + depthHist[depth]++; + allDepthHist[depth]++; + } + else if ((_eachBase == true) && (bedItr->zeroLength == false)) + { + _bedB->reportBedTab(*bedItr); + printf("%d\t%d\n", pos-bedItr->start, depth); + } + } + // decrement coverage if ends observed at this position. + if (depthItr != bedItr->depthMap.end()) + depth = depth - depthItr->second.ends; + } + + // handle the special case where the user wants "per-base" depth + // but the current feature is length = 0. + if ((_eachBase == true) && (bedItr->zeroLength == true)) { + _bedB->reportBedTab(*bedItr); + printf("1\t%d\n",depth); + } + // Summarize the coverage for the current interval, + // assuming the user has not requested "per-base" coverage. + else if (_eachBase == false) + { + CHRPOS length = bedItr->end - bedItr->start; + if (bedItr->zeroLength == true) { + length = 0; + } + totalLength += length; + int nonZeroBases = (length - zeroDepthCount); + + float fractCovered = 0.0; + if (bedItr->zeroLength == false) { + fractCovered = (float) nonZeroBases / length; + } + + // print a summary of the coverage + if (_writeHistogram == false) { + _bedB->reportBedTab(*bedItr); + printf("%d\t%d\t%d\t%0.7f\n", bedItr->count, nonZeroBases, length, fractCovered); + } + // HISTOGRAM + // report the number of bases with coverage == x + else { + // produce a histogram when not a zero length feature. + if (bedItr->zeroLength == false) { + map<unsigned int, unsigned int>::const_iterator histItr = depthHist.begin(); + map<unsigned int, unsigned int>::const_iterator histEnd = depthHist.end(); + for (; histItr != histEnd; ++histItr) + { + float fractAtThisDepth = (float) histItr->second / length; + _bedB->reportBedTab(*bedItr); + printf("%d\t%d\t%d\t%0.7f\n", histItr->first, histItr->second, length, fractAtThisDepth); + } + } + // special case when it is a zero length feauture. + else { + _bedB->reportBedTab(*bedItr); + printf("%d\t%d\t%d\t%0.7f\n", bedItr->count, 0, 0, 1.0000000); + } + } + } + } + } + } + // report a histogram of coverage among _all_ + // features in B. + if (_writeHistogram == true) { + map<unsigned int, unsigned int>::const_iterator histItr = allDepthHist.begin(); + map<unsigned int, unsigned int>::const_iterator histEnd = allDepthHist.end(); + for (; histItr != histEnd; ++histItr) { + float fractAtThisDepth = (float) histItr->second / totalLength; + printf("all\t%d\t%d\t%d\t%0.7f\n", histItr->first, histItr->second, totalLength, fractAtThisDepth); + } + } +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/coverageBed/coverageBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,83 @@ +/***************************************************************************** + coverageBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef COVERAGEBED_H +#define COVERAGEBED_H + +#include "bedFile.h" + +#include "api/BamReader.h" +#include "api/BamAux.h" +#include "BamAncillary.h" +using namespace BamTools; + +#include <vector> +#include <algorithm> +#include <iostream> +#include <iomanip> +#include <fstream> +#include <stdlib.h> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class BedCoverage { + +public: + + // constructor + BedCoverage(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand, bool writeHistogram, + bool bamInput, bool obeySplits, bool eachBase, bool countsOnly); + + // destructor + ~BedCoverage(void); + +private: + + // input files. + string _bedAFile; + string _bedBFile; + + // instance of a bed file class. + BedFile *_bedA, *_bedB; + + // do we care about same or opposite strandedness when counting coverage? + bool _sameStrand; + bool _diffStrand; + + // should we write a histogram for each feature in B? + bool _writeHistogram; + + // are we dealing with BAM input for "A"? + bool _bamInput; + + // should we split BED/BAM into discrete blocks? + bool _obeySplits; + + // should discrete coverage be reported for each base in each feature? + bool _eachBase; + + // should we just count overlaps and not try to describe the breadth? + bool _countsOnly; + + // private function for reporting coverage information + void ReportCoverage(); + + // private function for reporting overlap counts + void ReportCounts(); + + void CollectCoverageBed(); + + void CollectCoverageBam(string bamFile); +}; +#endif /* COVERAGEBED_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/coverageBed/coverageMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,182 @@ +/***************************************************************************** + coverageMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "coverageBed.h" +#include "version.h" + +using namespace std; + +// define the version +#define PROGRAM_NAME "coverageBed" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + + // parm flags + bool sameStrand = false; + bool diffStrand = false; + bool writeHistogram = false; + bool eachBase = false; + bool obeySplits = false; + bool bamInput = false; + bool haveBedA = false; + bool haveBedB = false; + bool countsOnly = false; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-abam", 5, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + bamInput = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + sameStrand = true; + } + else if (PARAMETER_CHECK("-S", 2, parameterLength)) { + diffStrand = true; + } + else if (PARAMETER_CHECK("-hist", 5, parameterLength)) { + writeHistogram = true; + } + else if(PARAMETER_CHECK("-d", 2, parameterLength)) { + eachBase = true; + } + else if (PARAMETER_CHECK("-split", 6, parameterLength)) { + obeySplits = true; + } + else if (PARAMETER_CHECK("-counts", 7, parameterLength)) { + countsOnly = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (sameStrand && diffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedCoverage *bg = new BedCoverage(bedAFile, bedBFile, sameStrand, diffStrand, + writeHistogram, bamInput, obeySplits, eachBase, countsOnly); + delete bg; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Returns the depth and breadth of coverage of features from A" << endl; + cerr << "\t on the intervals in B." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-abam\t" << "The A input file is in BAM format." << endl << endl; + + cerr << "\t-s\t" << "Require same strandedness. That is, only counts hits in A that" << endl; + cerr << "\t\toverlap B on the _same_ strand." << endl; + cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl; + + cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in A that" << endl; + cerr << "\t\toverlap B on the _opposite_ strand." << endl; + cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl; + + cerr << "\t-hist\t" << "Report a histogram of coverage for each feature in B" << endl; + cerr << "\t\tas well as a summary histogram for _all_ features in B." << endl << endl; + cerr << "\t\tOutput (tab delimited) after each feature in B:" << endl; + cerr << "\t\t 1) depth\n\t\t 2) # bases at depth\n\t\t 3) size of B\n\t\t 4) % of B at depth" << endl << endl; + + cerr << "\t-d\t" << "Report the depth at each position in each B feature." << endl; + cerr << "\t\tPositions reported are one based. Each position" << endl; + cerr << "\t\tand depth follow the complete B feature." << endl << endl; + + cerr << "\t-counts\t" << "Only report the count of overlaps, don't compute fraction, etc." << endl << endl; + + cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl; + cerr << "\t\twhen computing coverage." << endl; + cerr << "\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations " << endl; + cerr << "\t\tto infer the blocks for computing coverage." << endl; + cerr << "\t\tFor BED12 files, this uses the BlockCount, BlockStarts," << endl; + cerr << "\t\tand BlockEnds fields (i.e., columns 10,11,12)." << endl << endl; + + cerr << "Default Output: " << endl; + cerr << "\t" << " After each entry in B, reports: " << endl; + cerr << "\t 1) The number of features in A that overlapped the B interval." << endl; + cerr << "\t 2) The number of bases in B that had non-zero coverage." << endl; + cerr << "\t 3) The length of the entry in B." << endl; + cerr << "\t 4) The fraction of bases in B that had non-zero coverage." << endl << endl; + + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/cuffToTrans/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,44 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= cuffToTransMain.cpp cuffToTrans.cpp Fasta.cpp split.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= cuffToTrans + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fastaFromBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,52 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/sequenceUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/Fasta/ \ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o Fasta.o split.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= fastaFromBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/Fasta/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fastaFromBed/fastaFromBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,141 @@ +/***************************************************************************** + fastaFromBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "fastaFromBed.h" + + +Bed2Fa::Bed2Fa(bool useName, const string &dbFile, const string &bedFile, + const string &fastaOutFile, bool useFasta, bool useStrand) { + + _useName = useName; + _dbFile = dbFile; + _bedFile = bedFile; + _fastaOutFile = fastaOutFile; + _useFasta = useFasta; + _useStrand = useStrand; + + _bed = new BedFile(_bedFile); + + // Figure out what the output file should be. + if (fastaOutFile == "stdout") { + _faOut = &cout; + } + else { + // Make sure we can open the file. + ofstream fa(fastaOutFile.c_str(), ios::out); + if ( !fa ) { + cerr << "Error: The requested fasta output file (" << fastaOutFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + else { + fa.close(); + _faOut = new ofstream(fastaOutFile.c_str(), ios::out); + } + } + + // Extract the requested intervals from the FASTA input file. + ExtractDNA(); +} + + +Bed2Fa::~Bed2Fa(void) { +} + + +//****************************************************************************** +// ReportDNA +//****************************************************************************** +void Bed2Fa::ReportDNA(const BED &bed, string &dna) { + + // revcomp if necessary. Thanks to Thomas Doktor. + if ((_useStrand == true) && (bed.strand == "-")) + reverseComplement(dna); + + if (!(_useName)) { + if (_useFasta == true) { + if (_useStrand == true) + *_faOut << ">" << bed.chrom << ":" << bed.start << "-" << bed.end << "(" << bed.strand << ")" << endl << dna << endl; + else + *_faOut << ">" << bed.chrom << ":" << bed.start << "-" << bed.end << endl << dna << endl; + } + else { + if (_useStrand == true) + *_faOut << bed.chrom << ":" << bed.start << "-" << bed.end << "(" << bed.strand << ")" << "\t" << dna << endl; + else + *_faOut << bed.chrom << ":" << bed.start << "-" << bed.end << "\t" << dna << endl; + } + } + else { + if (_useFasta == true) + *_faOut << ">" << bed.name << endl << dna << endl; + else + *_faOut << bed.name << "\t" << dna << endl; + } +} + + + +//****************************************************************************** +// ExtractDNA +//****************************************************************************** +void Bed2Fa::ExtractDNA() { + + /* Make sure that we can oen all of the files successfully*/ + + // open the fasta database for reading + ifstream faDb(_dbFile.c_str(), ios::in); + if ( !faDb ) { + cerr << "Error: The requested fasta database file (" << _dbFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + + // open and memory-map genome file + FastaReference *fr = new FastaReference; + bool memmap = true; + fr->open(_dbFile, memmap); + + BED bed, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + string sequence; + + _bed->Open(); + while ((bedStatus = _bed->GetNextBed(bed, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + // make sure we are extracting >= 1 bp + if (bed.zeroLength == false) { + size_t seqLength = fr->sequenceLength(bed.chrom); + // make sure this feature will not exceed the end of the chromosome. + if ( (bed.start <= seqLength) && (bed.end <= seqLength) ) + { + int length = bed.end - bed.start; + sequence = fr->getSubSequence(bed.chrom, bed.start, length); + ReportDNA(bed, sequence); + } + else + { + cerr << "Feature (" << bed.chrom << ":" << bed.start << "-" << bed.end << ") beyond the length of " + << bed.chrom << " size (" << seqLength << " bp). Skipping." << endl; + } + } + // handle zeroLength + else { + cerr << "Feature (" << bed.chrom << ":" << bed.start+1 << "-" << bed.end-1 << ") has length = 0, Skipping." << endl; + } + bed = nullBed; + } + } + _bed->Close(); +} + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fastaFromBed/fastaFromBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,56 @@ +/***************************************************************************** + fastaFromBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef FASTAFROMBED_H +#define FASTAFROMBED_H + +#include "bedFile.h" +#include "sequenceUtils.h" +#include "Fasta.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class Bed2Fa { + +public: + + // constructor + Bed2Fa(bool useName, const string &dbFile, const string &bedFile, const string &fastaOutFile, + bool useFasta, bool useStrand); + + // destructor + ~Bed2Fa(void); + + void ExtractDNA(); + void ReportDNA(const BED &bed, string &dna); + + +private: + + bool _useName; + string _dbFile; + string _bedFile; + string _fastaOutFile; + bool _useFasta; + bool _useStrand; + + // instance of a bed file class. + BedFile *_bed; + ostream *_faOut; +}; + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fastaFromBed/fastaFromBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,146 @@ +/***************************************************************************** + fastaFromBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "fastaFromBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "fastaFromBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string fastaDbFile; + string bedFile; + + // output files + string fastaOutFile; + + // checks for existence of parameters + bool haveFastaDb = false; + bool haveBed = false; + bool haveFastaOut = false; + bool useNameOnly = false; + bool useFasta = true; + bool useStrand = false; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-fi", 3, parameterLength)) { + if ((i+1) < argc) { + haveFastaDb = true; + fastaDbFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-fo", 3, parameterLength)) { + if ((i+1) < argc) { + haveFastaOut = true; + fastaOutFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bed", 4, parameterLength)) { + if ((i+1) < argc) { + haveBed = true; + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-name", 5, parameterLength)) { + useNameOnly = true; + } + else if(PARAMETER_CHECK("-tab", 4, parameterLength)) { + useFasta = false; + } + else if(PARAMETER_CHECK("-s", 2, parameterLength)) { + useStrand = true; + } + else { + cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + if (!haveFastaDb || !haveFastaOut || !haveBed) { + showHelp = true; + } + + if (!showHelp) { + + Bed2Fa *b2f = new Bed2Fa(useNameOnly, fastaDbFile, bedFile, fastaOutFile, useFasta, useStrand); + delete b2f; + + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Extract DNA sequences into a fasta file based on feature coordinates." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> " << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-fi\tInput FASTA file" << endl; + cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl; + cerr << "\t-fo\tOutput file (can be FASTA or TAB-delimited)" << endl; + cerr << "\t-name\tUse the name field for the FASTA header" << endl; + + cerr << "\t-tab\tWrite output in TAB delimited format." << endl; + cerr << "\t\t- Default is FASTA format." << endl << endl; + + cerr << "\t-s\tForce strandedness. If the feature occupies the antisense strand," << endl; + cerr << "\t\tthe sequence will be reverse complemented." << endl; + cerr << "\t\t- By default, strand information is ignored." << endl << endl; + + + + // end the program here + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fjoin/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,42 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= fjoinMain.cpp fjoin.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= fjoin + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fjoin/fjoin.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,350 @@ +/***************************************************************************** + intersectBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "fjoin.h" +#include <queue> +#include <set> + +bool leftOf(const BED &a, const BED &b); + + +bool BedIntersect::processHits(BED &a, vector<BED> &hits) { + // how many overlaps are there b/w the bed and the set of hits? + int s, e, overlapBases; + int numOverlaps = 0; + bool hitsFound = false; + int aLength = (a.end - a.start); // the length of a in b.p. + + // loop through the hits and report those that meet the user's criteria + vector<BED>::const_iterator h = hits.begin(); + vector<BED>::const_iterator hitsEnd = hits.end(); + for (; h != hitsEnd; ++h) { + s = max(a.start, h->start); + e = min(a.end, h->end); + overlapBases = (e - s); // the number of overlapping bases b/w a and b + + // is there enough overlap relative to the user's request? (default ~ 1bp) + if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) { + // Report the hit if the user doesn't care about reciprocal overlap between A and B. + if (_reciprocal == false) { + hitsFound = true; + numOverlaps++; + if (_printable == true) + ReportOverlapDetail(overlapBases, a, *h, s, e); + } + // we require there to be sufficient __reciprocal__ overlap + else { + int bLength = (h->end - h->start); + float bOverlap = ( (float) overlapBases / (float) bLength ); + if (bOverlap >= _overlapFraction) { + hitsFound = true; + numOverlaps++; + if (_printable == true) + ReportOverlapDetail(overlapBases, a, *h, s, e); + } + } + } + } + // report the summary of the overlaps if requested. + ReportOverlapSummary(a, numOverlaps); + // were hits found for this BED feature? + return hitsFound; +} + +/* + Constructor +*/ +BedIntersect::BedIntersect(string bedAFile, string bedBFile, bool anyHit, + bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap, + float overlapFraction, bool noHit, bool writeCount, bool forceStrand, + bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput) { + + _bedAFile = bedAFile; + _bedBFile = bedBFile; + _anyHit = anyHit; + _noHit = noHit; + _writeA = writeA; + _writeB = writeB; + _writeOverlap = writeOverlap; + _writeAllOverlap = writeAllOverlap; + _writeCount = writeCount; + _overlapFraction = overlapFraction; + _forceStrand = forceStrand; + _reciprocal = reciprocal; + _obeySplits = obeySplits; + _bamInput = bamInput; + _bamOutput = bamOutput; + + if (_anyHit || _noHit || _writeCount) + _printable = false; + else + _printable = true; + + // create new BED file objects for A and B + _bedA = new BedFile(bedAFile); + _bedB = new BedFile(bedBFile); + + IntersectBed(); +} + + +/* + Destructor +*/ +BedIntersect::~BedIntersect(void) { +} + + +bool leftOf(const BED &a, const BED &b) { + return (a.end <= b.start); +} + + +void BedIntersect::ReportOverlapDetail(const int &overlapBases, const BED &a, const BED &b, + const CHRPOS &s, const CHRPOS &e) { + // default. simple intersection only + if (_writeA == false && _writeB == false && _writeOverlap == false) { + _bedA->reportBedRangeNewLine(a,s,e); + } + // -wa -wbwrite the original A and B + else if (_writeA == true && _writeB == true) { + _bedA->reportBedTab(a); + _bedB->reportBedNewLine(b); + } + // -wa write just the original A + else if (_writeA == true) { + _bedA->reportBedNewLine(a); + } + // -wb write the intersected portion of A and the original B + else if (_writeB == true) { + _bedA->reportBedRangeTab(a,s,e); + _bedB->reportBedNewLine(b); + } + // -wo write the original A and B plus the no. of overlapping bases. + else if (_writeOverlap == true) { + _bedA->reportBedTab(a); + _bedB->reportBedTab(b); + printf("%d\n", overlapBases); + } +} + + +void BedIntersect::ReportOverlapSummary(const BED &a, const int &numOverlapsFound) { + // -u just report the fact that there was >= 1 overlaps + if (_anyHit && (numOverlapsFound >= 1)) { + _bedA->reportBedNewLine(a); + } + // -c report the total number of features overlapped in B + else if (_writeCount) { + _bedA->reportBedTab(a); + printf("%d\n", numOverlapsFound); + } + // -v report iff there were no overlaps + else if (_noHit && (numOverlapsFound == 0)) { + _bedA->reportBedNewLine(a); + } + // -wao the user wants to force the reporting of 0 overlap + else if (_writeAllOverlap && (numOverlapsFound == 0)) { + _bedA->reportBedTab(a); + _bedB->reportNullBedTab(); + printf("0\n"); + } +} + + + +void BedIntersect::Scan(BED *x, vector<BED *> *windowX, BedLineStatus xStatus, + const BED &y, vector<BED *> *windowY, BedLineStatus yStatus) { + + if (xStatus != BED_VALID) { + return; + } + + std::vector<BED *>::iterator wYIter = windowY->begin(); + while (wYIter != windowY->end()) { + if (leftOf(*(*wYIter), *x) == true) { + (*wYIter)->finished = true; + wYIter = windowY->erase(wYIter); // erase auto-increments to the next position + } + else if (overlaps((*wYIter)->start, (*wYIter)->end, x->start, x->end) > 0) { + if (_lastPick == 0) { + AddHits(x, *(*wYIter)); + } + else { + AddHits(*wYIter, *x); + } + ++wYIter; // force incrementing + } + } + if (leftOf(*x,y) == false) + windowX->push_back(x); + else { + x->finished = true; + } + // dump the buffered results (if any) + FlushOutputBuffer(); +} + + +void BedIntersect::AddHits(BED *x, const BED &y) { + if (x->overlaps.empty() == true) + _outputBuffer.push(x); + x->overlaps.push_back(y); +} + + +void BedIntersect::FlushOutputBuffer(bool final) { + while (_outputBuffer.empty() == false) + { + if (final == false && _outputBuffer.front()->finished == false) + break; + + processHits(*_outputBuffer.front(), _outputBuffer.front()->overlaps); + // remove the finished BED entry from the heap + delete _outputBuffer.front(); + _outputBuffer.pop(); + } +} + + +vector<BED*>* BedIntersect::GetWindow(const string &chrom, bool isA) { + + // iterator to test if a window for a given chrom exists. + map<string, vector<BED*> >::iterator it; + + // grab the current window for A or B, depending on + // the request. if a window hasn't yet been created + // for the requested chrom, create one. + + if (isA) { + it = _windowA.find(chrom); + if (it != _windowA.end()) { + return & _windowA[chrom]; + } + else { + _windowA.insert(pair<string, vector<BED *> >(chrom, vector<BED *>())); + return & _windowA[chrom]; + } + } + else { + it = _windowB.find(chrom); + if (it != _windowB.end()) { + return & _windowB[chrom]; + } + else { + _windowB.insert(pair<string, vector<BED *> >(chrom, vector<BED *>())); + return & _windowB[chrom]; + } + } +} + + +void BedIntersect::ChromSwitch(const string &chrom) { + + vector<BED*>::iterator windowAIter = _windowA[chrom].begin(); + vector<BED*>::iterator windowAEnd = _windowA[chrom].end(); + for (; windowAIter != windowAEnd; ++windowAIter) + (*windowAIter)->finished = true; + + vector<BED*>::iterator windowBIter = _windowB[chrom].begin(); + vector<BED*>::iterator windowBEnd = _windowB[chrom].end(); + for (; windowBIter != windowBEnd; ++windowBIter) + (*windowBIter)->finished = true; + + FlushOutputBuffer(); +} + + +void BedIntersect::IntersectBed() { + + int aLineNum = 0; + int bLineNum = 0; + + // current feature from each file + BED *a, *b, *prevA, *prevB; + + // status of the current lines + BedLineStatus aStatus, bStatus; + + // open the files; get the first line from each + _bedA->Open(); + _bedB->Open(); + + prevA = NULL; + prevB = NULL; + a = new BED(); + b = new BED(); + aStatus = _bedA->GetNextBed(*a, aLineNum); + bStatus = _bedB->GetNextBed(*b, bLineNum); + + cout << a->chrom << " " << a->start << " " << a->chrom << " " << b->start << endl; + while (aStatus != BED_INVALID || bStatus != BED_INVALID) { + + if ((a->start <= b->start) && (a->chrom == b->chrom)) { + prevA = a; + _lastPick = 0; + Scan(a, GetWindow(a->chrom, true), aStatus, + *b, GetWindow(a->chrom, false), bStatus); + + a = new BED(); + aStatus = _bedA->GetNextBed(*a, aLineNum); + } + else if ((a->start > b->start) && (a->chrom == b->chrom)) { + prevB = b; + _lastPick = 1; + Scan(b, GetWindow(b->chrom, false), bStatus, + *a, GetWindow(b->chrom, true), aStatus); + + b = new BED(); + bStatus = _bedB->GetNextBed(*b, bLineNum); + } + else if (a->chrom != b->chrom) { + // A was most recently read + if (_lastPick == 0) { + prevB = b; + while (b->chrom == prevA->chrom){ + _windowB[prevA->chrom].push_back(b); + b = new BED(); + bStatus = _bedB->GetNextBed(*b, bLineNum); + } + Scan(prevA, GetWindow(prevA->chrom, true), aStatus, + *prevB, GetWindow(prevA->chrom, false), bStatus); + } + // B was most recently read + else { + prevA = a; + while (a->chrom == prevB->chrom) { + _windowA[prevB->chrom].push_back(a); + a = new BED(); + aStatus = _bedA->GetNextBed(*a, aLineNum); + } + Scan(prevB, GetWindow(prevB->chrom, false), bStatus, + *prevA, GetWindow(prevB->chrom, true), aStatus); + } + FlushOutputBuffer(true); + } + if (prevA!=NULL&&prevB!=NULL) + //cout << prevA->chrom << " " << a->chrom << " " << a->start << " " + // << prevB->chrom << " " << b->chrom << " " << b->start << "\n"; + if (aStatus == BED_INVALID) a->start = INT_MAX; + if (bStatus == BED_INVALID) b->start = INT_MAX; + } + + // clear out the final bit of staged output + FlushOutputBuffer(true); + + // close the files + _bedA->Close(); + _bedB->Close(); +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fjoin/fjoin.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,114 @@ +/***************************************************************************** + intersectBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef INTERSECTBED_H +#define INTERSECTBED_H + +#include "bedFile.h" +// #include "BamReader.h" +// #include "BamWriter.h" +// #include "BamAncillary.h" +// #include "BamAux.h" +// using namespace BamTools; + + +#include <vector> +#include <queue> +#include <iostream> +#include <fstream> +#include <stdlib.h> +using namespace std; + + + +class BedIntersect { + +public: + + // constructor + BedIntersect(string bedAFile, string bedBFile, bool anyHit, + bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap, + float overlapFraction, bool noHit, bool writeCount, bool forceStrand, + bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput); + + // destructor + ~BedIntersect(void); + +private: + + //------------------------------------------------ + // private attributes + //------------------------------------------------ + string _bedAFile; + string _bedBFile; + + bool _writeA; // should the original A feature be reported? + bool _writeB; // should the original B feature be reported? + bool _writeOverlap; + bool _writeAllOverlap; + + bool _forceStrand; + bool _reciprocal; + float _overlapFraction; + + bool _anyHit; + bool _noHit; + bool _writeCount; // do we want a count of the number of overlaps in B? + bool _obeySplits; + bool _bamInput; + bool _bamOutput; + + bool _printable; + + queue<BED*> _outputBuffer; + bool _lastPick; + + map<string, vector<BED*> > _windowA; + map<string, vector<BED*> > _windowB; + + // instance of a bed file class. + BedFile *_bedA, *_bedB; + + //------------------------------------------------ + // private methods + //------------------------------------------------ + void IntersectBed(istream &bedInput); + + void Scan(BED *x, vector<BED *> *windowX, BedLineStatus xStatus, + const BED &y, vector<BED *> *windowY, BedLineStatus yStatus); + + void AddHits(BED *x, const BED &y); + + void FlushOutputBuffer(bool final = false); + + vector<BED*>* GetWindow(const string &chrom, bool isA); + + void ChromSwitch(const string &chrom); + + void IntersectBed(); + + void IntersectBam(string bamFile); + + bool processHits(BED &a, vector<BED> &hits); + + bool FindOverlaps(const BED &a, vector<BED> &hits); + + bool FindOneOrMoreOverlap(const BED &a); + + void ReportOverlapDetail(const int &overlapBases, const BED &a, const BED &b, + const CHRPOS &s, const CHRPOS &e); + void ReportOverlapSummary(const BED &a, const int &numOverlapsFound); + + void ReportHits(set<BED> &A, set<BED> &B); + +}; + +#endif /* INTERSECTBED_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/fjoin/fjoinMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,271 @@ +/***************************************************************************** + intersectMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "fjoin.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "fjoin" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + + // input arguments + float overlapFraction = 1E-9; + + bool haveBedA = false; + bool haveBedB = false; + bool noHit = false; + bool anyHit = false; + bool writeA = false; + bool writeB = false; + bool writeCount = false; + bool writeOverlap = false; + bool writeAllOverlap = false; + bool haveFraction = false; + bool reciprocalFraction = false; + bool forceStrand = false; + bool obeySplits = false; + bool inputIsBam = false; + bool outputIsBam = true; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + outputIsBam = false; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-abam", 5, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + inputIsBam = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bed", 4, parameterLength)) { + outputIsBam = false; + } + else if(PARAMETER_CHECK("-u", 2, parameterLength)) { + anyHit = true; + } + else if(PARAMETER_CHECK("-f", 2, parameterLength)) { + if ((i+1) < argc) { + haveFraction = true; + overlapFraction = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-wa", 3, parameterLength)) { + writeA = true; + } + else if(PARAMETER_CHECK("-wb", 3, parameterLength)) { + writeB = true; + } + else if(PARAMETER_CHECK("-wo", 3, parameterLength)) { + writeOverlap = true; + } + else if(PARAMETER_CHECK("-wao", 4, parameterLength)) { + writeAllOverlap = true; + writeOverlap = true; + } + else if(PARAMETER_CHECK("-c", 2, parameterLength)) { + writeCount = true; + } + else if(PARAMETER_CHECK("-r", 2, parameterLength)) { + reciprocalFraction = true; + } + else if (PARAMETER_CHECK("-v", 2, parameterLength)) { + noHit = true; + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + forceStrand = true; + } + else if (PARAMETER_CHECK("-split", 6, parameterLength)) { + obeySplits = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && noHit) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeB && writeCount) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeCount && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeA && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wa OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeB && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (reciprocalFraction && !haveFraction) { + cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && writeCount) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && writeB) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wb, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + + if (!showHelp) { + + BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, writeOverlap, + writeAllOverlap, overlapFraction, noHit, writeCount, forceStrand, + reciprocalFraction, obeySplits, inputIsBam, outputIsBam); + delete bi; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Report overlaps between two feature files." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl; + + cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl; + cerr << "\t\tis to write output in BAM when using -abam." << endl << endl; + + cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl; + + cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl; + cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl; + + cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl; + cerr << "\t\tpairs of overlap between the two features." << endl; + cerr << "\t\t- Overlaps restricted by -f and -r." << endl; + cerr << "\t\t Only A features with overlap are reported." << endl << endl; + + cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl; + cerr << "\t\tpairs of overlap between the two features." << endl; + cerr << "\t\t- Overlapping features restricted by -f and -r." << endl; + cerr << "\t\t However, A features w/o overlap are also reported" << endl; + cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl; + + cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl; + cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl; + cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl; + + cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl; + cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl; + cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl; + + cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl; + cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl; + + cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl; + cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl; + cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl; + + cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl; + cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl; + cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl; + + cerr << "\t-s\t" << "Force strandedness. That is, only report hits in B that" << endl; + cerr << "\t\toverlap A on the same strand." << endl; + cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + + cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl; + + + // end the program here + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/flankBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,50 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= flankBedMain.cpp flankBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= flankBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/flankBed/flankBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,163 @@ +/***************************************************************************** + flankBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "flankBed.h" + + +BedFlank::BedFlank(string &bedFile, string &genomeFile, bool forceStrand, float leftFlank, float rightFlank, bool fractional) { + + _bedFile = bedFile; + _genomeFile = genomeFile; + _forceStrand = forceStrand; + _leftFlank = leftFlank; + _rightFlank = rightFlank; + _fractional = fractional; + + _bed = new BedFile(bedFile); + _genome = new GenomeFile(genomeFile); + + // get going, slop it up. + FlankBed(); +} + + +BedFlank::~BedFlank(void) { + +} + + +void BedFlank::FlankBed() { + + int lineNum = 0; + BED bedEntry, nullBed; // used to store the current BED line from the BED file. + BedLineStatus bedStatus; + + _bed->Open(); + bedStatus = _bed->GetNextBed(bedEntry, lineNum); + while (bedStatus != BED_INVALID) { + if (bedStatus == BED_VALID) { + + int leftFlank = _leftFlank; + int rightFlank = _rightFlank; + if (_fractional == true) { + leftFlank = (int) (_leftFlank * bedEntry.size()); + rightFlank = (int) (_rightFlank * bedEntry.size()); + } + + if ((_forceStrand == false) || (bedEntry.strand == "+")) + { + AddFlank(bedEntry, leftFlank, rightFlank); + } + else if ((_forceStrand == true) && (bedEntry.strand == "-" )) + { + AddStrandedFlank(bedEntry, leftFlank, rightFlank); + } + bedEntry = nullBed; + } + bedStatus = _bed->GetNextBed(bedEntry, lineNum); + } + _bed->Close(); +} + + +void BedFlank::AddFlank(BED &bed, int leftFlank, int rightFlank) { + + int chromSize = _genome->getChromSize(bed.chrom); + if (chromSize == -1) { + cerr << "ERROR: chrom \"" << bed.chrom << "\" not found in genome file. Exiting." << endl; + exit(1); + } + + // init. our left and right flanks to the original BED entry. + // we'll create the flanks from these coordinates. + BED left = bed; + BED right = bed; + + // make the left flank (if necessary) + if (leftFlank > 0) { + if ( (static_cast<int>(left.start) - leftFlank) > 0) + { + left.end = left.start; + left.start -= leftFlank; + } + else + { + left.end = left.start; + left.start = 0; + } + // report the left flank + _bed->reportBedNewLine(left); + } + + // make the left flank (if necessary) + if (rightFlank > 0) { + if ( (static_cast<int>(right.end) + (rightFlank+1)) <= static_cast<int>(chromSize)) + { + right.start = right.end; + right.end += (rightFlank); + } + else { + right.start = right.end; + right.end += chromSize; + } + // report the right flank + _bed->reportBedNewLine(right); + } +} + + +void BedFlank::AddStrandedFlank(BED &bed, int leftFlank, int rightFlank) { + + int chromSize = _genome->getChromSize(bed.chrom); + if (chromSize == -1) { + cerr << "ERROR: chrom \"" << bed.chrom << "\" not found in genome file. Exiting." << endl; + exit(1); + } + + // init. our left and right flanks to the original BED entry. + // we'll create the flanks from these coordinates. + BED left = bed; + BED right = bed; + + // make the left flank (if necessary) + if (rightFlank > 0) { + if ( (static_cast<int>(left.start) - rightFlank) > 0) + { + left.end = left.start; + left.start -= rightFlank; + } + else + { + left.end = left.start; + left.start = 0; + } + // report the left flank + _bed->reportBedNewLine(left); + } + + // make the left flank (if necessary) + if (leftFlank > 0) { + if ( (static_cast<int>(right.end) + leftFlank) <= static_cast<int>(chromSize)) + { + right.start = right.end; + right.end += leftFlank; + } + else { + right.start = right.end; + right.end = chromSize; + } + // report the right flank + _bed->reportBedNewLine(right); + } +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/flankBed/flankBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,63 @@ +/***************************************************************************** + flankBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ + +#include "bedFile.h" +#include "genomeFile.h" + +#include <vector> +#include <iostream> +#include <fstream> +#include <map> +#include <cstdlib> +#include <ctime> +using namespace std; + + +//************************************************ +// Class methods and elements +//************************************************ +class BedFlank { + +public: + + // constructor + BedFlank(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional); + + // destructor + ~BedFlank(void); + + + +private: + + string _bedFile; + string _genomeFile; + + bool _forceStrand; + float _leftFlank; + float _rightFlank; + bool _fractional; + + BedFile *_bed; + GenomeFile *_genome; + + // methods + + void FlankBed(); + + // method to grab requested flank w.r.t. a single BED entry + void AddFlank(BED &bed, int leftSlop, int rightSlop); + + // method to grab requested flank w.r.t. a single BED entry, + // while choosing flanks based on strand + void AddStrandedFlank(BED &bed, int leftSlop, int rightSlop); +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/flankBed/flankBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,190 @@ +/***************************************************************************** + flankBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "flankBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "flankBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + string genomeFile; + + bool haveBed = true; + bool haveGenome = false; + bool haveLeft = false; + bool haveRight = false; + bool haveBoth = false; + + bool forceStrand = false; + float leftSlop = 0.0; + float rightSlop = 0.0; + bool fractional = false; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-l", 2, parameterLength)) { + if ((i+1) < argc) { + haveLeft = true; + leftSlop = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-r", 2, parameterLength)) { + if ((i+1) < argc) { + haveRight = true; + rightSlop = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBoth = true; + leftSlop = atof(argv[i + 1]); + rightSlop = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-s", 2, parameterLength)) { + forceStrand = true; + } + else if(PARAMETER_CHECK("-pct", 4, parameterLength)) { + fractional = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed || !haveGenome) { + cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl; + showHelp = true; + } + if (!haveLeft && !haveRight && !haveBoth) { + cerr << endl << "*****" << endl << "*****ERROR: Need -l and -r together or -b alone. " << endl << "*****" << endl; + showHelp = true; + } + if ((!haveLeft && haveRight) || (haveLeft && !haveRight)) { + cerr << endl << "*****" << endl << "*****ERROR: Need both -l and -r. " << endl << "*****" << endl; + showHelp = true; + } + if (forceStrand && (!(haveLeft) || !(haveRight))) { + cerr << endl << "*****" << endl << "*****ERROR: Must supply -l and -r with -s. " << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedFlank *bc = new BedFlank(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional); + delete bc; + + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Creates flanking interval(s) for each BED/GFF/VCF feature." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome> [-b <int> or (-l and -r)]" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-b\t" << "Create flanking intervak using -b base pairs in each direction." << endl; + cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl; + + cerr << "\t-l\t" << "The number of base pairs that a flank should start from orig. start coordinate." << endl; + cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl; + + cerr << "\t-r\t" << "The number of base pairs that a flank should end from orig. end coordinate." << endl; + cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl; + + cerr << "\t-s\t" << "Define -l and -r based on strand." << endl; + cerr << "\t\tE.g. if used, -l 500 for a negative-stranded feature, " << endl; + cerr << "\t\tit will start the flank 500 bp downstream. Default = false." << endl << endl; + + cerr << "\t-pct\t" << "Define -l and -r as a fraction of the feature's length." << endl; + cerr << "\t\tE.g. if used on a 1000bp feature, -l 0.50, " << endl; + cerr << "\t\twill add 500 bp \"upstream\". Default = false." << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) Starts will be set to 0 if options would force it below 0." << endl; + cerr << "\t(2) Ends will be set to the chromosome length if requested flank would" << endl; + cerr << "\tforce it above the max chrom length." << endl; + + cerr << "\t(3) The genome file should tab delimited and structured as follows:" << endl; + cerr << "\n\t<chromName><TAB><chromSize>" << endl << endl; + cerr << "\tFor example, Human (hg19):" << endl; + cerr << "\tchr1\t249250621" << endl; + cerr << "\tchr2\t243199373" << endl; + cerr << "\t..." << endl; + cerr << "\tchr18_gl000207_random\t4262" << endl << endl; + + + cerr << "Tips: " << endl; + cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl; + cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl; + cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl; + cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl; + + + // end the program here + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/genomeCoverageBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,52 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamAncillary.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= genomeCoverageBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/genomeCoverageBed/genomeCoverageBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,396 @@ +/***************************************************************************** +genomeCoverage.cpp + +(c) 2009 - Aaron Quinlan +Hall Laboratory +Department of Biochemistry and Molecular Genetics +University of Virginia +aaronquinlan@gmail.com + +Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "genomeCoverageBed.h" + + +BedGenomeCoverage::BedGenomeCoverage(string bedFile, string genomeFile, + bool eachBase, bool startSites, + bool bedGraph, bool bedGraphAll, + int max, float scale, + bool bamInput, bool obeySplits, + bool filterByStrand, string requestedStrand, + bool only_5p_end, bool only_3p_end, + bool eachBaseZeroBased, + bool add_gb_track_line, string gb_track_line_opts) { + + _bedFile = bedFile; + _genomeFile = genomeFile; + _eachBase = eachBase; + _eachBaseZeroBased = eachBaseZeroBased; + _startSites = startSites; + _bedGraph = bedGraph; + _bedGraphAll = bedGraphAll; + _max = max; + _scale = scale; + _bamInput = bamInput; + _obeySplits = obeySplits; + _filterByStrand = filterByStrand; + _requestedStrand = requestedStrand; + _only_3p_end = only_3p_end; + _only_5p_end = only_5p_end; + _add_gb_track_line = add_gb_track_line; + _gb_track_line_opts = gb_track_line_opts; + _currChromName = ""; + _currChromSize = 0 ; + + + if (_bamInput == false) { + _genome = new GenomeFile(genomeFile); + } + + PrintTrackDefinitionLine(); + + if (_bamInput == false) { + _bed = new BedFile(bedFile); + CoverageBed(); + } + else { + CoverageBam(_bedFile); + } +} + +void BedGenomeCoverage::PrintTrackDefinitionLine() +{ + //Print Track Definition line (if requested) + if ( (_bedGraph||_bedGraphAll) && _add_gb_track_line) { + string line = "track type=bedGraph"; + if (!_gb_track_line_opts.empty()) { + line += " " ; + line += _gb_track_line_opts ; + } + cout << line << endl; + } + +} + + +BedGenomeCoverage::~BedGenomeCoverage(void) { + delete _bed; + delete _genome; +} + + +void BedGenomeCoverage::ResetChromCoverage() { + _currChromName = ""; + _currChromSize = 0 ; + std::vector<DEPTH>().swap(_currChromCoverage); +} + + +void BedGenomeCoverage::StartNewChrom(const string& newChrom) { + // If we've moved beyond the first encountered chromosomes, + // process the results of the previous chromosome. + if (_currChromName.length() > 0) { + ReportChromCoverage(_currChromCoverage, _currChromSize, + _currChromName, _currChromDepthHist); + } + + // empty the previous chromosome and reserve new + std::vector<DEPTH>().swap(_currChromCoverage); + + if (_visitedChromosomes.find(newChrom) != _visitedChromosomes.end()) { + cerr << "Input error: Chromosome " << _currChromName + << " found in non-sequential lines. This suggests that the input file is not sorted correctly." << endl; + + } + _visitedChromosomes.insert(newChrom); + + _currChromName = newChrom; + + // get the current chrom size and allocate space + _currChromSize = _genome->getChromSize(_currChromName); + + if (_currChromSize >= 0) + _currChromCoverage.resize(_currChromSize); + else { + cerr << "Input error: Chromosome " << _currChromName << " found in your input file but not in your genome file." << endl; + exit(1); + } +} + + +void BedGenomeCoverage::AddCoverage(int start, int end) { + // process the first line for this chromosome. + // make sure the coordinates fit within the chrom + if (start < _currChromSize) + _currChromCoverage[start].starts++; + if (end < _currChromSize) + _currChromCoverage[end].ends++; + else + _currChromCoverage[_currChromSize-1].ends++; +} + + +void BedGenomeCoverage::AddBlockedCoverage(const vector<BED> &bedBlocks) { + vector<BED>::const_iterator bedItr = bedBlocks.begin(); + vector<BED>::const_iterator bedEnd = bedBlocks.end(); + for (; bedItr != bedEnd; ++bedItr) { + // the end - 1 must be done because BamAncillary::getBamBlocks + // returns ends uncorrected for the genomeCoverageBed data structure. + // ugly, but necessary. + AddCoverage(bedItr->start, bedItr->end - 1); + } +} + + +void BedGenomeCoverage::CoverageBed() { + + BED a, nullBed; + int lineNum = 0; // current input line number + BedLineStatus bedStatus; + + ResetChromCoverage(); + + _bed->Open(); + while ( (bedStatus = _bed->GetNextBed(a, lineNum)) != BED_INVALID ) { + if (bedStatus == BED_VALID) { + if (_filterByStrand == true) { + if (a.strand.empty()) { + cerr << "Input error: Interval is missing a strand value on line " << lineNum << "." <<endl; + exit(1); + } + if ( ! (a.strand == "-" || a.strand == "+") ) { + cerr << "Input error: Invalid strand value (" << a.strand << ") on line " << lineNum << "." << endl; + exit(1); + } + // skip if the strand is not what the user requested. + if (a.strand != _requestedStrand) + continue; + } + + // are we on a new chromosome? + if (a.chrom != _currChromName) + StartNewChrom(a.chrom); + + if (_obeySplits == true) { + bedVector bedBlocks; // vec to store the discrete BED "blocks" + splitBedIntoBlocks(a, lineNum, bedBlocks); + AddBlockedCoverage(bedBlocks); + } + else if (_only_5p_end) { + int pos = ( a.strand=="+" ) ? a.start : a.end-1; + AddCoverage(pos,pos); + } + else if (_only_3p_end) { + int pos = ( a.strand=="-" ) ? a.start : a.end-1; + AddCoverage(pos,pos); + } + else + AddCoverage(a.start, a.end-1); + } + } + _bed->Close(); + PrintFinalCoverage(); +} + + +void BedGenomeCoverage::PrintFinalCoverage() +{ + + + // process the results of the last chromosome. + ReportChromCoverage(_currChromCoverage, _currChromSize, + _currChromName, _currChromDepthHist); + if (_eachBase == false && _bedGraph == false && _bedGraphAll == false) { + ReportGenomeCoverage(_currChromDepthHist); + } +} + + +void BedGenomeCoverage::CoverageBam(string bamFile) { + + ResetChromCoverage(); + + // open the BAM file + BamReader reader; + reader.Open(bamFile); + + // get header & reference information + string header = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // load the BAM header references into a BEDTools "genome file" + _genome = new GenomeFile(refs); + // convert each aligned BAM entry to BED + // and compute coverage on B + BamAlignment bam; + while (reader.GetNextAlignment(bam)) { + // skip if the read is unaligned + if (bam.IsMapped() == false) + continue; + + // skip if we care about strands and the strand isn't what + // the user wanted + if ( (_filterByStrand == true) && + ((_requestedStrand == "-") != bam.IsReverseStrand()) ) + continue; + + // extract the chrom, start and end from the BAM alignment + string chrom(refs.at(bam.RefID).RefName); + CHRPOS start = bam.Position; + CHRPOS end = bam.GetEndPosition(false, false) - 1; + + // are we on a new chromosome? + if ( chrom != _currChromName ) + StartNewChrom(chrom); + + // add coverage accordingly. + if (_obeySplits) { + bedVector bedBlocks; + // since we are counting coverage, we do want to split blocks when a + // deletion (D) CIGAR op is encountered (hence the true for the last parm) + getBamBlocks(bam, refs, bedBlocks, true); + AddBlockedCoverage(bedBlocks); + } + else if (_only_5p_end) { + int pos = ( !bam.IsReverseStrand() ) ? start : end; + AddCoverage(pos,pos); + } + else if (_only_3p_end) { + int pos = ( bam.IsReverseStrand() ) ? start : end; + AddCoverage(pos,pos); + } + else + AddCoverage(start, end); + } + // close the BAM + reader.Close(); + PrintFinalCoverage(); +} + + +void BedGenomeCoverage::ReportChromCoverage(const vector<DEPTH> &chromCov, const int &chromSize, const string &chrom, chromHistMap &chromDepthHist) { + + if (_eachBase) { + int depth = 0; // initialize the depth + int offset = (_eachBaseZeroBased)?0:1; + for (int pos = 0; pos < chromSize; pos++) { + + depth += chromCov[pos].starts; + // report the depth for this position. + if (depth>0 || !_eachBaseZeroBased) + cout << chrom << "\t" << pos+offset << "\t" << depth * _scale << endl; + depth = depth - chromCov[pos].ends; + } + } + else if (_bedGraph == true || _bedGraphAll == true) { + ReportChromCoverageBedGraph(chromCov, chromSize, chrom); + } + else { + + int depth = 0; // initialize the depth + + for (int pos = 0; pos < chromSize; pos++) { + + depth += chromCov[pos].starts; + + // add the depth at this position to the depth histogram + // for this chromosome. if the depth is greater than the + // maximum bin requested, then readjust the depth to be the max + if (depth >= _max) { + chromDepthHist[chrom][_max]++; + } + else { + chromDepthHist[chrom][depth]++; + } + depth = depth - chromCov[pos].ends; + } + // report the histogram for each chromosome + histMap::const_iterator depthIt = chromDepthHist[chrom].begin(); + histMap::const_iterator depthEnd = chromDepthHist[chrom].end(); + for (; depthIt != depthEnd; ++depthIt) { + int depth = depthIt->first; + unsigned int numBasesAtDepth = depthIt->second; + cout << chrom << "\t" << depth << "\t" << numBasesAtDepth << "\t" + << chromSize << "\t" << (float) ((float)numBasesAtDepth / (float)chromSize) << endl; + } + } +} + + + +void BedGenomeCoverage::ReportGenomeCoverage(chromHistMap &chromDepthHist) { + + // get the list of chromosome names in the genome + vector<string> chromList = _genome->getChromList(); + + unsigned int genomeSize = 0; + vector<string>::const_iterator chromItr = chromList.begin(); + vector<string>::const_iterator chromEnd = chromList.end(); + for (; chromItr != chromEnd; ++chromItr) { + string chrom = *chromItr; + genomeSize += _genome->getChromSize(chrom); + // if there were no reads for a give chromosome, then + // add the length of the chrom to the 0 bin. + if ( chromDepthHist.find(chrom) == chromDepthHist.end() ) { + chromDepthHist[chrom][0] += _genome->getChromSize(chrom); + } + } + + histMap genomeHist; // depth histogram for the entire genome + + // loop through each chromosome and add the depth and number of bases at each depth + // to the aggregate histogram for the entire genome + for (chromHistMap::iterator chromIt = chromDepthHist.begin(); chromIt != chromDepthHist.end(); ++chromIt) { + string chrom = chromIt->first; + for (histMap::iterator depthIt = chromDepthHist[chrom].begin(); depthIt != chromDepthHist[chrom].end(); ++depthIt) { + int depth = depthIt->first; + unsigned int numBasesAtDepth = depthIt->second; + genomeHist[depth] += numBasesAtDepth; + } + } + + // loop through the depths for the entire genome + // and report the number and fraction of bases in + // the entire genome that are at said depth. + for (histMap::iterator genomeDepthIt = genomeHist.begin(); genomeDepthIt != genomeHist.end(); ++genomeDepthIt) { + int depth = genomeDepthIt->first; + unsigned int numBasesAtDepth = genomeDepthIt->second; + + cout << "genome" << "\t" << depth << "\t" << numBasesAtDepth << "\t" + << genomeSize << "\t" << (float) ((float)numBasesAtDepth / (float)genomeSize) << endl; + } +} + + +void BedGenomeCoverage::ReportChromCoverageBedGraph(const vector<DEPTH> &chromCov, const int &chromSize, const string &chrom) { + + int depth = 0; // initialize the depth + int lastStart = -1; + int lastDepth = -1; + + for (int pos = 0; pos < chromSize; pos++) { + depth += chromCov[pos].starts; + + if (depth != lastDepth) { + // Coverage depth has changed, print the last interval coverage (if any) + // Print if: + // (1) depth>0 (the default running mode), + // (2) depth==0 and the user requested to print zero covered regions (_bedGraphAll) + if ( (lastDepth != -1) && (lastDepth > 0 || _bedGraphAll) ) { + cout << chrom << "\t" << lastStart << "\t" << pos << "\t" << lastDepth * _scale << endl; + } + //Set current position as the new interval start + depth + lastDepth = depth; + lastStart = pos; + } + // Default: the depth has not changed, so we will not print anything. + // Proceed until the depth changes. + // Update depth + depth = depth - chromCov[pos].ends; + } + //Print information about the last position + if ( (lastDepth != -1) && (lastDepth > 0 || _bedGraphAll) ) { + cout << chrom << "\t" << lastStart << "\t" << chromSize << "\t" << lastDepth * _scale << endl; + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/genomeCoverageBed/genomeCoverageBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,104 @@ +/***************************************************************************** +genomeCoverage.h + +(c) 2009 - Aaron Quinlan +Hall Laboratory +Department of Biochemistry and Molecular Genetics +University of Virginia +aaronquinlan@gmail.com + +Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" +#include "genomeFile.h" + +#include "BamAncillary.h" +#include "api/BamReader.h" +#include "api/BamAux.h" +using namespace BamTools; + +#include <vector> +#include <set> +#include <iostream> +#include <fstream> +using namespace std; + + +//*********************************************** +// Typedefs +//*********************************************** +typedef map<int, DEPTH, less<int> > depthMap; +typedef map<string, depthMap, less<string> > chromDepthMap; + +typedef map<int, unsigned int, less<int> > histMap; +typedef map<string, histMap, less<string> > chromHistMap; + +//************************************************ +// Class methods and elements +//************************************************ +class BedGenomeCoverage { + +public: + + // constructor + BedGenomeCoverage(string bedFile, string genomeFile, + bool eachBase, bool startSites, + bool bedGraph, bool bedGraphAll, + int max, float scale, + bool bamInput, bool obeySplits, + bool filterByStrand, string requestedStrand, + bool only_5p_end, bool only_3p_end, + bool eachBaseZeroBased, + bool add_gb_track_line, string gb_track_line_opts); + + // destructor + ~BedGenomeCoverage(void); + +private: + + // data (parms) + string _bedFile; + string _genomeFile; + bool _bamInput; + bool _eachBase; + bool _eachBaseZeroBased; + bool _startSites; + bool _bedGraph; + bool _bedGraphAll; + int _max; + float _scale; + bool _obeySplits; + bool _filterByStrand; + bool _only_5p_end; + bool _only_3p_end; + bool _add_gb_track_line; + string _gb_track_line_opts; + string _requestedStrand; + + BedFile *_bed; + GenomeFile *_genome; + + // data for internal processing + chromDepthMap _chromCov; + string _currChromName ; + vector<DEPTH> _currChromCoverage; + chromHistMap _currChromDepthHist; + int _currChromSize ; + set<string> _visitedChromosomes; + + + // methods + void CoverageBed(); + void CoverageBam(string bamFile); + void LoadBamHeaderIntoGenomeFile(const string &bamFile); + void ReportChromCoverage(const vector<DEPTH> &, const int &chromSize, const string &chrom, chromHistMap&); + void ReportGenomeCoverage(chromHistMap &chromDepthHist); + void ReportChromCoverageBedGraph(const vector<DEPTH> &chromCov, const int &chromSize, const string &chrom); + void ResetChromCoverage(); + void StartNewChrom (const string& chrom); + void AddCoverage (int start, int end); + void AddBlockedCoverage(const vector<BED> &bedBlocks); + void PrintFinalCoverage(); + void PrintTrackDefinitionLine(); +}; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/genomeCoverageBed/genomeCoverageMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,312 @@ +/***************************************************************************** +genomeCoverageMain.cpp + +(c) 2009 - Aaron Quinlan +Hall Laboratory +Department of Biochemistry and Molecular Genetics +University of Virginia +aaronquinlan@gmail.com + +Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "genomeCoverageBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "genomeCoverageBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile; + string genomeFile; + int max = INT_MAX; + float scale = 1.0; + + bool haveBed = false; + bool bamInput = false; + bool haveGenome = false; + bool startSites = false; + bool bedGraph = false; + bool bedGraphAll = false; + bool eachBase = false; + bool eachBaseZeroBased = false; + bool obeySplits = false; + bool haveScale = false; + bool filterByStrand = false; + bool only_5p_end = false; + bool only_3p_end = false; + bool add_gb_track_line = false; + string gb_track_opts; + string requestedStrand = "X"; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + haveBed = true; + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-ibam", 5, parameterLength)) { + if ((i+1) < argc) { + haveBed = true; + bamInput = true; + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-d", 2, parameterLength)) { + eachBase = true; + } + else if(PARAMETER_CHECK("-dz", 3, parameterLength)) { + eachBase = true; + eachBaseZeroBased = true; + } + else if(PARAMETER_CHECK("-bg", 3, parameterLength)) { + bedGraph = true; + } + else if(PARAMETER_CHECK("-bga", 4, parameterLength)) { + bedGraphAll = true; + } + else if(PARAMETER_CHECK("-max", 4, parameterLength)) { + if ((i+1) < argc) { + max = atoi(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-scale", 6, parameterLength)) { + if ((i+1) < argc) { + haveScale = true; + scale = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-split", 6, parameterLength)) { + obeySplits = true; + } + else if(PARAMETER_CHECK("-strand", 7, parameterLength)) { + if ((i+1) < argc) { + filterByStrand = true; + requestedStrand = argv[i+1][0]; + if (!(requestedStrand == "-" || requestedStrand == "+")) { + cerr << "*****ERROR: invalid -strand value (" << requestedStrand << "). Allowed options are + or -" << endl; + showHelp = true; + } + i++; + } + else { + cerr << "*****ERROR: -strand options requires a value: + or -" << endl; + showHelp = true; + } + } + else if(PARAMETER_CHECK("-3", 2, parameterLength)) { + only_3p_end = true; + } + else if(PARAMETER_CHECK("-5", 2, parameterLength)) { + only_5p_end = true; + } + else if(PARAMETER_CHECK("-trackline", 10, parameterLength)) { + add_gb_track_line = true; + } + else if(PARAMETER_CHECK("-trackopts", 10, parameterLength)) { + if ((i+1) < argc) { + add_gb_track_line = true; + gb_track_opts = argv[i+1]; + i++; + } else { + cerr << "*****ERROR: -trackopts options requires a value (UCSC/GB track definition parameters)" << endl; + showHelp = true; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed && !haveGenome && !bamInput) { + cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl; + showHelp = true; + } + if (bedGraph && eachBase) { + cerr << endl << "*****" << endl << "*****ERROR: Use -d/-dz or -bg, not both" << endl << "*****" << endl; + showHelp = true; + } + if (bedGraphAll && eachBase) { + cerr << endl << "*****" << endl << "*****ERROR: Use -d/-dz or -bga, not both" << endl << "*****" << endl; + showHelp = true; + } + + if (only_3p_end && only_5p_end) { + cerr << endl << "*****" << endl << "*****ERROR: Use -3 or -5, not both " << endl << "*****" << endl; + showHelp = true; + } + + if ( (only_3p_end||only_5p_end) && obeySplits) { + cerr << endl << "*****" << endl << "*****ERROR: Use -split can't be used with -3 or -5." << endl << "*****" << endl; + showHelp = true; + } + + if (add_gb_track_line && !(bedGraph||bedGraphAll)) { + cerr << endl << "*****" << endl << "*****ERROR: Using -trackline requires bedGraph output (use -bg or -bga)." << endl << "*****" << endl; + showHelp = true; + } + + if (haveScale && !(bedGraph||bedGraphAll||eachBase)) { + cerr << endl << "*****" << endl << "*****ERROR: Using -scale requires bedGraph output (use -bg or -bga) or per base depth (-d)." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedGenomeCoverage *bc = new BedGenomeCoverage(bedFile, genomeFile, eachBase, + startSites, bedGraph, bedGraphAll, + max, scale, bamInput, obeySplits, + filterByStrand, requestedStrand, + only_5p_end, only_3p_end, + eachBaseZeroBased, + add_gb_track_line, gb_track_opts); + delete bc; + + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Authors: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + cerr << " Assaf Gordon, CSHL" << endl << endl; + + cerr << "Summary: Compute the coverage of a feature file among a genome." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-ibam\t\t" << "The input file is in BAM format." << endl; + cerr << "\t\t\tNote: BAM _must_ be sorted by position" << endl << endl; + + cerr << "\t-d\t\t" << "Report the depth at each genome position (with one-based coordinates)." << endl; + cerr << "\t\t\tDefault behavior is to report a histogram." << endl << endl; + + cerr << "\t-dz\t\t" << "Report the depth at each genome position (with zero-based coordinates)." << endl; + cerr << "\t\t\tReports only non-zero positions." << endl; + cerr << "\t\t\tDefault behavior is to report a histogram." << endl << endl; + + cerr << "\t-bg\t\t" << "Report depth in BedGraph format. For details, see:" << endl; + cerr << "\t\t\tgenome.ucsc.edu/goldenPath/help/bedgraph.html" << endl << endl; + + cerr << "\t-bga\t\t" << "Report depth in BedGraph format, as above (-bg)." << endl; + cerr << "\t\t\tHowever with this option, regions with zero " << endl; + cerr << "\t\t\tcoverage are also reported. This allows one to" << endl; + cerr << "\t\t\tquickly extract all regions of a genome with 0 " << endl; + cerr << "\t\t\tcoverage by applying: \"grep -w 0$\" to the output." << endl << endl; + + cerr << "\t-split\t\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl; + cerr << "\t\t\twhen computing coverage." << endl; + cerr << "\t\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations " << endl; + cerr << "\t\t\tto infer the blocks for computing coverage." << endl; + cerr << "\t\t\tFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds" << endl; + cerr << "\t\t\tfields (i.e., columns 10,11,12)." << endl << endl; + + cerr << "\t-strand\t\t" << "Calculate coverage of intervals from a specific strand." << endl; + cerr << "\t\t\tWith BED files, requires at least 6 columns (strand is column 6). " << endl; + cerr << "\t\t\t- (STRING): can be + or -" << endl << endl; + + cerr << "\t-5\t\t" << "Calculate coverage of 5\" positions (instead of entire interval)." << endl << endl; + + cerr << "\t-3\t\t" << "Calculate coverage of 3\" positions (instead of entire interval)." << endl << endl; + + cerr << "\t-max\t\t" << "Combine all positions with a depth >= max into" << endl; + cerr << "\t\t\ta single bin in the histogram. Irrelevant" << endl; + cerr << "\t\t\tfor -d and -bedGraph" << endl; + cerr << "\t\t\t- (INTEGER)" << endl << endl; + + cerr << "\t-scale\t\t" << "Scale the coverage by a constant factor." << endl; + cerr << "\t\t\tEach coverage value is multiplied by this factor before being reported." << endl; + cerr << "\t\t\tUseful for normalizing coverage by, e.g., reads per million (RPM)." << endl; + cerr << "\t\t\t- Default is 1.0; i.e., unscaled." << endl; + cerr << "\t\t\t- (FLOAT)" << endl << endl; + + cerr << "\t-trackline\t" << "Adds a UCSC/Genome-Browser track line definition in the first line of the output." << endl; + cerr <<"\t\t\t- See here for more details about track line definition:" << endl; + cerr <<"\t\t\t http://genome.ucsc.edu/goldenPath/help/bedgraph.html" << endl; + cerr <<"\t\t\t- NOTE: When adding a trackline definition, the output BedGraph can be easily" << endl; + cerr <<"\t\t\t uploaded to the Genome Browser as a custom track," << endl; + cerr <<"\t\t\t BUT CAN NOT be converted into a BigWig file (w/o removing the first line)." << endl << endl; + + cerr << "\t-trackopts\t"<<"Writes additional track line definition parameters in the first line." << endl; + cerr <<"\t\t\t- Example:" << endl; + cerr <<"\t\t\t -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'" << endl; + cerr <<"\t\t\t Note the use of single-quotes if you have spaces in your parameters." << endl; + cerr <<"\t\t\t- (TEXT)" << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl; + cerr << "\t <chromName><TAB><chromSize>" << endl << endl; + cerr << "\tFor example, Human (hg19):" << endl; + cerr << "\tchr1\t249250621" << endl; + cerr << "\tchr2\t243199373" << endl; + cerr << "\t..." << endl; + cerr << "\tchr18_gl000207_random\t4262" << endl << endl; + + cerr << "\t(2) The input BED (-i) file must be grouped by chromosome." << endl; + cerr << "\t A simple \"sort -k 1,1 <BED> > <BED>.sorted\" will suffice."<< endl << endl; + + cerr << "\t(3) The input BAM (-ibam) file must be sorted by position." << endl; + cerr << "\t A \"samtools sort <BAM>\" should suffice."<< endl << endl; + + cerr << "Tips: " << endl; + cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl; + cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl; + cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl; + cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl; + + + // end the program here + exit(1); +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/intersectBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,53 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary \ + -I$(UTILITIES_DIR)/chromsweep \ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= intersectMain.cpp intersectBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamAncillary.o gzstream.o fileType.o chromsweep.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= intersectBed + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/chromsweep/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/intersectBed/intersectBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,367 @@ +/***************************************************************************** + intersectBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "intersectBed.h" + +/************************************ +Helper functions +************************************/ +bool BedIntersect::processHits(const BED &a, const vector<BED> &hits) { + + // how many overlaps are there b/w the bed and the set of hits? + CHRPOS s, e; + int overlapBases; + int numOverlaps = 0; + bool hitsFound = false; + int aLength = (a.end - a.start); // the length of a in b.p. + + // loop through the hits and report those that meet the user's criteria + vector<BED>::const_iterator h = hits.begin(); + vector<BED>::const_iterator hitsEnd = hits.end(); + for (; h != hitsEnd; ++h) { + s = max(a.start, h->start); + e = min(a.end, h->end); + overlapBases = (e - s); // the number of overlapping bases b/w a and b + + // is there enough overlap relative to the user's request? (default ~ 1bp) + if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) { + // Report the hit if the user doesn't care about reciprocal overlap between A and B. + if (_reciprocal == false) { + hitsFound = true; + numOverlaps++; + if (_printable == true) + ReportOverlapDetail(overlapBases, a, *h, s, e); + } + // we require there to be sufficient __reciprocal__ overlap + else { + int bLength = (h->end - h->start); + float bOverlap = ( (float) overlapBases / (float) bLength ); + if (bOverlap >= _overlapFraction) { + hitsFound = true; + numOverlaps++; + if (_printable == true) + ReportOverlapDetail(overlapBases, a, *h, s, e); + } + } + } + } + // report the summary of the overlaps if requested. + ReportOverlapSummary(a, numOverlaps); + // were hits found for this BED feature? + return hitsFound; +} + + +/* + Constructor +*/ +BedIntersect::BedIntersect(string bedAFile, string bedBFile, bool anyHit, + bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap, + float overlapFraction, bool noHit, bool writeCount, bool sameStrand, bool diffStrand, + bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam, + bool sortedInput) { + + _bedAFile = bedAFile; + _bedBFile = bedBFile; + _anyHit = anyHit; + _noHit = noHit; + _writeA = writeA; + _writeB = writeB; + _writeOverlap = writeOverlap; + _writeAllOverlap = writeAllOverlap; + _writeCount = writeCount; + _overlapFraction = overlapFraction; + _sameStrand = sameStrand; + _diffStrand = diffStrand; + _reciprocal = reciprocal; + _obeySplits = obeySplits; + _bamInput = bamInput; + _bamOutput = bamOutput; + _isUncompressedBam = isUncompressedBam; + _sortedInput = sortedInput; + + // should we print each overlap, or does the user want summary information? + _printable = true; + if (_anyHit || _noHit || _writeCount) + _printable = false; + + if (_bamInput == false) + IntersectBed(); + else + IntersectBam(bedAFile); +} + + +/* + Destructor +*/ +BedIntersect::~BedIntersect(void) { +} + + +bool BedIntersect::FindOverlaps(const BED &a, vector<BED> &hits) { + bool hitsFound = false; + + // collect and report the sufficient hits + _bedB->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, _sameStrand, _diffStrand); + hitsFound = processHits(a, hits); + return hitsFound; +} + + +void BedIntersect::ReportOverlapDetail(int overlapBases, const BED &a, const BED &b, CHRPOS s, CHRPOS e) { + // default. simple intersection only + if (_writeA == false && _writeB == false && _writeOverlap == false) { + _bedA->reportBedRangeNewLine(a,s,e); + } + // -wa -wb write the original A and B + else if (_writeA == true && _writeB == true) { + _bedA->reportBedTab(a); + _bedB->reportBedNewLine(b); + } + // -wa write just the original A + else if (_writeA == true) { + _bedA->reportBedNewLine(a); + } + // -wb write the intersected portion of A and the original B + else if (_writeB == true) { + _bedA->reportBedRangeTab(a,s,e); + _bedB->reportBedNewLine(b); + } + // -wo write the original A and B plus the no. of overlapping bases. + else if (_writeOverlap == true) { + _bedA->reportBedTab(a); + _bedB->reportBedTab(b); + if (b.zeroLength == false) printf("%d\n", overlapBases); + else printf("0\n"); + } +} + + +void BedIntersect::ReportOverlapSummary(const BED &a, const int &numOverlapsFound) { + // -u just report the fact that there was >= 1 overlaps + if (_anyHit && (numOverlapsFound >= 1)) { + _bedA->reportBedNewLine(a); + } + // -c report the total number of features overlapped in B + else if (_writeCount) { + _bedA->reportBedTab(a); + printf("%d\n", numOverlapsFound); + } + // -v report iff there were no overlaps + else if (_noHit && (numOverlapsFound == 0)) { + _bedA->reportBedNewLine(a); + } + // -wao the user wants to force the reporting of 0 overlap + else if (_writeAllOverlap && (numOverlapsFound == 0)) { + _bedA->reportBedTab(a); + _bedB->reportNullBedTab(); + printf("0\n"); + } +} + + +bool BedIntersect::FindOneOrMoreOverlap(const BED &a) { + bool overlapsFound = false; + if (_reciprocal == false) { + overlapsFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, + _sameStrand, _diffStrand, _overlapFraction); + } + else { + overlapsFound = _bedB->FindOneOrMoreReciprocalOverlapsPerBin(a.chrom, a.start, a.end, a.strand, + _sameStrand, _diffStrand, _overlapFraction); + } + return overlapsFound; +} + + +void BedIntersect::IntersectBed() { + + // create new BED file objects for A and B + _bedA = new BedFile(_bedAFile); + _bedB = new BedFile(_bedBFile); + + if (_sortedInput == false) { + // load the "B" file into a map in order to + // compare each entry in A to it in search of overlaps. + _bedB->loadBedFileIntoMap(); + + int lineNum = 0; + vector<BED> hits; + hits.reserve(100); + BED a, nullBed; + BedLineStatus bedStatus; + + // open the "A" file, process each BED entry and searh for overlaps. + _bedA->Open(); + while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + // treat the BED as a single "block" + if (_obeySplits == false) { + FindOverlaps(a, hits); + hits.clear(); + } + // split the BED12 into blocks and look for overlaps in each discrete block + else { + bedVector bedBlocks; // vec to store the discrete BED "blocks" + splitBedIntoBlocks(a, lineNum, bedBlocks); + + vector<BED>::const_iterator bedItr = bedBlocks.begin(); + vector<BED>::const_iterator bedEnd = bedBlocks.end(); + for (; bedItr != bedEnd; ++bedItr) { + FindOverlaps(*bedItr, hits); + hits.clear(); + } + } + } + a = nullBed; + } + _bedA->Close(); + } + else { + // use the chromsweep algorithm to detect overlaps on the fly. + ChromSweep sweep = ChromSweep(_bedA, _bedB, _sameStrand, _diffStrand); + + pair<BED, vector<BED> > hit_set; + hit_set.second.reserve(10000); + while (sweep.Next(hit_set)) { + processHits(hit_set.first, hit_set.second); + } + } +} + + +void BedIntersect::IntersectBam(string bamFile) { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB = new BedFile(_bedBFile); + _bedB->loadBedFileIntoMap(); + + // create a dummy BED A file for printing purposes if not + // using BAM output. + if (_bamOutput == false) { + _bedA = new BedFile(_bedAFile); + _bedA->bedType = 6; + } + + // open the BAM file + BamReader reader; + BamWriter writer; + + reader.Open(bamFile); + + // get header & reference information + string bamHeader = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // open a BAM output to stdout if we are writing BAM + if (_bamOutput == true) { + // set compression mode + BamWriter::CompressionMode compressionMode = BamWriter::Compressed; + if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed; + writer.SetCompressionMode(compressionMode); + // open our BAM writer + writer.Open("stdout", bamHeader, refs); + } + + vector<BED> hits; + // reserve some space + hits.reserve(100); + + + BamAlignment bam; + // get each set of alignments for each pair. + while (reader.GetNextAlignment(bam)) { + + if (bam.IsMapped()) { + BED a; + a.chrom = refs.at(bam.RefID).RefName; + a.start = bam.Position; + a.end = bam.GetEndPosition(false, false); + + // build the name field from the BAM alignment. + a.name = bam.Name; + if (bam.IsFirstMate()) a.name += "/1"; + if (bam.IsSecondMate()) a.name += "/2"; + + a.score = ToString(bam.MapQuality); + + a.strand = "+"; + if (bam.IsReverseStrand()) a.strand = "-"; + + if (_bamOutput == true) { + bool overlapsFound = false; + // treat the BAM alignment as a single "block" + if (_obeySplits == false) { + overlapsFound = FindOneOrMoreOverlap(a); + } + // split the BAM alignment into discrete blocks and + // look for overlaps only within each block. + else { + bool overlapFoundForBlock; + bedVector bedBlocks; // vec to store the discrete BED "blocks" from a + // we don't want to split on "D" ops, hence the "false" + getBamBlocks(bam, refs, bedBlocks, false); + + vector<BED>::const_iterator bedItr = bedBlocks.begin(); + vector<BED>::const_iterator bedEnd = bedBlocks.end(); + for (; bedItr != bedEnd; ++bedItr) { + overlapFoundForBlock = FindOneOrMoreOverlap(*bedItr); + if (overlapFoundForBlock == true) + overlapsFound = true; + } + } + if (overlapsFound == true) { + if (_noHit == false) + writer.SaveAlignment(bam); + } + else { + if (_noHit == true) { + writer.SaveAlignment(bam); + } + } + } + else { + // treat the BAM alignment as a single BED "block" + if (_obeySplits == false) { + FindOverlaps(a, hits); + hits.clear(); + } + // split the BAM alignment into discrete BED blocks and + // look for overlaps only within each block. + else { + bedVector bedBlocks; // vec to store the discrete BED "blocks" from a + getBamBlocks(bam, refs, bedBlocks, false); + + vector<BED>::const_iterator bedItr = bedBlocks.begin(); + vector<BED>::const_iterator bedEnd = bedBlocks.end(); + for (; bedItr != bedEnd; ++bedItr) { + FindOverlaps(*bedItr, hits); + hits.clear(); + } + } + } + } + // BAM IsMapped() is false + else if (_noHit == true) { + writer.SaveAlignment(bam); + } + } + + // close the relevant BAM files. + reader.Close(); + if (_bamOutput == true) { + writer.Close(); + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/intersectBed/intersectBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,98 @@ +/***************************************************************************** + intersectBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef INTERSECTBED_H +#define INTERSECTBED_H + +#include "bedFile.h" +#include "chromsweep.h" +#include "api/BamReader.h" +#include "api/BamWriter.h" +#include "api/BamAux.h" +#include "BamAncillary.h" +using namespace BamTools; + + +#include <vector> +#include <iostream> +#include <fstream> +#include <stdlib.h> +using namespace std; + + + +class BedIntersect { + +public: + + // constructor + BedIntersect(string bedAFile, string bedBFile, bool anyHit, + bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap, + float overlapFraction, bool noHit, bool writeCount, bool sameStrand, bool diffStrand, + bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam, + bool sortedInput); + + // destructor + ~BedIntersect(void); + +private: + + //------------------------------------------------ + // private attributes + //------------------------------------------------ + string _bedAFile; + string _bedBFile; + + bool _writeA; // should the original A feature be reported? + bool _writeB; // should the original B feature be reported? + bool _writeOverlap; + bool _writeAllOverlap; + + bool _sameStrand; + bool _diffStrand; + bool _reciprocal; + float _overlapFraction; + + bool _anyHit; + bool _noHit; + bool _writeCount; // do we want a count of the number of overlaps in B? + bool _obeySplits; + bool _bamInput; + bool _bamOutput; + bool _isUncompressedBam; + bool _sortedInput; + bool _printable; + + // instance of a bed file class. + BedFile *_bedA, *_bedB; + + //------------------------------------------------ + // private methods + //------------------------------------------------ + void IntersectBed(istream &bedInput); + + void IntersectBed(); + + void IntersectBam(string bamFile); + + bool processHits(const BED &a, const vector<BED> &hits); + + bool FindOverlaps(const BED &a, vector<BED> &hits); + + bool FindOneOrMoreOverlap(const BED &a); + + void ReportOverlapDetail(int overlapBases, const BED &a, const BED &b, CHRPOS s, CHRPOS e); + + void ReportOverlapSummary(const BED &a, const int &numOverlapsFound); + +}; + +#endif /* INTERSECTBED_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/intersectBed/intersectMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,294 @@ +/***************************************************************************** + intersectMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "intersectBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "intersectBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + + // input arguments + float overlapFraction = 1E-9; + + bool haveBedA = false; + bool haveBedB = false; + bool noHit = false; + bool anyHit = false; + bool writeA = false; + bool writeB = false; + bool writeCount = false; + bool writeOverlap = false; + bool writeAllOverlap = false; + bool haveFraction = false; + bool reciprocalFraction = false; + bool sameStrand = false; + bool diffStrand = false; + bool obeySplits = false; + bool inputIsBam = false; + bool outputIsBam = true; + bool uncompressedBam = false; + bool sortedInput = false; + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + outputIsBam = false; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-abam", 5, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + inputIsBam = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bed", 4, parameterLength)) { + outputIsBam = false; + } + else if(PARAMETER_CHECK("-u", 2, parameterLength)) { + anyHit = true; + } + else if(PARAMETER_CHECK("-f", 2, parameterLength)) { + if ((i+1) < argc) { + haveFraction = true; + overlapFraction = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-wa", 3, parameterLength)) { + writeA = true; + } + else if(PARAMETER_CHECK("-wb", 3, parameterLength)) { + writeB = true; + } + else if(PARAMETER_CHECK("-wo", 3, parameterLength)) { + writeOverlap = true; + } + else if(PARAMETER_CHECK("-wao", 4, parameterLength)) { + writeAllOverlap = true; + writeOverlap = true; + } + else if(PARAMETER_CHECK("-c", 2, parameterLength)) { + writeCount = true; + } + else if(PARAMETER_CHECK("-r", 2, parameterLength)) { + reciprocalFraction = true; + } + else if (PARAMETER_CHECK("-v", 2, parameterLength)) { + noHit = true; + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + sameStrand = true; + } + else if (PARAMETER_CHECK("-S", 2, parameterLength)) { + diffStrand = true; + } + else if (PARAMETER_CHECK("-split", 6, parameterLength)) { + obeySplits = true; + } + else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) { + uncompressedBam = true; + } + else if(PARAMETER_CHECK("-sorted", 7, parameterLength)) { + sortedInput = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && noHit) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeB && writeCount) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeCount && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeA && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wa OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (writeB && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (reciprocalFraction && !haveFraction) { + cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && writeCount) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && writeB) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wb, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && writeOverlap) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wo, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (sameStrand && diffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + + BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, writeOverlap, + writeAllOverlap, overlapFraction, noHit, writeCount, sameStrand, diffStrand, + reciprocalFraction, obeySplits, inputIsBam, outputIsBam, uncompressedBam, sortedInput); + delete bi; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Report overlaps between two feature files." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl; + + cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl; + + cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl; + cerr << "\t\tis to write output in BAM when using -abam." << endl << endl; + + cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl; + + cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl; + cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl; + + cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl; + cerr << "\t\tpairs of overlap between the two features." << endl; + cerr << "\t\t- Overlaps restricted by -f and -r." << endl; + cerr << "\t\t Only A features with overlap are reported." << endl << endl; + + cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl; + cerr << "\t\tpairs of overlap between the two features." << endl; + cerr << "\t\t- Overlapping features restricted by -f and -r." << endl; + cerr << "\t\t However, A features w/o overlap are also reported" << endl; + cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl; + + cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl; + cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl; + cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl; + + cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl; + cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl; + cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl; + + cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl; + cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl; + + cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl; + cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl; + cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl; + + cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl; + cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl; + cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl; + + cerr << "\t-s\t" << "Require same strandedness. That is, only report hits in B that" << endl; + cerr << "\t\toverlap A on the _same_ strand." << endl; + cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + + cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in B that" << endl; + cerr << "\t\toverlap A on the _opposite_ strand." << endl; + cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + + cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl; + + cerr << "\t-sorted\t" << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input" << endl; + cerr << "\t\tNOTE: this will trust, but not enforce that data is sorted. Caveat emptor." << endl << endl; + + // end the program here + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/linksBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,43 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= linksMain.cpp linksBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= linksBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/linksBed/linksBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,122 @@ +/***************************************************************************** + linksBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "linksBed.h" + +// +// Constructor +// +BedLinks::BedLinks(string &bedFile, string &base, string &org, string &db) { + _bedFile = bedFile; + _bed = new BedFile(bedFile); + + _base = base; + _org = org; + _db = db; + + CreateLinks(); +} + +// +// Destructor +// +BedLinks::~BedLinks(void) { +} + + +void BedLinks::WriteURL(BED &bed, string &base) { + + string position = bed.chrom; + std::stringstream posStream; + posStream << ":" << bed.start << "-" << bed.end; + position.append(posStream.str()); + + cout << "<tr>" << endl; + cout << "\t<td>" << endl; + cout << "\t\t<a href=" << base << position << ">"; + cout << bed.chrom << ":" << bed.start << "-" << bed.end; + cout << "</a>" << endl; + cout << "\t</td>" << endl; + + if (_bed->bedType == 4) { + cout << "\t<td>" << endl; + cout << bed.name << endl; + cout << "\t</td>" << endl; + } + else if (_bed->bedType == 5) { + cout << "\t<td>" << endl; + cout << bed.name << endl; + cout << "\t</td>" << endl; + + cout << "\t<td>" << endl; + cout << bed.score << endl; + cout << "\t</td>" << endl; + } + else if ((_bed->bedType == 6) || (_bed->bedType == 9) || (_bed->bedType == 12)) { + cout << "\t<td>" << endl; + cout << bed.name << endl; + cout << "\t</td>" << endl; + + cout << "\t<td>" << endl; + cout << bed.score << endl; + cout << "\t</td>" << endl; + + cout << "\t<td>" << endl; + cout << bed.strand << endl; + cout << "\t</td>" << endl; + } + cout << "</tr>" << endl; +} + + +void BedLinks::CreateLinks() { + + + // construct the html base. + string org = _org; + string db = _db; + string base = _base; + base.append("/cgi-bin/hgTracks?org="); + base.append(org); + base.append("&db="); + base.append(db); + base.append("&position="); + + // create the HTML header + cout << "<html>" << endl <<"\t<body>" << endl; + cout << "<title>" << _bedFile << "</title>" << endl; + + // start the table of entries + cout << "<br>Firefox users: Press and hold the \"apple\" or \"alt\" key and click link to open in new tab." << endl; + cout << "<p style=\"font-family:courier\">" << endl; + cout << "<table border=\"0\" align=\"justify\"" << endl; + cout << "<h3>BED Entries from: stdin </h3>" << endl; + + int lineNum = 0; + BED bedEntry, nullBed; + BedLineStatus bedStatus; + + _bed->Open(); + while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + WriteURL(bedEntry, base); + bedEntry = nullBed; + } + } + _bed->Close(); + + cout << "</table>" << endl; + cout << "</p>" << endl; + cout << "\t</body>" << endl <<"</html>" << endl; +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/linksBed/linksBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,44 @@ +/***************************************************************************** + linksBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" +#include <vector> +#include <algorithm> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class BedLinks { + +public: + + // constructor + BedLinks(string &bedFile, string &base, string &org, string &db); + + // destructor + ~BedLinks(void); + +private: + string _bedFile; + string _base; + string _org; + string _db; + + // instance of a bed file class. + BedFile *_bed; + + void WriteURL(BED &bed, string &base); + void CreateLinks(); // the default. sorts by chrom (asc.) then by start (asc.) +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/linksBed/linksMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,129 @@ +/***************************************************************************** + linksBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "linksBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "linksBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + bool haveBed = true; + + /* Defaults for everyone else */ + string org = "human"; + string db = "hg18"; + string base = "http://genome.ucsc.edu"; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-base", 5, parameterLength)) { + if ((i+1) < argc) { + base = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-org", 4, parameterLength)) { + if ((i+1) < argc) { + org = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-db", 3, parameterLength)) { + if ((i+1) < argc) { + db = argv[i + 1]; + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedLinks *bl = new BedLinks(bedFile, base, org, db); + delete bl; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Creates HTML links to an UCSC Genome Browser from a feature file." << endl << endl; + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> > out.html" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-base\t" << "The browser basename. Default: http://genome.ucsc.edu " << endl; + cerr << "\t-org\t" << "The organism. Default: human" << endl; + cerr << "\t-db\t" << "The build. Default: hg18" << endl << endl; + + cerr << "Example: " << endl; + cerr << "\t" << "By default, the links created will point to human (hg18) UCSC browser." << endl; + cerr << "\tIf you have a local mirror, you can override this behavior by supplying" << endl; + cerr << "\tthe -base, -org, and -db options." << endl << endl; + cerr << "\t" << "For example, if the URL of your local mirror for mouse MM9 is called: " << endl; + cerr << "\thttp://mymirror.myuniversity.edu, then you would use the following:" << endl; + cerr << "\t" << "-base http://mymirror.myuniversity.edu" << endl; + cerr << "\t" << "-org mouse" << endl; + cerr << "\t" << "-db mm9" << endl; + + + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/maskFastaFromBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,43 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= maskFastaFromBedMain.cpp maskFastaFromBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= maskFastaFromBed + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,155 @@ +/***************************************************************************** + maskFastaFromBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "maskFastaFromBed.h" + + +MaskFastaFromBed::MaskFastaFromBed(const string &fastaInFile, const string &bedFile, + const string &fastaOutFile, bool softMask, char maskChar) { + _softMask = softMask; + _fastaInFile = fastaInFile; + _bedFile = bedFile; + _fastaOutFile = fastaOutFile; + _maskChar = maskChar; + _bed = new BedFile(_bedFile); + + _bed->loadBedFileIntoMapNoBin(); + // start masking. + MaskFasta(); +} + + +MaskFastaFromBed::~MaskFastaFromBed(void) { +} + + +//****************************************************************************** +// Mask the Fasta file based on the coordinates in the BED file. +//****************************************************************************** +void MaskFastaFromBed::MaskFasta() { + + /* Make sure that we can open all of the files successfully*/ + + // open the fasta database for reading + ifstream fa(_fastaInFile.c_str(), ios::in); + if ( !fa ) { + cerr << "Error: The requested fasta file (" << _fastaInFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + + // open the fasta database for reading + ofstream faOut(_fastaOutFile.c_str(), ios::out); + if ( !faOut ) { + cerr << "Error: The requested fasta output file (" << _fastaOutFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + + + /* Read the fastaDb chromosome by chromosome*/ + string fastaInLine; + string currChrom; + string currDNA = ""; + currDNA.reserve(500000000); + int fastaWidth = -1; + bool widthSet = false; + int start, end, length; + string replacement; + + while (getline(fa,fastaInLine)) { + + if (fastaInLine.find(">",0) != 0 ) { + if (widthSet == false) { + fastaWidth = fastaInLine.size(); + widthSet = true; + } + currDNA += fastaInLine; + } + else { + if (currDNA.size() > 0) { + + vector<BED> bedList = _bed->bedMapNoBin[currChrom]; + + /* + loop through each BED entry for this chrom and + mask the requested sequence in the FASTA file. + */ + for (unsigned int i = 0; i < bedList.size(); i++) { + start = bedList[i].start; + end = bedList[i].end; + length = end - start; + + /* + (1) if soft masking, extract the sequence, lowercase it, + then put it back + (2) otherwise replace with Ns + */ + if (_softMask) { + replacement = currDNA.substr(start, length); + toLowerCase(replacement); + currDNA.replace(start, length, replacement); + } + else { + string hardmask(length, _maskChar); + currDNA.replace(start, length, hardmask); + } + } + // write the masked chrom to the output file + PrettyPrintChrom(faOut, currChrom, currDNA, fastaWidth); + } + + // reset for the next chromosome. + currChrom = fastaInLine.substr(1, fastaInLine.find_first_of(" ")-1); + currDNA = ""; + } + } + + // process the last chromosome. + // exact same logic as in the main loop. + if (currDNA.size() > 0) { + + vector<BED> bedList = _bed->bedMapNoBin[currChrom]; + + for (unsigned int i = 0; i < bedList.size(); i++) { + start = bedList[i].start; + end = bedList[i].end; + length = end - start; + + if (_softMask) { + replacement = currDNA.substr(start, length); + toLowerCase(replacement); + currDNA.replace(start, length, replacement); + } + else { + string hardmask(length, _maskChar); + currDNA.replace(start, length, hardmask); + } + } + PrettyPrintChrom(faOut, currChrom, currDNA, fastaWidth); + } + + // closed for business. + fa.close(); + faOut.close(); +} + + +void MaskFastaFromBed::PrettyPrintChrom(ofstream &out, string chrom, const string &sequence, int width) { + + int seqLength = sequence.size(); + + out << ">" << chrom << endl; + for(int i = 0; i < seqLength; i += width) { + if (i + width < seqLength) out << sequence.substr(i, width) << endl; + else out << sequence.substr(i, seqLength-i) << endl; + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,56 @@ +/***************************************************************************** + maskFastaFromBed.h + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef MASKFASTAFROMBED_H +#define MASKFASTAFROMBED_H + +#include "bedFile.h" +#include "sequenceUtils.h" +#include <vector> +#include <iostream> +#include <fstream> +#include <cctype> /* for tolower */ + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class MaskFastaFromBed { + +public: + + // constructor + MaskFastaFromBed(const string &fastaInFile, const string &bedFile, + const string &fastaOutFile, bool softMask, char maskChar); + + // destructor + ~MaskFastaFromBed(void); + + +private: + + bool _softMask; + + string _fastaInFile; + string _bedFile; + string _fastaOutFile; + char _maskChar; // typically "N", but user's can choose something else, e.g., "X" + + // instance of a bed file class. + BedFile *_bed; + + void MaskFasta(); + + void PrettyPrintChrom(ofstream &out, string chrom, const string &sequence, int width); + +}; + +#endif /* MASKFASTAFROMBED */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,146 @@ +/***************************************************************************** + maskFastaFromBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "maskFastaFromBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "maskFastaFromBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string fastaInFile; + string bedFile; + + // output files + string fastaOutFile; + + // defaults for parameters + bool haveFastaIn = false; + bool haveBed = false; + bool haveFastaOut = false; + bool softMask = false; + char maskChar = 'N'; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-fi", 3, parameterLength)) { + if ((i+1) < argc) { + haveFastaIn = true; + fastaInFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-fo", 3, parameterLength)) { + if ((i+1) < argc) { + haveFastaOut = true; + fastaOutFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bed", 4, parameterLength)) { + if ((i+1) < argc) { + haveBed = true; + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-soft", 5, parameterLength)) { + softMask = true; + } + else if(PARAMETER_CHECK("-mc", 3, parameterLength)) { + if ((i+1) < argc) { + string mask = argv[i + 1]; + if (mask.size() > 1) { + cerr << "*****ERROR: The mask character (-mc) should be a single character.*****" << endl << endl; + showHelp = true; + } + else { + maskChar = mask[0]; + } + i++; + } + } + else { + cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + if (!haveFastaIn || !haveFastaOut || !haveBed) { + showHelp = true; + } + + if (!showHelp) { + + MaskFastaFromBed *maskFasta = new MaskFastaFromBed(fastaInFile, bedFile, fastaOutFile, softMask, maskChar); + delete maskFasta; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Mask a fasta file based on feature coordinates." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -out <fasta> -bed <bed/gff/vcf>" << endl << endl; + + cerr << "Options:" << endl; + cerr << "\t-fi\tInput FASTA file" << endl; + cerr << "\t-bed\tBED/GFF/VCF file of ranges to mask in -fi" << endl; + cerr << "\t-fo\tOutput FASTA file" << endl; + cerr << "\t-soft\tEnforce \"soft\" masking. That is, instead of masking with Ns," << endl; + cerr << "\t\tmask with lower-case bases." << endl; + cerr << "\t-mc\tReplace masking character. That is, instead of masking with Ns, use another character." << endl; + + // end the program here + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/mergeBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,44 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= mergeMain.cpp mergeBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= mergeBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/mergeBed/mergeBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,364 @@ +/***************************************************************************** + mergeBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "mergeBed.h" + + + +void BedMerge::ReportMergedNames(const vector<string> &names) { + if (names.size() > 0) { + printf("\t"); + vector<string>::const_iterator nameItr = names.begin(); + vector<string>::const_iterator nameEnd = names.end(); + for (; nameItr != nameEnd; ++nameItr) { + if (nameItr < (nameEnd - 1)) + cout << *nameItr << ";"; + else + cout << *nameItr; + } + } + else { + cerr << endl + << "*****" << endl + << "*****ERROR: No names found to report for the -names option. Exiting." << endl + << "*****" << endl; + exit(1); + } +} + + +void BedMerge::ReportMergedScores(const vector<string> &scores) { + if (scores.size() > 0) { + printf("\t"); + + // convert the scores to floats + vector<float> data; + for (size_t i = 0 ; i < scores.size() ; i++) { + data.push_back(atof(scores[i].c_str())); + } + + if (_scoreOp == "sum") { + printf("%.3f", accumulate(data.begin(), data.end(), 0.0)); + } + else if (_scoreOp == "min") { + printf("%.3f", *min_element( data.begin(), data.end() )); + } + else if (_scoreOp == "max") { + printf("%.3f", *max_element( data.begin(), data.end() )); + } + else if (_scoreOp == "mean") { + double total = accumulate(data.begin(), data.end(), 0.0); + double mean = total / data.size(); + printf("%.3f", mean); + } + else if (_scoreOp == "median") { + double median = 0.0; + sort(data.begin(), data.end()); + int totalLines = data.size(); + if ((totalLines % 2) > 0) { + long mid; + mid = totalLines / 2; + median = data[mid]; + } + else { + long midLow, midHigh; + midLow = (totalLines / 2) - 1; + midHigh = (totalLines / 2); + median = (data[midLow] + data[midHigh]) / 2.0; + } + printf("%.3f", median); + } + else if ((_scoreOp == "mode") || (_scoreOp == "antimode")) { + // compute the frequency of each unique value + map<string, int> freqs; + vector<string>::const_iterator dIt = scores.begin(); + vector<string>::const_iterator dEnd = scores.end(); + for (; dIt != dEnd; ++dIt) { + freqs[*dIt]++; + } + + // grab the mode and the anti mode + string mode, antiMode; + int count = 0; + int minCount = INT_MAX; + for(map<string,int>::const_iterator iter = freqs.begin(); iter != freqs.end(); ++iter) { + if (iter->second > count) { + mode = iter->first; + count = iter->second; + } + if (iter->second < minCount) { + antiMode = iter->first; + minCount = iter->second; + } + } + // report + if (_scoreOp == "mode") { + printf("%s", mode.c_str()); + } + else if (_scoreOp == "antimode") { + printf("%s", antiMode.c_str()); + } + } + else if (_scoreOp == "collapse") { + vector<string>::const_iterator scoreItr = scores.begin(); + vector<string>::const_iterator scoreEnd = scores.end(); + for (; scoreItr != scoreEnd; ++scoreItr) { + if (scoreItr < (scoreEnd - 1)) + cout << *scoreItr << ";"; + else + cout << *scoreItr; + } + } + } + else { + cerr << endl + << "*****" << endl + << "*****ERROR: No scores found to report for the -scores option. Exiting." << endl + << "*****" << endl; + exit(1); + } +} + +// =============== +// = Constructor = +// =============== +BedMerge::BedMerge(string &bedFile, + bool numEntries, + int maxDistance, + bool forceStrand, + bool reportNames, + bool reportScores, + const string &scoreOp) : + _bedFile(bedFile), + _numEntries(numEntries), + _forceStrand(forceStrand), + _reportNames(reportNames), + _reportScores(reportScores), + _scoreOp(scoreOp), + _maxDistance(maxDistance) +{ + _bed = new BedFile(bedFile); + + if (_forceStrand == false) + MergeBed(); + else + MergeBedStranded(); +} + + +// ================= +// = Destructor = +// ================= +BedMerge::~BedMerge(void) { +} + + +// =============================================== +// Convenience method for reporting merged blocks +// ================================================ +void BedMerge::Report(string chrom, int start, int end, + const vector<string> &names, const vector<string> &scores, int mergeCount) +{ + // ARQ: removed to force all output to be zero-based, BED format, reagrdless of input type + //if (_bed->isZeroBased == false) {start++;} + + printf("%s\t%d\t%d", chrom.c_str(), start, end); + // just the merged intervals + if (_numEntries == false && _reportNames == false && _reportScores == false) { + printf("\n"); + } + // merged intervals and counts + else if (_numEntries == true && _reportNames == false && _reportScores == false) { + printf("\t%d\n", mergeCount); + } + // merged intervals and names + else if (_numEntries == false && _reportNames == true && _reportScores == false) { + ReportMergedNames(names); + printf("\n"); + } + // merged intervals and scores + else if (_numEntries == false && _reportNames == false && _reportScores == true) { + ReportMergedScores(scores); + printf("\n"); + } + // merged intervals, names, and scores + else if (_numEntries == false && _reportNames == true && _reportScores == true) { + ReportMergedNames(names); + ReportMergedScores(scores); + printf("\n"); + } +} + + +// ========================================================= +// Convenience method for reporting merged blocks by strand +// ========================================================= +void BedMerge::ReportStranded(string chrom, int start, int end, + const vector<string> &names, const vector<string> &scores, + int mergeCount, string strand) +{ + // ARQ: removed to force all output to be zero-based, BED format, reagrdless of input type + //if (_bed->isZeroBased == false) {start++;} + + printf("%s\t%d\t%d", chrom.c_str(), start, end); + // just the merged intervals + if (_numEntries == false && _reportNames == false && _reportScores == false) { + printf("\t%s\n", strand.c_str()); + } + // merged intervals and counts + else if (_numEntries == true && _reportNames == false && _reportScores == false) { + printf("\t%d\t%s\n", mergeCount, strand.c_str()); + } + // merged intervals and names + else if (_numEntries == false && _reportNames == true && _reportScores == false) { + ReportMergedNames(names); + printf("\t%s\n", strand.c_str()); + } + // merged intervals and scores + else if (_numEntries == false && _reportNames == false && _reportScores == true) { + ReportMergedScores(scores); + printf("\t%s\n", strand.c_str()); + } + // merged intervals, names, and scores + else if (_numEntries == false && _reportNames == true && _reportScores == true) { + ReportMergedNames(names); + ReportMergedScores(scores); + printf("\t%s\n", strand.c_str()); + } +} + + +// ===================================================== +// = Merge overlapping BED entries into a single entry = +// ===================================================== +void BedMerge::MergeBed() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + // loop through each chromosome and merge their BED entries + masterBedMapNoBin::const_iterator m = _bed->bedMapNoBin.begin(); + masterBedMapNoBin::const_iterator mEnd = _bed->bedMapNoBin.end(); + for (; m != mEnd; ++m) { + + // bedList is already sorted by start position. + string chrom = m->first; + vector<BED> bedList = m->second; + int mergeCount = 1; + vector<string> names; + vector<string> scores; + + // merge overlapping features for this chromosome. + int start = -1; + int end = -1; + vector<BED>::const_iterator bedItr = bedList.begin(); + vector<BED>::const_iterator bedEnd = bedList.end(); + for (; bedItr != bedEnd; ++bedItr) { + // new block, no overlap + if ( (((int) bedItr->start - end) > _maxDistance) || (end < 0)) { + if (start >= 0) { + Report(chrom, start, end, names, scores, mergeCount); + // reset + mergeCount = 1; + names.clear(); + scores.clear(); + } + start = bedItr->start; + end = bedItr->end; + if (!bedItr->name.empty()) names.push_back(bedItr->name); + if (!bedItr->score.empty()) scores.push_back(bedItr->score); + } + // same block, overlaps + else { + if ((int) bedItr-> end > end) end = bedItr->end; + mergeCount++; + if (!bedItr->name.empty()) names.push_back(bedItr->name); + if (!bedItr->score.empty()) scores.push_back(bedItr->score); + } + } + if (start >= 0) { + Report(chrom, start, end, names, scores, mergeCount); + } + } +} + + +// ================================================================================== +// = Merge overlapping BED entries into a single entry, accounting for strandedness = +// ================================================================================== +void BedMerge::MergeBedStranded() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + // loop through each chromosome and merge their BED entries + masterBedMapNoBin::const_iterator m = _bed->bedMapNoBin.begin(); + masterBedMapNoBin::const_iterator mEnd = _bed->bedMapNoBin.end(); + for (; m != mEnd; ++m) { + + // bedList is already sorted by start position. + string chrom = m->first; + vector<BED> bedList = m->second; + + // make a list of the two strands to merge separately. + vector<string> strands(2); + strands[0] = "+"; + strands[1] = "-"; + + // do two passes, one for each strand. + for (unsigned int s = 0; s < strands.size(); s++) { + + int mergeCount = 1; + int numOnStrand = 0; + vector<string> names; + vector<string> scores; + + // merge overlapping features for this chromosome. + int start = -1; + int end = -1; + vector<BED>::const_iterator bedItr = bedList.begin(); + vector<BED>::const_iterator bedEnd = bedList.end(); + for (; bedItr != bedEnd; ++bedItr) { + + // if forcing strandedness, move on if the hit + // is not on the current strand. + if (bedItr->strand != strands[s]) { continue; } + else { numOnStrand++; } + + if ( (((int) bedItr->start - end) > _maxDistance) || (end < 0)) { + if (start >= 0) { + ReportStranded(chrom, start, end, names, scores, mergeCount, strands[s]); + // reset + mergeCount = 1; + names.clear(); + scores.clear(); + } + start = bedItr->start; + end = bedItr->end; + if (!bedItr->name.empty()) names.push_back(bedItr->name); + if (!bedItr->score.empty()) scores.push_back(bedItr->score); + } + else { + if ((int) bedItr-> end > end) end = bedItr->end; + mergeCount++; + if (!bedItr->name.empty()) names.push_back(bedItr->name); + if (!bedItr->score.empty()) scores.push_back(bedItr->score); + } + } + if (start >= 0) { + ReportStranded(chrom, start, end, names, scores, mergeCount, strands[s]); + } + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/mergeBed/mergeBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,59 @@ +/***************************************************************************** + mergeBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" +#include <vector> +#include <algorithm> +#include <numeric> +#include <iostream> +#include <fstream> +#include <limits.h> +#include <stdlib.h> + +using namespace std; + + +//************************************************ +// Class methods and elements +//************************************************ +class BedMerge { + +public: + + // constructor + BedMerge(string &bedFile, bool numEntries, + int maxDistance, bool forceStrand, + bool reportNames, bool reportScores, const string &scoreOp); + + // destructor + ~BedMerge(void); + + void MergeBed(); + void MergeBedStranded(); + +private: + + string _bedFile; + bool _numEntries; + bool _forceStrand; + bool _reportNames; + bool _reportScores; + string _scoreOp; + int _maxDistance; + // instance of a bed file class. + BedFile *_bed; + + void Report(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount); + void ReportStranded(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount, string strand); + void ReportMergedNames(const vector<string> &names); + void ReportMergedScores(const vector<string> &scores); + +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/mergeBed/mergeMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,163 @@ +/***************************************************************************** + mergeMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "mergeBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "mergeBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + int maxDistance = 0; + string scoreOp = ""; + + // input arguments + bool haveBed = true; + bool numEntries = false; + bool haveMaxDistance = false; + bool forceStrand = false; + bool reportNames = false; + bool reportScores = false; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-n", 2, parameterLength)) { + numEntries = true; + } + else if(PARAMETER_CHECK("-d", 2, parameterLength)) { + if ((i+1) < argc) { + haveMaxDistance = true; + maxDistance = atoi(argv[i + 1]); + i++; + } + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + forceStrand = true; + } + else if (PARAMETER_CHECK("-nms", 4, parameterLength)) { + reportNames = true; + } + else if (PARAMETER_CHECK("-scores", 7, parameterLength)) { + reportScores = true; + if ((i+1) < argc) { + scoreOp = argv[i + 1]; + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl; + showHelp = true; + } + if (reportNames && numEntries) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -n OR -nms, not both." << endl << "*****" << endl; + showHelp = true; + } + if ((reportScores == true) && (scoreOp != "sum") && (scoreOp != "max") && (scoreOp != "min") && (scoreOp != "mean") && + (scoreOp != "mode") && (scoreOp != "median") && (scoreOp != "antimode") && (scoreOp != "collapse")) + { + cerr << endl << "*****" << endl << "*****ERROR: Invalid scoreOp selection \"" << scoreOp << endl << "\" *****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedMerge *bm = new BedMerge(bedFile, numEntries, maxDistance, forceStrand, reportNames, reportScores, scoreOp); + delete bm; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Merges overlapping BED/GFF/VCF entries into a single interval." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-s\t" << "Force strandedness. That is, only merge features" << endl; + cerr << "\t\tthat are the same strand." << endl; + cerr << "\t\t- By default, merging is done without respect to strand." << endl << endl; + + cerr << "\t-n\t" << "Report the number of BED entries that were merged." << endl; + cerr << "\t\t- Note: \"1\" is reported if no merging occurred." << endl << endl; + + + cerr << "\t-d\t" << "Maximum distance between features allowed for features" << endl; + cerr << "\t\tto be merged." << endl; + cerr << "\t\t- Def. 0. That is, overlapping & book-ended features are merged." << endl; + cerr << "\t\t- (INTEGER)" << endl << endl; + + cerr << "\t-nms\t" << "Report the names of the merged features separated by semicolons." << endl << endl; + + cerr << "\t-scores\t" << "Report the scores of the merged features. Specify one of " << endl; + cerr << "\t\tthe following options for reporting scores:" << endl; + cerr << "\t\t sum, min, max," << endl; + cerr << "\t\t mean, median, mode, antimode," << endl; + cerr << "\t\t collapse (i.e., print a semicolon-separated list)," << endl; + cerr << "\t\t- (INTEGER)" << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) All output, regardless of input type (e.g., GFF or VCF)" << endl; + cerr << "\t will in BED format with zero-based starts" << endl << endl; + + + // end the program here + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiBamCov/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,48 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= multiBamCovMain.cpp multiBamCov.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= multiBamCov + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiBamCov/multiBamCov.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,134 @@ +/***************************************************************************** + multiBamCov.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "multiBamCov.h" +#include "api/BamMultiReader.h" + + +/* + Constructor +*/ +MultiCovBam::MultiCovBam(const vector<string> &bam_files, const string bed_file, + int minQual, bool properOnly, + bool keepDuplicates, bool keepFailedQC) +: +_bam_files(bam_files), +_bed_file(bed_file), +_minQual(minQual), +_properOnly(properOnly), +_keepDuplicates(keepDuplicates), +_keepFailedQC(keepFailedQC) +{ + _bed = new BedFile(_bed_file); + LoadBamFileMap(); +} + + +/* + Destructor +*/ +MultiCovBam::~MultiCovBam(void) +{} + + + +void MultiCovBam::CollectCoverage() +{ + BamMultiReader reader; + + if ( !reader.Open(_bam_files) ) + { + cerr << "Could not open input BAM files." << endl; + exit(1); + } + else + { + // attempt to find index files + reader.LocateIndexes(); + + // if index data available for all BAM files, we can use SetRegion + if ( reader.HasIndexes() ) { + BED bed, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + + _bed->Open(); + // loop through each BED entry, jump to it, + // and collect coverage from each BAM + while ((bedStatus = _bed->GetNextBed(bed, lineNum)) != BED_INVALID) + { + if (bedStatus == BED_VALID) + { + // initialize counts for each file to 0 + vector<int> counts(_bam_files.size(), 0); + // get the BAM refId for this chrom. + int refId = reader.GetReferenceID(bed.chrom); + // set up a BamRegion to which to attempt to jump + BamRegion region(refId, (int)bed.start, refId, (int)bed.end); + + // everything checks out, just iterate through specified region, counting alignments + if ( (refId != -1) && (reader.SetRegion(region)) ) { + BamAlignment al; + while ( reader.GetNextAlignment(al) ) + { + bool duplicate = al.IsDuplicate(); + bool failedQC = al.IsFailedQC(); + if (_keepDuplicates) duplicate = false; + if (_keepFailedQC) failedQC = false; + // map qual must exceed minimum + if ((al.MapQuality >= _minQual) && (!duplicate) && (!failedQC)) { + // ignore if not properly paired and we actually care. + if (_properOnly && !al.IsProperPair()) + continue; + + // lookup the offset of the file name and tabulate + //coverage for the appropriate file + counts[bamFileMap[al.Filename]]++; + } + } + } + // report the cov at this interval for each file and reset + _bed->reportBedTab(bed); + ReportCounts(counts); + bed = nullBed; + } + } + _bed->Close(); + } + else { + cerr << "Could not find indexes." << endl; + reader.Close(); + exit(1); + } + } +} + + +void MultiCovBam::LoadBamFileMap(void) +{ + for (size_t i = 0; i < _bam_files.size(); ++i) + { + bamFileMap[_bam_files[i]] = i; + } +} + +void MultiCovBam::ReportCounts(const vector<int> &counts) +{ + for (size_t i = 0; i < counts.size(); ++i) + { + if (i < counts.size() - 1) + cout << counts[i] << "\t"; + else + cout << counts[i]; + } + cout << endl; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiBamCov/multiBamCov.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,64 @@ +/***************************************************************************** + multiBamCov.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef MULTICOVBAM_H +#define MULTICOVBAM_H + +#include "bedFile.h" +#include "api/BamMultiReader.h" +using namespace BamTools; + + +#include <vector> +#include <iostream> +#include <fstream> +#include <stdlib.h> +using namespace std; + + + +class MultiCovBam { + +public: + + // constructor + MultiCovBam(const vector<string> &bam_files, const string bed_file, + int minQual, bool properOnly, + bool keepDuplicates, bool keepFailedQC); + + // destructor + ~MultiCovBam(void); + + void CollectCoverage(); + +private: + + //------------------------------------------------ + // private attributes + //------------------------------------------------ + vector<string> _bam_files; + string _bed_file; + BedFile *_bed; + + // attributes to control what is counted + int _minQual; + bool _properOnly; + bool _keepDuplicates; + bool _keepFailedQC; + + + map<string, int> bamFileMap; + + void LoadBamFileMap(void); + void ReportCounts(const vector<int> &counts); +}; + +#endif /* MULTIBAMCOV_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiBamCov/multiBamCovMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,145 @@ +/***************************************************************************** + multiBamCovMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "multiBamCov.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "multiBamCov" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile; + vector<string> bamFiles; + int minQual = 0; + + // input arguments + bool haveBed = false; + bool haveBams = false; + bool properOnly = false; + bool keepDuplicates = false; + bool keepFailedQC = false; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-bed", 4, parameterLength)) { + if ((i+1) < argc) { + haveBed = true; + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bams", 5, parameterLength)) { + if ((i+1) < argc) { + haveBams = true; + i = i+1; + string file = argv[i]; + while (file[0] != '-' && i < argc) { + bamFiles.push_back(file); + i++; + if (i < argc) + file = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-q", 2, parameterLength)) { + if ((i+1) < argc) { + minQual = atoi(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-p", 2, parameterLength)) { + properOnly = true; + } + else if(PARAMETER_CHECK("-D", 2, parameterLength)) { + keepDuplicates = true; + } + + else if(PARAMETER_CHECK("-F", 2, parameterLength)) { + keepFailedQC = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + if (!showHelp) { + MultiCovBam *mc = new MultiCovBam(bamFiles, bedFile, minQual, properOnly, keepDuplicates, keepFailedQC); + mc->CollectCoverage(); + delete mc; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Counts sequence coverage for multiple bams at specific loci." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-bams\t" << "The bam files." << endl << endl; + + cerr << "\t-bed\t" << "The bed file." << endl << endl; + + cerr << "\t-q\t" << "Minimum mapping quality allowed. Default is 0." << endl << endl; + + cerr << "\t-D\t" << "Include duplicate-marked reads. Default is to count non-duplicates only" << endl << endl; + + cerr << "\t-F\t" << "Include failed-QC reads. Default is to count pass-QC reads only" << endl << endl; + + cerr << "\t-p\t" << "Only count proper pairs. Default is to count all alignments with MAPQ" << endl; + cerr << "\t\t" << "greater than the -q argument, regardless of the BAM FLAG field." << endl << endl; + + // end the program here + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiIntersectBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,49 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= multiIntersectBed.cpp multiIntersectBedMain.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= multiIntersectBed + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedGraphFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiIntersectBed/intervalItem.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,64 @@ +/***************************************************************************** + intervalItem.h + + (c) 2010 - Assaf Gordon + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef INTERVALITEM_H +#define INTERVALITEM_H + +#include <string> +#include <queue> + +enum COORDINATE_TYPE { + START, + END +}; + +/* + An interval item in the priority queue. + + An IntervalItem can mark either a START position or an END position. + */ +class IntervalItem +{ + + +public: + int source_index; // which source BedGraph file this came from + COORDINATE_TYPE coord_type; // is this the start or the end position? + CHRPOS coord; + + IntervalItem () : + source_index(-1), + coord_type(START), + coord(0) + {} + + IntervalItem(int _index, COORDINATE_TYPE _type, CHRPOS _coord) : + source_index(_index), + coord_type(_type), + coord(_coord) + {} + + IntervalItem(const IntervalItem &other) : + source_index(other.source_index), + coord_type(other.coord_type), + coord(other.coord) + {} + + bool operator< ( const IntervalItem& other ) const + { + return this->coord > other.coord; + } +}; + +// our priority queue +typedef std::priority_queue<IntervalItem> INTERVALS_PRIORITY_QUEUE; + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiIntersectBed/multiIntersectBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,289 @@ +/***************************************************************************** + unionBedGraphs.cpp + + (c) 2010 - Assaf Gordon, CSHL + - Aaron Quinlan, UVA + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include <cassert> +#include <cstring> +#include <cstdlib> +#include <iostream> +#include <algorithm> + +#include "bedFile.h" +#include "multiIntersectBed.h" + +using namespace std; + + +MultiIntersectBed::MultiIntersectBed(std::ostream& _output, + const vector<string>& _filenames, + const vector<string>& _titles, + bool _print_empty_regions, + const std::string& _genome_size_filename, + const std::string& _no_coverage_value ) : + filenames(_filenames), + titles(_titles), + output(_output), + current_non_zero_inputs(0), + print_empty_regions(_print_empty_regions), + haveTitles(false), + genome_sizes(NULL), + no_coverage_value(_no_coverage_value) +{ + if (print_empty_regions) { + assert(!_genome_size_filename.empty()); + + genome_sizes = new GenomeFile(_genome_size_filename); + } + + if (titles.size() > 0) { + haveTitles = true; + } +} + + +MultiIntersectBed::~MultiIntersectBed() { + CloseFiles(); + if (genome_sizes) { + delete genome_sizes; + genome_sizes = NULL ; + } +} + + +void MultiIntersectBed::MultiIntersect() { + OpenFiles(); + + // Add the first interval from each file + for(size_t i = 0;i < input_files.size(); ++i) + LoadNextItem(i); + + // Chromosome loop - once per chromosome + do { + // Find the first chromosome to use + current_chrom = DetermineNextChrom(); + + // Populate the queue with initial values from all files + // (if they belong to the correct chromosome) + for(size_t i = 0; i < input_files.size(); ++i) + AddInterval(i); + + CHRPOS current_start = ConsumeNextCoordinate(); + + // User wanted empty regions, and the first coordinate is not 0 - print a dummy empty coverage + if (print_empty_regions && current_start > 0) + PrintEmptyCoverage(0,current_start); + + // Intervals loop - until all intervals (of current chromosome) from all files are used. + do { + CHRPOS current_end = queue.top().coord; + PrintCoverage(current_start, current_end); + current_start = ConsumeNextCoordinate(); + } while (!queue.empty()); + + // User wanted empty regions, and the last coordinate is not the last coordinate of the chromosome + // print a dummy empty coverage + if (print_empty_regions) { + CHRPOS chrom_size = genome_sizes->getChromSize(current_chrom); + if (current_start < chrom_size) + PrintEmptyCoverage(current_start, chrom_size); + } + + } while (!AllFilesDone()); +} + + +CHRPOS MultiIntersectBed::ConsumeNextCoordinate() { + assert(!queue.empty()); + + CHRPOS new_position = queue.top().coord; + do { + IntervalItem item = queue.top(); + UpdateInformation(item); + queue.pop(); + } while (!queue.empty() && queue.top().coord == new_position); + + return new_position; +} + + +void MultiIntersectBed::UpdateInformation(const IntervalItem &item) { + // Update the depth coverage for this file + + // Which coordinate is it - start or end? + switch (item.coord_type) + { + case START: + current_depth[item.source_index] = 1; + current_non_zero_inputs++; + files_with_coverage[item.source_index] = true; + break; + case END: + //Read the next interval from this file + AddInterval(item.source_index); + current_depth[item.source_index] = 0; + current_non_zero_inputs--; + files_with_coverage.erase(item.source_index); + break; + default: + assert(0); + } +} + + +void MultiIntersectBed::AddInterval(int index) { + assert(static_cast<unsigned int>(index) < input_files.size()); + + //This file has no more intervals + if (current_item[index].chrom.empty()) + return; + + //If the next interval belongs to a different chrom, don't add it + if (current_item[index].chrom!=current_chrom) + return; + + const BED &bed(current_item[index]); + + IntervalItem start_item(index, START, bed.start); + IntervalItem end_item(index, END, bed.end); + + queue.push(start_item); + queue.push(end_item); + + LoadNextItem(index); +} + + +void MultiIntersectBed::PrintHeader() { + output << "chrom\tstart\tend\tnum\tlist" ; + for (size_t i=0;i<titles.size();++i) + output << "\t" <<titles[i]; + output << endl; +} + + +void MultiIntersectBed::PrintCoverage(CHRPOS start, CHRPOS end) { + if ( current_non_zero_inputs == 0 && ! print_empty_regions ) + return ; + + output << current_chrom << "\t" + << start << "\t" + << end << "\t" + << current_non_zero_inputs << "\t"; + + ostringstream file_list_string; + ostringstream file_bool_string; + int depth_count = 0; + for (size_t i = 0; i < current_depth.size(); ++i) + { + if (current_depth[i] > 0) { + if (depth_count < current_non_zero_inputs - 1) { + if (!haveTitles) + file_list_string << i+1 << ","; + else + file_list_string << titles[i] << ","; + } + else { + if (!haveTitles) + file_list_string << i+1; + else + file_list_string << titles[i]; + } + depth_count++; + } + file_bool_string << "\t" << current_depth[i]; + } + if (current_non_zero_inputs > 0) { + cout << file_list_string.str() << file_bool_string.str() << endl; + } + else { + cout << "none" << file_bool_string.str() << endl; + } +} + + +void MultiIntersectBed::PrintEmptyCoverage(CHRPOS start, CHRPOS end) { + output << current_chrom << "\t" + << start << "\t" + << end << "\t" + << "0" << "\t" << "none"; + + for (size_t i=0;i<current_depth.size();++i) + output << "\t0"; + + output << endl; +} + + +void MultiIntersectBed::LoadNextItem(int index) { + assert(static_cast<unsigned int>(index) < input_files.size()); + + current_item[index].chrom=""; + + BedFile *file = input_files[index]; + BED merged_bed; + int lineNum = 0; + // + // TO DO: Do the mergeing on the fly. How best to do this? + // + // IDEA: Implement a Merge class with GetNextMerge element. + // + + while (file->GetNextMergedBed(merged_bed, lineNum)) + { + current_item[index] = merged_bed; + break; + } +} + + +bool MultiIntersectBed::AllFilesDone() { + for (size_t i=0;i<current_item.size();++i) + if (!current_item[i].chrom.empty()) + return false; + return true; +} + + +string MultiIntersectBed::DetermineNextChrom() { + string next_chrom; + for (size_t i=0;i<current_item.size();++i) { + if (current_item[i].chrom.empty()) + continue; + + if (next_chrom.empty()) + next_chrom = current_item[i].chrom; + else + if (current_item[i].chrom < next_chrom) + next_chrom = current_item[i].chrom ; + } + return next_chrom; +} + + +void MultiIntersectBed::OpenFiles() { + for (size_t i = 0; i < filenames.size(); ++i) { + BedFile *file = new BedFile(filenames[i]); + file->Open(); + input_files.push_back(file); + current_depth.push_back(0); + } + current_item.resize(filenames.size()); +} + + +void MultiIntersectBed::CloseFiles() { + for (size_t i=0; i < input_files.size(); ++i) { + BedFile *file = input_files[i]; + delete file; + input_files[i] = NULL ; + } + input_files.clear(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiIntersectBed/multiIntersectBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,125 @@ +/***************************************************************************** + multiIntersectBed.h + + (c) 2010 - Aaron Quinlan, UVA + - Assaf Gordon, CSHL + Quinlan Laboratory + Department of Public Health Sciences + Center for Public Health Genomics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef MULTIINTERSECTBED_H +#define MULTIINTERSECTBED_H + +#include <vector> +#include <string> +#include "bedFile.h" +#include "genomeFile.h" +#include "intervalItem.h" + +class MultiIntersectBed +{ +private: + + vector<string> filenames; + vector<string> titles; + + vector<BedFile*> input_files; + vector<int> current_depth; + vector<BED> current_item; + + std::ostream &output; + + INTERVALS_PRIORITY_QUEUE queue; + std::string current_chrom; + map<int, bool> files_with_coverage; + int current_non_zero_inputs; + bool print_empty_regions; + bool haveTitles; + + GenomeFile* genome_sizes; + + std::string no_coverage_value; + +public: + MultiIntersectBed(std::ostream& _output, + const vector<string>& _filenames, + const vector<string>& _titles, + bool _print_empty_regions, + const std::string& _genomeFileName, + const std::string& _no_coverage_value); + + virtual ~MultiIntersectBed(); + + // Combines all interval files + void MultiIntersect(); + + // Print the header line: chrom/start/end + name of each bedgraph file. + void PrintHeader(); + + +private: + + // Open all input files, initialize "current_XXX" vectors + void OpenFiles(); + + // Close the input files. + void CloseFiles(); + + /* + Add an interval from BedGraph file 'index' into the queue. + will only be added if it belongs to the current chromosome. + + If the interval was added (=consumed), the next interval will be read from the file + using 'LoadNextItem' + */ + void AddInterval(int index); + + /* + Loads the next interval from Bed file 'index'. + Stores it in 'current_bed_item' vector. + */ + void LoadNextItem(int index); + + /* + Scans the 'current_bedgraph_item' vector, + find the 'first' chromosome to use (different BedGraph files can start with different chromosomes). + */ + std::string DetermineNextChrom(); + + /* + Returns 'true' if ALL intervals from ALL BedGraph files were used + */ + bool AllFilesDone(); + + /* + Extract the next coordinate from the queue, and updates the current coverage information. + If multiple interval share the same coordinate values, all of them are handled. + If an END coordinate is consumed, the next interval (from the corresponding file) is read. + */ + CHRPOS ConsumeNextCoordinate(); + + /* + Updates the coverage information based on the given item. + Item can be a START coordinate or an END coordiante. + */ + void UpdateInformation(const IntervalItem &item); + + /* + prints chrom/start/end and the current depth coverage values of all the files. + */ + void PrintCoverage(CHRPOS start, CHRPOS end); + + /* + prints chrom/start/end and the ZERO depth coverage values of all the files. + */ + void PrintEmptyCoverage(CHRPOS start, CHRPOS end); + + void DebugPrintQueue(); +}; + + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/multiIntersectBed/multiIntersectBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,294 @@ +/***************************************************************************** + unionBedGraphsMain.cpp + + (c) 2010 - Assaf Gordon, CSHL + - Aaron Quinlan, UVA + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include <climits> +#include <cstring> +#include <cstdlib> +#include <vector> +#include <string> +#include <iostream> +#include <getopt.h> +#include <libgen.h> //for basename() +#include "version.h" + +#include "genomeFile.h" +#include "multiIntersectBed.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "multiIntersectBed" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +//STLized version of basename() +// (because POSIX basename() modifies the input string pointer) +// Additionally: removes any extension the basename might have. +std::string stl_basename(const std::string& path); + +// function declarations +void ShowHelp(void); +void ShowExamples(void); + + +int main(int argc, char* argv[]) +{ + bool haveFiles = false; + bool haveTitles = false; + bool haveGenome = false; + bool haveFiller = true; + bool printHeader = false; + bool printEmptyRegions = false; + bool showHelp = false; + string genomeFile; + string basePath; + string noCoverageValue = "0"; + vector<string> inputFiles; + vector<string> inputTitles; + + //Parse command line options + if(argc <= 1) + ShowHelp(); + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp == true) { + ShowHelp(); + exit(1); + } + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + haveFiles = true; + i = i+1; + string file = argv[i]; + while (file[0] != '-' && i < argc) { + inputFiles.push_back(file); + i++; + if (i < argc) + file = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-names", 6, parameterLength)) { + if ((i+1) < argc) { + haveTitles = true; + i = i+1; + string title = argv[i]; + while (title[0] != '-' && i < argc) { + inputTitles.push_back(title); + i++; + if (i < argc) + title = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-filler", 7, parameterLength)) { + if ((i+1) < argc) { + haveFiller = true; + noCoverageValue = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-header", 7, parameterLength)) { + printHeader = true; + } + else if(PARAMETER_CHECK("-empty", 6, parameterLength)) { + printEmptyRegions = true; + } + else if(PARAMETER_CHECK("-examples", 9, parameterLength)) { + ShowHelp(); + ShowExamples(); + exit(1); + } + } + + //Sanity checks + if (inputFiles.empty() == true) { + cerr << "Error: missing BedGraph file names (-i) to combine." << endl; + exit(1); + } + if (inputFiles.size() == 1) { + cerr << "Error: Only a single BedGraph file was specified. Nothing to combine, exiting." << endl; + exit(1); + } + if (printEmptyRegions && (genomeFile.empty() == true)) { + cerr << "Error: when using -empty, the genome sizes file (-g) must be specified using '-g FILE'." << endl; + exit(1); + } + if ((haveTitles == true) && (inputFiles.size() != inputTitles.size())) { + cerr << "Error: The number of file titles (-names) does not match the number of files (-i)." << endl; + exit(1); + } + + MultiIntersectBed mbi(cout, inputFiles, inputTitles, printEmptyRegions, genomeFile, noCoverageValue); + if (printHeader) + mbi.PrintHeader(); + mbi.MultiIntersect(); +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Authors: Assaf Gordon, CSHL" << endl; + cerr << " Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl; + + cerr << "Summary: Combines multiple BedGraph files into a single file," << endl; + cerr << "\t allowing coverage comparisons between them." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i FILE1 FILE2 .. FILEn" << endl; + cerr << "\t Assumes that each BedGraph file is sorted by chrom/start " << endl; + cerr << "\t and that the intervals in each are non-overlapping." << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-header\t\t" << "Print a header line." << endl; + cerr << "\t\t\t(chrom/start/end + names of each file)." << endl << endl; + + cerr << "\t-names\t\t" << "A list of names (one / file) to describe each file in -i." << endl; + cerr << "\t\t\tThese names will be printed in the header line." << endl << endl; + + cerr << "\t-g\t\t" << "Use genome file to calculate empty regions." << endl; + cerr << "\t\t\t- STRING." << endl << endl; + + cerr << "\t-empty\t\t" << "Report empty regions (i.e., start/end intervals w/o" << endl; + cerr << "\t\t\tvalues in all files)." << endl; + cerr << "\t\t\t- Requires the '-g FILE' parameter.\n" << endl; + + cerr << "\t-filler TEXT\t" << "Use TEXT when representing intervals having no value." << endl; + cerr << "\t\t\t- Default is '0', but you can use 'N/A' or any other text." << endl << endl; + + cerr << "\t-examples\t" << "Show detailed usage examples." << endl << endl; +} + + + +void ShowExamples() +{ + cerr << "Example usage:\n\n" \ +"== Input files: ==\n" \ +"\n" \ +" $ cat 1.bg\n" \ +" chr1 1000 1500 10\n" \ +" chr1 2000 2100 20\n" \ +"\n" \ +" $ cat 2.bg\n" \ +" chr1 900 1600 60\n" \ +" chr1 1700 2050 50\n" \ +"\n" \ +" $ cat 3.bg\n" \ +" chr1 1980 2070 80\n" \ +" chr1 2090 2100 20\n" \ +"\n" \ +" $ cat sizes.txt\n" \ +" chr1 5000\n" \ +"\n" \ +"== Union/combine the files: ==\n" \ +"\n" \ +" $ unionBedGraphs -i 1.bg 2.bg 3.bg\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +"\n" \ +"== Union/combine the files, with a header line (titles are the file names): ==\n" \ +"\n" \ +" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg\n" \ +" chrom start end 1 2 3\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +"\n" \ +"== Union/combine the files, with a header line and custom names: ==\n" \ +"\n" \ +" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg -names WT-1 WT-2 KO-1\n" \ +" chrom start end WT-1 WT-2 KO-1\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +"\n" \ +"== Union/combine, showing empty regions (note, requires -g): ==\n" \ +"\n" \ +" $ unionBedGraphs -header -empty -g sizes.TXT -i 1.bg 2.bg 3.bg\n" \ +" chrom start end 1 2 3\n" \ +" chr1 0 900 0 0 0\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1600 1700 0 0 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +" chr1 2100 5000 0 0 0\n" \ +"\n" \ +; +} + +std::string stl_basename(const std::string& path) +{ + string result; + + char* path_dup = strdup(path.c_str()); + char* basename_part = basename(path_dup); + result = basename_part; + free(path_dup); + + size_t pos = result.find_last_of('.'); + if (pos != string::npos ) + result = result.substr(0,pos); + + return result; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/nucBed/LargeFileSupport.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,13 @@ +#pragma once + +#define _FILE_OFFSET_BITS 64 + +#ifdef WIN32 +#define ftell64(a) _ftelli64(a) +#define fseek64(a,b,c) _fseeki64(a,b,c) +typedef __int64_t off_type; +#else +#define ftell64(a) ftello(a) +#define fseek64(a,b,c) fseeko(a,b,c) +typedef off_t off_type; +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/nucBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,52 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/sequenceUtilities/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/Fasta/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= nucBedMain.cpp nucBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o Fasta.o split.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= nucBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/Fasta/ + + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/nucBed/nucBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,158 @@ +/***************************************************************************** + nucBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "nucBed.h" + + +NucBed::NucBed(string &dbFile, string &bedFile, bool printSeq, + bool hasPattern, const string &pattern, bool forceStrand) { + + _dbFile = dbFile; + _bedFile = bedFile; + _printSeq = printSeq; + _hasPattern = hasPattern; + _pattern = pattern; + _forceStrand = forceStrand; + + _bed = new BedFile(_bedFile); + + // Compute the DNA content in each BED/GFF/VCF interval + ProfileDNA(); +} + + +NucBed::~NucBed(void) +{} + + +void NucBed::ReportDnaProfile(const BED& bed, const string &sequence, int seqLength) +{ + int a,c,g,t,n,other,userPatternCount; + a = c = g = t = n = other = userPatternCount = 0; + + getDnaContent(sequence,a,c,g,t,n,other); + + if (_hasPattern) + userPatternCount = countPattern(sequence, _pattern); + + + // report the original interval + _bed->reportBedTab(bed); + // report AT and GC content + printf("%f\t%f\t",(float)(a+t)/seqLength, (float)(c+g)/seqLength); + // report raw nucleotide counts + printf("%d\t%d\t%d\t%d\t%d\t%d\t%d",a,c,g,t,n,other,seqLength); + // add the original sequence if requested. + + if (_printSeq) + printf("\t%s",sequence.c_str()); + if (_hasPattern) + printf("\t%d",userPatternCount); + printf("\n"); + +} + + +void NucBed::PrintHeader(void) { + printf("#"); + + int numOrigColumns = (int) _bed->bedType; + for (int i = 1; i <= numOrigColumns; ++i) { + printf("%d_usercol\t", i); + } + printf("%d_pct_at\t", numOrigColumns + 1); + printf("%d_pct_gc\t", numOrigColumns + 2); + printf("%d_num_A\t", numOrigColumns + 3); + printf("%d_num_C\t", numOrigColumns + 4); + printf("%d_num_G\t", numOrigColumns + 5); + printf("%d_num_T\t", numOrigColumns + 6); + printf("%d_num_N\t", numOrigColumns + 7); + printf("%d_num_oth\t", numOrigColumns + 8); + printf("%d_seq_len\t", numOrigColumns + 9); + + if (_printSeq) + printf("%d_seq", numOrigColumns + 10); + if (_hasPattern && !_printSeq) + printf("%d_user_patt_count", numOrigColumns + 10); + else if (_hasPattern && _printSeq) + printf("\t%d_user_patt_count", numOrigColumns + 11); + printf("\n"); + +} + + +//****************************************************************************** +// ExtractDNA +//****************************************************************************** +void NucBed::ProfileDNA() { + + /* Make sure that we can oen all of the files successfully*/ + + // open the fasta database for reading + ifstream faDb(_dbFile.c_str(), ios::in); + if ( !faDb ) { + cerr << "Error: The requested fasta database file (" << _dbFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + + // open and memory-map genome file + FastaReference fr; + bool memmap = true; + fr.open(_dbFile, memmap); + + bool headerReported = false; + BED bed, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + string sequence; + + _bed->Open(); + while ((bedStatus = _bed->GetNextBed(bed, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + if (headerReported == false) { + PrintHeader(); + headerReported = true; + } + // make sure we are extracting >= 1 bp + if (bed.zeroLength == false) { + size_t seqLength = fr.sequenceLength(bed.chrom); + // make sure this feature will not exceed the end of the chromosome. + if ( (bed.start <= seqLength) && (bed.end <= seqLength) ) + { + // grab the dna at this interval + int length = bed.end - bed.start; + // report the sequence's content + string dna = fr.getSubSequence(bed.chrom, bed.start, length); + // rev comp si necessaire + if ((_forceStrand == true) && (bed.strand == "-")) + reverseComplement(dna); + ReportDnaProfile(bed, dna, length); + bed = nullBed; + } + else + { + cerr << "Feature (" << bed.chrom << ":" << bed.start << "-" << bed.end << ") beyond the length of " + << bed.chrom << " size (" << seqLength << " bp). Skipping." << endl; + } + } + // handle zeroLength + else { + cerr << "Feature (" << bed.chrom << ":" << bed.start+1 << "-" << bed.end-1 << ") has length = 0, Skipping." << endl; + } + bed = nullBed; + } + } + _bed->Close(); +} + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/nucBed/nucBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,55 @@ +/***************************************************************************** + nucBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef NUCBED_H +#define NUCBED_H + +#include "bedFile.h" +#include "sequenceUtils.h" +#include "Fasta.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class NucBed { + +public: + + // constructor + NucBed(string &dbFile, string &bedFile, bool printSeq, + bool hasPattern, const string &pattern, + bool forceStrand); + // destructor + ~NucBed(void); + + void ProfileDNA(); + + +private: + string _dbFile; + string _bedFile; + bool _printSeq; + bool _hasPattern; + string _pattern; + bool _forceStrand; + + // instance of a bed file class. + BedFile *_bed; + void PrintHeader(void); + void ReportDnaProfile(const BED& bed, const string &sequence, int seqLength); +}; + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/nucBed/nucBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,147 @@ +/***************************************************************************** + nucBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "nucBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "nucBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string fastaDbFile; + string bedFile; + string pattern; + + // checks for existence of parameters + bool haveFastaDb = false; + bool haveBed = false; + bool printSeq = false; + bool hasPattern = false; + bool forceStrand = false; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-fi", 3, parameterLength)) { + if ((i+1) < argc) { + haveFastaDb = true; + fastaDbFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bed", 4, parameterLength)) { + if ((i+1) < argc) { + haveBed = true; + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-seq", 4, parameterLength)) { + printSeq = true; + } + else if(PARAMETER_CHECK("-s", 2, parameterLength)) { + forceStrand = true; + } + else if(PARAMETER_CHECK("-pattern", 8, parameterLength)) { + if ((i+1) < argc) { + hasPattern = true; + pattern = argv[i + 1]; + i++; + } + } + else { + cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + if (!haveFastaDb || !haveBed) { + showHelp = true; + } + + if (!showHelp) { + + NucBed *nuc = new NucBed(fastaDbFile, bedFile, printSeq, hasPattern, pattern, forceStrand); + delete nuc; + + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Profiles the nucleotide content of intervals in a fasta file." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-fi\tInput FASTA file" << endl << endl; + cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl << endl; + cerr << "\t-s\tProfile the sequence according to strand." << endl << endl; + cerr << "\t-seq\tPrint the extracted sequence" << endl << endl; + cerr << "\t-pattern\tReport the number of times a user-defined sequence is observed (case-insensitive)." << endl << endl; + + + cerr << "Output format: " << endl; + cerr << "\tThe following information will be reported after each original BED entry:" << endl; + cerr << "\t 1) %AT content" << endl; + cerr << "\t 2) %GC content" << endl; + cerr << "\t 3) Number of As observed" << endl; + cerr << "\t 4) Number of Cs observed" << endl; + cerr << "\t 5) Number of Gs observed" << endl; + cerr << "\t 6) Number of Ts observed" << endl; + cerr << "\t 7) Number of Ns observed" << endl; + cerr << "\t 8) Number of other bases observed" << endl; + cerr << "\t 9) The length of the explored sequence/interval." << endl; + cerr << "\t 10) The sequence extracted from the FASTA file. (optional, if -seq is used)" << endl; + cerr << "\t 11) The number of times a user defined pattern was observed. (optional, if -pattern is used.)" << endl; + + // end the program here + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/overlap/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,47 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= overlap.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= overlap + + +all: $(PROGRAM) + +.PHONY: all + + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + + + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/overlap/overlap.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,202 @@ +/***************************************************************************** + overlap.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include <vector> +#include <iostream> +#include <fstream> +#include <stdlib.h> + +#include "version.h" +#include "lineFileUtilities.h" +#include "bedFile.h" +using namespace std; + + +// define our program name +#define PROGRAM_NAME "overlap" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + + +// function declarations +void ShowHelp(void); +void DetermineInput(string &inFile, short &s1Col, short &e1Col, short &s2Col, short &e2Col); +void ComputeOverlaps(istream &input, short &s1Col, short &e1Col, short &s2Col, short &e2Col); + +int main(int argc, char* argv[]) { + + // input files + string inFile = "stdin"; + string columns; + + // our configuration variables + bool showHelp = false; + bool haveInFile = true; + bool haveColumns = false; + + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + inFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-cols", 5, parameterLength)) { + haveColumns = true; + columns = argv[i + 1]; + i++; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have an input files + if (!haveInFile ) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i file. " << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + + // Split the column string sent by the user into discrete column numbers + // A comma separated string is expected. + vector<string> posColumns; + Tokenize(columns, posColumns, ","); + + if (posColumns.size() != 4) { + cerr << endl << "*****" << endl << "*****ERROR: Please specify 4, comma-separated position columns. " << endl << "*****" << endl; + ShowHelp(); + } + else { + short s1, e1, s2, e2; + s1 = atoi(posColumns[0].c_str()); + e1 = atoi(posColumns[1].c_str()); + s2 = atoi(posColumns[2].c_str()); + e2 = atoi(posColumns[3].c_str()); + + DetermineInput(inFile, s1, e1, s2, e2); + } + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Computes the amount of overlap (positive values)" << endl; + cerr << "\t or distance (negative values) between genome features" << endl; + cerr << "\t and reports the result at the end of the same line." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input> -cols s1,e1,s2,e2 " << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-i\t" << "Input file. Use \"stdin\" for pipes." << endl << endl; + + cerr << "\t-cols\t" << "Specify the columns (1-based) for the starts and ends of the" << endl; + cerr << "\t\tfeatures for which you'd like to compute the overlap/distance." << endl; + cerr << "\t\tThe columns must be listed in the following order: " << endl << endl; + cerr << "\t\tstart1,end1,start2,end2" << endl << endl; + + cerr << "Example: " << endl; + cerr << "\t$ windowBed -a A.bed -b B.bed -w 10" << endl; + cerr << "\tchr1 10 20 A chr1 15 25 B" << endl; + cerr << "\tchr1 10 20 C chr1 25 35 D" << endl << endl; + cerr << "\t$ windowBed -a A.bed -b B.bed -w 10 | overlap -i stdin -cols 2,3,6,7" << endl; + cerr << "\tchr1 10 20 A chr1 15 25 B 5" << endl; + cerr << "\tchr1 10 20 C chr1 25 35 D -5" << endl; + + // end the program here + exit(1); + +} + + +void DetermineInput(string &inFile, short &s1Col, short &e1Col, short &s2Col, short &e2Col) { + + + if (inFile != "stdin") { // process a file + + ifstream in(inFile.c_str(), ios::in); + if ( !in ) { + cerr << "Error: The requested input file (" << inFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + ComputeOverlaps(in, s1Col, e1Col, s2Col, e2Col); + } + else ComputeOverlaps(cin, s1Col, e1Col, s2Col, e2Col); +} + + +void ComputeOverlaps(istream &input, short &s1Col, short &e1Col, short &s2Col, short &e2Col) { + + int lineNum = 0; + string inLine; + vector<string> inFields; + + int overlap; + + char *s1End, *e1End, *s2End, *e2End; + long s1, e1, s2, e2; + + while (getline(input, inLine)) { + lineNum++; + Tokenize(inLine, inFields); + + if (inFields.size() > 1) { + + // test if columns 2 and 3 are integers. If so, assume BED. + s1 = strtol(inFields[s1Col-1].c_str(), &s1End, 10); + e1 = strtol(inFields[e1Col-1].c_str(), &e1End, 10); + s2 = strtol(inFields[s2Col-1].c_str(), &s2End, 10); + e2 = strtol(inFields[e2Col-1].c_str(), &e2End, 10); + + // strtol will set pointers to the start of the string if non-integral, base 10 + // if they all check out, we have valid numeric columns. Otherwise, complain. + if (s1End != inFields[s1Col-1].c_str() && + e1End != inFields[e1Col-1].c_str() && + s2End != inFields[s2Col-1].c_str() && + e2End != inFields[e2Col-1].c_str()) { + + overlap = overlaps(s1, e1, s2, e2); + printf("%s\t%d\n", inLine.c_str(), overlap); + } + else { + cerr << "One of your columns appears to be non-numeric at line " << lineNum << ". Exiting..." << endl << endl; + exit(1); + } + } + inFields.clear(); + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,52 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ \ + -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= pairToBedMain.cpp pairToBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= pairToBed + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToBed/pairToBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,525 @@ +/***************************************************************************** + pairToBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "pairToBed.h" + + +bool IsCorrectMappingForBEDPE (const BamAlignment &bam) { + + if ( (bam.RefID == bam.MateRefID) && (bam.InsertSize > 0) ) { + return true; + } + else if ( (bam.RefID == bam.MateRefID) && (bam.InsertSize == 0) && bam.IsFirstMate() ) { + return true; + } + else if ( (bam.RefID != bam.MateRefID) && bam.IsFirstMate() ) { + return true; + } + else return false; +} + + +/* + Constructor +*/ + + +BedIntersectPE::BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction, + string searchType, bool sameStrand, bool diffStrand, bool bamInput, + bool bamOutput, bool uncompressedBam, bool useEditDistance) { + + _bedAFilePE = bedAFilePE; + _bedBFile = bedBFile; + _overlapFraction = overlapFraction; + _sameStrand = sameStrand; + _diffStrand = diffStrand; + _useEditDistance = useEditDistance; + _searchType = searchType; + _bamInput = bamInput; + _bamOutput = bamOutput; + _isUncompressedBam = uncompressedBam; + + _bedA = new BedFilePE(bedAFilePE); + _bedB = new BedFile(bedBFile); + + if (_bamInput == false) + IntersectBedPE(); + else + IntersectBamPE(_bedAFilePE); +} + + +/* + Destructor +*/ + +BedIntersectPE::~BedIntersectPE(void) { +} + + + +void BedIntersectPE::FindOverlaps(const BEDPE &a, vector<BED> &hits1, vector<BED> &hits2, const string &type) { + + // list of hits on each end of BEDPE + // that exceed the requested overlap fraction + vector<BED> qualityHits1; + vector<BED> qualityHits2; + + // count of hits on each end of BEDPE + // that exceed the requested overlap fraction + int numOverlapsEnd1 = 0; + int numOverlapsEnd2 = 0; + + // make sure we have a valid chromosome before we search + if (a.chrom1 != ".") { + // Find the quality hits between ***end1*** of the BEDPE and the B BED file + _bedB->FindOverlapsPerBin(a.chrom1, a.start1, a.end1, a.strand1, hits1, _sameStrand, _diffStrand); + + vector<BED>::const_iterator h = hits1.begin(); + vector<BED>::const_iterator hitsEnd = hits1.end(); + for (; h != hitsEnd; ++h) { + + int s = max(a.start1, h->start); + int e = min(a.end1, h->end); + int overlapBases = (e - s); // the number of overlapping bases b/w a and b + int aLength = (a.end1 - a.start1); // the length of a in b.p. + + // is there enough overlap relative to the user's request? (default ~ 1bp) + if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) { + numOverlapsEnd1++; + + if (type == "either") { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*h); + } + else { + qualityHits1.push_back(*h); + } + } + } + } + + + // make sure we have a valid chromosome before we search + if (a.chrom2 != ".") { + // Now find the quality hits between ***end2*** of the BEDPE and the B BED file + _bedB->FindOverlapsPerBin(a.chrom2, a.start2, a.end2, a.strand2, hits2, _sameStrand, _diffStrand); + + vector<BED>::const_iterator h = hits2.begin(); + vector<BED>::const_iterator hitsEnd = hits2.end(); + for (; h != hitsEnd; ++h) { + + int s = max(a.start2, h->start); + int e = min(a.end2, h->end); + int overlapBases = (e - s); // the number of overlapping bases b/w a and b + int aLength = (a.end2 - a.start2); // the length of a in b.p. + + // is there enough overlap relative to the user's request? (default ~ 1bp) + if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) { + numOverlapsEnd2++; + + if (type == "either") { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*h); + } + else { + qualityHits2.push_back(*h); + } + } + } + } + + // Now report the hits depending on what the user has requested. + if (type == "neither") { + if ( (numOverlapsEnd1 == 0) && (numOverlapsEnd2 == 0) ) { + _bedA->reportBedPENewLine(a); + } + } + else if (type == "notboth") { + if ( (numOverlapsEnd1 == 0) && (numOverlapsEnd2 == 0) ) { + _bedA->reportBedPENewLine(a); + } + else if ( (numOverlapsEnd1 > 0) && (numOverlapsEnd2 == 0) ) { + for (vector<BED>::iterator q = qualityHits1.begin(); q != qualityHits1.end(); ++q) { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*q); + } + } + else if ( (numOverlapsEnd1 == 0) && (numOverlapsEnd2 > 0) ) { + for (vector<BED>::iterator q = qualityHits2.begin(); q != qualityHits2.end(); ++q) { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*q); + } + } + } + else if (type == "xor") { + if ( (numOverlapsEnd1 > 0) && (numOverlapsEnd2 == 0) ) { + for (vector<BED>::iterator q = qualityHits1.begin(); q != qualityHits1.end(); ++q) { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*q); + } + } + else if ( (numOverlapsEnd1 == 0) && (numOverlapsEnd2 > 0) ) { + for (vector<BED>::iterator q = qualityHits2.begin(); q != qualityHits2.end(); ++q) { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*q); + } + } + } + else if (type == "both") { + if ( (numOverlapsEnd1 > 0) && (numOverlapsEnd2 > 0) ) { + for (vector<BED>::iterator q = qualityHits1.begin(); q != qualityHits1.end(); ++q) { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*q); + } + for (vector<BED>::iterator q = qualityHits2.begin(); q != qualityHits2.end(); ++q) { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*q); + } + } + } +} + + +bool BedIntersectPE::FindOneOrMoreOverlaps(const BEDPE &a, const string &type) { + + // flags for the existence of hits on each end of BEDPE + // that exceed the requested overlap fraction + bool end1Found = false; + bool end2Found = false; + + // Look for overlaps in end 1 assuming we have an aligned chromosome. + if (a.chrom1 != ".") { + end1Found = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom1, a.start1, a.end1, a.strand1, + _sameStrand, _diffStrand, _overlapFraction); + + // can we bail out without checking end2? + if ((type == "either") && (end1Found == true)) return true; + else if ((type == "neither") && (end1Found == true)) return false; + else if ((type == "notboth") && (end1Found == false)) return true; + else if ((type == "both") && (end1Found == false)) return false; + } + + // Now look for overlaps in end 2 assuming we have an aligned chromosome. + if (a.chrom2 != ".") { + end2Found = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom2, a.start2, a.end2, a.strand2, + _sameStrand, _diffStrand, _overlapFraction); + + if ((type == "either") && (end2Found == true)) return true; + else if ((type == "neither") && (end2Found == true)) return false; + else if ((type == "notboth") && (end2Found == false)) return true; + else if ((type == "both") && (end2Found == false)) return false; + } + + // Now report the hits depending on what the user has requested. + if (type == "notboth") { + if ( (end1Found == false) || (end2Found == false) ) return true; + else return false; + } + else if (type == "either") { + if ( (end1Found == false) && (end2Found == false) ) return false; + } + else if (type == "neither") { + if ( (end1Found == false) && (end2Found == false) ) return true; + else return false; + } + else if (type == "xor") { + if ( (end1Found == true) && (end2Found == false) ) return true; + else if ( (end1Found == false) && (end2Found == true) ) return true; + else return false; + } + else if (type == "both") { + if ( (end1Found == true) && (end2Found == true) ) return true; + return false; + } + return false; +} + + +void BedIntersectPE::FindSpanningOverlaps(const BEDPE &a, vector<BED> &hits, const string &type) { + + // count of hits on _between_ end of BEDPE + // that exceed the requested overlap fraction + int numOverlaps = 0; + CHRPOS spanStart = 0; + CHRPOS spanEnd = 0; + CHRPOS spanLength = 0; + + if ((type == "ispan") || (type == "notispan")) { + spanStart = a.end1; + spanEnd = a.start2; + if (a.end1 > a.start2) { + spanStart = a.end2; + spanEnd = a.start1; + } + } + else if ((type == "ospan") || (type == "notospan")) { + spanStart = a.start1; + spanEnd = a.end2; + if (a.start1 > a.start2) { + spanStart = a.start2; + spanEnd = a.end1; + } + } + spanLength = spanEnd - spanStart; + + // get the hits for the span + _bedB->FindOverlapsPerBin(a.chrom1, spanStart, spanEnd, a.strand1, hits, _sameStrand, _diffStrand); + + vector<BED>::const_iterator h = hits.begin(); + vector<BED>::const_iterator hitsEnd = hits.end(); + for (; h != hitsEnd; ++h) { + + int s = max(spanStart, h->start); + int e = min(spanEnd, h->end); + int overlapBases = (e - s); // the number of overlapping bases b/w a and b + int spanLength = (spanEnd - spanStart); // the length of a in b.p. + + // is there enough overlap relative to the user's request? (default ~ 1bp) + if ( ( (float) overlapBases / (float) spanLength ) >= _overlapFraction ) { + numOverlaps++; + if ((type == "ispan") || (type == "ospan")) { + _bedA->reportBedPETab(a); + _bedB->reportBedNewLine(*h); + } + } + } + + if ( ( (type == "notispan") || (type == "notospan") ) && numOverlaps == 0 ) { + _bedA->reportBedPENewLine(a); + } +} + + +bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE &a, const string &type) { + + int spanStart = 0; + int spanEnd = 0; + int spanLength = 0; + bool overlapFound; + + if ((type == "ispan") || (type == "notispan")) { + spanStart = a.end1; + spanEnd = a.start2; + if (a.end1 > a.start2) { + spanStart = a.end2; + spanEnd = a.start1; + } + } + else if ((type == "ospan") || (type == "notospan")) { + spanStart = a.start1; + spanEnd = a.end2; + if (a.start1 > a.start2) { + spanStart = a.start2; + spanEnd = a.end1; + } + } + spanLength = spanEnd - spanStart; + + overlapFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom1, spanStart, spanEnd, a.strand1, + _sameStrand, _diffStrand, _overlapFraction); + + return overlapFound; +} + + +void BedIntersectPE::IntersectBedPE() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedFileIntoMap(); + + int lineNum = 0; // current input line number + vector<BED> hits, hits1, hits2; // vector of potential hits + + // reserve some space + hits.reserve(100); + hits1.reserve(100); + hits2.reserve(100); + + BEDPE a, nullBedPE; + BedLineStatus bedStatus; + + _bedA->Open(); + while ((bedStatus = _bedA->GetNextBedPE(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + if ( (_searchType == "ispan") || (_searchType == "ospan") || + (_searchType == "notispan") || (_searchType == "notospan") ) { + if (a.chrom1 == a.chrom2) { + FindSpanningOverlaps(a, hits, _searchType); + hits.clear(); + } + } + else { + FindOverlaps(a, hits1, hits2, _searchType); + hits1.clear(); + hits2.clear(); + } + a = nullBedPE; + } + } + _bedA->Close(); +} + + +void BedIntersectPE::IntersectBamPE(string bamFile) { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedFileIntoMap(); + + // open the BAM file + BamReader reader; + BamWriter writer; + reader.Open(bamFile); + + // get header & reference information + string bamHeader = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // open a BAM output to stdout if we are writing BAM + if (_bamOutput == true) { + // set compression mode + BamWriter::CompressionMode compressionMode = BamWriter::Compressed; + if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed; + writer.SetCompressionMode(compressionMode); + // open our BAM writer + writer.Open("stdout", bamHeader, refs); + } + + // track the previous and current sequence + // names so that we can identify blocks of + // alignments for a given read ID. + string prevName, currName; + prevName = currName = ""; + + vector<BamAlignment> alignments; // vector of BAM alignments for a given ID in a BAM file. + alignments.reserve(100); + + _bedA->bedType = 10; // it's a full BEDPE given it's BAM + + // rip through the BAM file and convert each mapped entry to BEDPE + BamAlignment bam1, bam2; + while (reader.GetNextAlignment(bam1)) { + // the alignment must be paired + if (bam1.IsPaired() == true) { + // grab the second alignment for the pair. + reader.GetNextAlignment(bam2); + + // require that the alignments are from the same query + if (bam1.Name == bam2.Name) { + ProcessBamBlock(bam1, bam2, refs, writer); + } + else { + cerr << "*****ERROR: BAM must be sorted by query name. " << endl; + exit(1); + } + } + } + // close up + reader.Close(); + if (_bamOutput == true) { + writer.Close(); + } +} + + +void BedIntersectPE::ProcessBamBlock (const BamAlignment &bam1, const BamAlignment &bam2, + const RefVector &refs, BamWriter &writer) { + + vector<BED> hits, hits1, hits2; // vector of potential hits + hits.reserve(1000); // reserve some space + hits1.reserve(1000); + hits2.reserve(1000); + + bool overlapsFound; // flag to indicate if overlaps were found + + if ( (_searchType == "either") || (_searchType == "xor") || + (_searchType == "both") || (_searchType == "notboth") || + (_searchType == "neither") ) { + + // create a new BEDPE feature from the BAM alignments. + BEDPE a; + ConvertBamToBedPE(bam1, bam2, refs, a); + if (_bamOutput == true) { // BAM output + // write to BAM if correct hits found + overlapsFound = FindOneOrMoreOverlaps(a, _searchType); + if (overlapsFound == true) { + writer.SaveAlignment(bam1); + writer.SaveAlignment(bam2); + } + } + else { // BEDPE output + FindOverlaps(a, hits1, hits2, _searchType); + hits1.clear(); + hits2.clear(); + } + } + else if ( (_searchType == "ispan") || (_searchType == "ospan") ) { + // only look for ispan and ospan when both ends are mapped. + if (bam1.IsMapped() && bam2.IsMapped()) { + // only do an inspan or outspan check if the alignment is intrachromosomal + if (bam1.RefID == bam2.RefID) { + // create a new BEDPE feature from the BAM alignments. + BEDPE a; + ConvertBamToBedPE(bam1, bam2, refs, a); + if (_bamOutput == true) { // BAM output + // look for overlaps, and write to BAM if >=1 were found + overlapsFound = FindOneOrMoreSpanningOverlaps(a, _searchType); + if (overlapsFound == true) { + writer.SaveAlignment(bam1); + writer.SaveAlignment(bam2); + } + } + else { // BEDPE output + FindSpanningOverlaps(a, hits, _searchType); + hits.clear(); + } + } + } + } + else if ( (_searchType == "notispan") || (_searchType == "notospan") ) { + // only look for notispan and notospan when both ends are mapped. + if (bam1.IsMapped() && bam2.IsMapped()) { + // only do an inspan or outspan check if the alignment is intrachromosomal + if (bam1.RefID == bam2.RefID) { + // create a new BEDPE feature from the BAM alignments. + BEDPE a; + ConvertBamToBedPE(bam1, bam2, refs, a); + if (_bamOutput == true) { // BAM output + // write to BAM if there were no overlaps + overlapsFound = FindOneOrMoreSpanningOverlaps(a, _searchType); + if (overlapsFound == false) { + writer.SaveAlignment(bam1); + writer.SaveAlignment(bam2); + } + } + else { // BEDPE output + FindSpanningOverlaps(a, hits, _searchType); + hits.clear(); + } + } + // if inter-chromosomal or orphaned, we know it's not ispan and not ospan + else if (_bamOutput == true) { + writer.SaveAlignment(bam1); + writer.SaveAlignment(bam2); + } + } + // if both ends aren't mapped, we know that it's notispan and not ospan + else if (_bamOutput == true) { + writer.SaveAlignment(bam1); + writer.SaveAlignment(bam2); + } + } +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToBed/pairToBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,161 @@ +/***************************************************************************** + pairToBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef INTERSECTBED_H +#define INTERSECTBED_H + +#include "api/BamReader.h" +#include "api/BamWriter.h" +#include "api/BamAux.h" +using namespace BamTools; + +#include "bedFile.h" +#include "bedFilePE.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + + + +/************************************************** +Helper function protoypes +**************************************************/ +void IsCorrectMappingForBEDPE (const BamAlignment &bam, const RefVector &refs, BEDPE &a); + + + +//************************************************ +// Class methods and elements +//************************************************ +class BedIntersectPE { + +public: + + // constructor + BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction, + string searchType, bool sameStrand, bool diffStrand, bool bamInput, bool bamOutput, bool uncompressedBam, bool useEditDistance); + // destructor + ~BedIntersectPE(void); + + void FindOverlaps(const BEDPE &, vector<BED> &hits1, vector<BED> &hits2, const string &type); + + bool FindOneOrMoreOverlaps(const BEDPE &, const string &type); + + void FindSpanningOverlaps(const BEDPE &a, vector<BED> &hits, const string &type); + bool FindOneOrMoreSpanningOverlaps(const BEDPE &a, const string &type); + + void IntersectBedPE(); + void IntersectBamPE(string bamFile); + + void DetermineBedPEInput(); + +private: + + string _bedAFilePE; + string _bedBFile; + float _overlapFraction; + string _searchType; + bool _sameStrand; + bool _diffStrand; + bool _useEditDistance; + bool _bamInput; + bool _bamOutput; + bool _isUncompressedBam; + + // instance of a paired-end bed file class. + BedFilePE *_bedA; + + // instance of a bed file class. + BedFile *_bedB; + + inline + void ConvertBamToBedPE(const BamAlignment &bam1, const BamAlignment &bam2, const RefVector &refs, BEDPE &a) { + + // initialize BEDPE variables + a.start1 = a.start2 = a.end1 = a.end2 = -1; + a.chrom1 = a.chrom2 = "."; + a.strand1 = a.strand2 = '.'; + uint32_t editDistance1, editDistance2; + editDistance1 = editDistance2 = 0; + + // take the qname from end 1. + a.name = bam1.Name; + + // end 1 + if (bam1.IsMapped()) { + a.chrom1 = refs.at(bam1.RefID).RefName; + a.start1 = bam1.Position; + a.end1 = bam1.GetEndPosition(false, false); + a.strand1 = "+"; + if (bam1.IsReverseStrand()) a.strand1 = "-"; + + // extract the edit distance from the NM tag + // if possible. otherwise, complain. + if (_useEditDistance == true) { + if (bam1.GetTag("NM", editDistance1) == false) { + cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n"; + exit(1); + } + } + } + + // end 2 + if (bam2.IsMapped()) { + a.chrom2 = refs.at(bam2.RefID).RefName; + a.start2 = bam2.Position; + a.end2 = bam2.GetEndPosition(false, false); + a.strand2 = "+"; + if (bam2.IsReverseStrand()) a.strand2 = "-"; + + // extract the edit distance from the NM tag + // if possible. otherwise, complain. + if (_useEditDistance == true) { + if (bam2.GetTag("NM", editDistance2) == false) { + cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n"; + exit(1); + } + } + } + + // swap the ends if necessary + if ( a.chrom1 > a.chrom2 || ((a.chrom1 == a.chrom2) && (a.start1 > a.start2)) ) { + swap(a.chrom1, a.chrom2); + swap(a.start1, a.start2); + swap(a.end1, a.end2); + swap(a.strand1, a.strand2); + } + + // compute the minimum mapping quality b/w the two ends of the pair. + a.score = "0"; + if (_useEditDistance == false) { + if (bam1.IsMapped() == true && bam2.IsMapped() == true) + a.score = ToString(min(bam1.MapQuality, bam2.MapQuality)); + } + // BEDPE using edit distance + else { + if (bam1.IsMapped() == true && bam2.IsMapped() == true) + a.score = ToString((int) (editDistance1 + editDistance2)); + else if (bam1.IsMapped() == true) + a.score = ToString((int) editDistance1); + else if (bam2.IsMapped() == true) + a.score = ToString((int) editDistance2); + } + }; + + inline + void ProcessBamBlock (const BamAlignment &bam1, const BamAlignment &bam2, + const RefVector &refs, + BamWriter &writer); +}; + +#endif /* PEINTERSECTBED_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToBed/pairToBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,237 @@ +/***************************************************************************** + pairToBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "pairToBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "pairToBed" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + + // input arguments + float overlapFraction = 1E-9; + string searchType = "either"; + + // flags to track parameters + bool haveBedA = false; + bool haveBedB = false; + bool haveSearchType = false; + bool haveFraction = false; + bool sameStrand = false; + bool diffStrand = false; + bool useEditDistance = false; + bool inputIsBam = false; + bool outputIsBam = true; + bool uncompressedBam = false; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + outputIsBam = false; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-abam", 5, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + inputIsBam = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) { + outputIsBam = false; + } + else if(PARAMETER_CHECK("-ed", 3, parameterLength)) { + useEditDistance = true; + } + else if(PARAMETER_CHECK("-type", 5, parameterLength)) { + if ((i+1) < argc) { + haveSearchType = true; + searchType = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-f", 2, parameterLength)) { + if ((i+1) < argc) { + haveFraction = true; + overlapFraction = atof(argv[i + 1]); + i++; + } + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + sameStrand = true; + } + else if (PARAMETER_CHECK("-S", 2, parameterLength)) { + diffStrand = true; + } + else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) { + uncompressedBam = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (haveSearchType && (searchType != "either") && (searchType != "neither") && (searchType != "both") + && (searchType != "xor") && (searchType != "notboth") && (searchType != "ispan") + && (searchType != "ospan") && (searchType != "notispan") && (searchType != "notospan")) { + cerr << endl << "*****" << endl << "*****ERROR: Request \"either\" or \"both\" or \"neither\" or \"xor\" or \"notboth\" or \"ispan\" or \"ospan\" or \"notispan\" or \"notospan\"" << endl << "*****" << endl; + showHelp = true; + } + + if ( ((searchType == "ispan") || (searchType == "ospan") || (searchType == "notispan") || (searchType == "notospan")) + && (sameStrand || diffStrand) ) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl; + showHelp = true; + } + + if (useEditDistance && (inputIsBam == false || outputIsBam == true)) { + cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl; + showHelp = true; + } + + if (sameStrand && diffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl; + showHelp = true; + } + if (!showHelp) { + + BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction, + searchType, sameStrand, diffStrand, inputIsBam, + outputIsBam, uncompressedBam, useEditDistance); + delete bi; + return 0; + } + else { + ShowHelp(); + } +} + + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bedpe> -b <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl; + cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl; + + cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl; + cerr << "\t\tis to write output in BAM when using -abam." << endl << endl; + + cerr << "\t-bedpe\t" << "When using BAM input (-abam), write output as BEDPE. The default" << endl; + cerr << "\t\tis to write output in BAM when using -abam." << endl << endl; + + cerr << "\t-ed\t" << "Use BAM total edit distance (NM tag) for BEDPE score." << endl; + cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl; + cerr << "\t\t of the two mapping qualities for the pair." << endl; + cerr << "\t\t- When -ed is used the total edit distance" << endl; + cerr << "\t\t from the two mates is reported as the score." << endl << endl; + + cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl; + cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl; + + cerr << "\t-s\t" << "Require same strandedness when finding overlaps." << endl; + cerr << "\t\tDefault is to ignore stand." << endl; + cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl; + + cerr << "\t-S\t" << "Require different strandedness when finding overlaps." << endl; + cerr << "\t\tDefault is to ignore stand." << endl; + cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl; + + cerr << "\t-type \t" << "Approach to reporting overlaps between BEDPE and BED." << endl << endl; + cerr << "\t\teither\tReport overlaps if either end of A overlaps B." << endl; + cerr << "\t\t\t- Default." << endl; + + cerr << "\t\tneither\tReport A if neither end of A overlaps B." << endl; + + cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl; + + cerr << "\t\txor\tReport overlaps if one and only one end of A overlaps B." << endl; + + cerr << "\t\tnotboth\tReport overlaps if neither end or one and only one " << endl; + cerr << "\t\t\tend of A overlap B. That is, xor + neither." << endl << endl; + + cerr << "\t\tispan\tReport overlaps between [end1, start2] of A and B." << endl; + cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; + + cerr << "\t\tospan\tReport overlaps between [start1, end2] of A and B." << endl; + cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; + + cerr << "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl; + cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; + + cerr << "\t\tnotospan\tReport A if ospan of A doesn't overlap B." << endl; + cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; + + cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl; + + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToPair/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,44 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= pairToPairMain.cpp pairToPair.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= pairToPair + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToPair/pairToPair.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,216 @@ +/***************************************************************************** + pairToPair.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "pairToPair.h" + + +/* + Constructor +*/ +PairToPair::PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction, + string searchType, bool ignoreStrand, bool reqDiffNames, int slop, bool strandedSlop) { + + _bedAFilePE = bedAFilePE; + _bedBFilePE = bedBFilePE; + _overlapFraction = overlapFraction; + _searchType = searchType; + _ignoreStrand = ignoreStrand; + _reqDiffNames = reqDiffNames; + _slop = slop; + _strandedSlop = strandedSlop; + + _bedA = new BedFilePE(bedAFilePE); + _bedB = new BedFilePE(bedBFilePE); + + IntersectPairs(); +} + + +/* + Destructor +*/ +PairToPair::~PairToPair(void) { +} + + + +void PairToPair::IntersectPairs() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedPEFileIntoMap(); + + int lineNum = 0; + BedLineStatus bedStatus; + BEDPE a, nullBedPE; + + _bedA->Open(); + while ((bedStatus = _bedA->GetNextBedPE(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + // identify overlaps b/w the pairs + FindOverlaps(a); + a = nullBedPE; + } + } + _bedA->Close(); +} +// END IntersectPE + + + +void PairToPair::FindOverlaps(const BEDPE &a) { + // + vector<MATE> hitsA1B1, hitsA1B2, hitsA2B1, hitsA2B2; + + // add the appropriate slop to the starts and ends + int start1 = a.start1; + int end1 = a.end1; + int start2 = a.start2; + int end2 = a.end2; + + if (_strandedSlop == true) { + if (a.strand1 == "+") + end1 += _slop; + else + start1 -= _slop; + if (a.strand2 == "+") + end2 += _slop; + else + start2 -= _slop; + } + else { + (start1 - _slop) >= 0 ? start1 -= _slop : start1 = 0; + (start2 - _slop) >= 0 ? start2 -= _slop : start2 = 0; + end1 += _slop; + end2 += _slop; + } + + // Find the _potential_ hits between each end of A and B + _bedB->FindOverlapsPerBin(1, a.chrom1, start1, end1, a.name, a.strand1, hitsA1B1, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A1 & B1 + _bedB->FindOverlapsPerBin(1, a.chrom2, start2, end2, a.name, a.strand2, hitsA2B1, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A2 & B1 + _bedB->FindOverlapsPerBin(2, a.chrom1, start1, end1, a.name, a.strand1, hitsA1B2, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A1 & B2 + _bedB->FindOverlapsPerBin(2, a.chrom2, start2, end2, a.name, a.strand2, hitsA2B2, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A2 & B2 + + unsigned int matchCount1 = (hitsA1B1.size() + hitsA2B2.size()); + unsigned int matchCount2 = (hitsA2B1.size() + hitsA1B2.size()); + + + // report the fact that no hits were found iff _searchType is neither. + if ((matchCount1 == 0) && (matchCount2 == 0) && (_searchType == "neither")) { + _bedA->reportBedPENewLine(a); + } + else if (_searchType == "both") { + bool found1 = false; + bool found2 = false; + if ((hitsA1B1.size() > 0) || (hitsA2B2.size() > 0)) + found1 = FindHitsOnBothEnds(a, hitsA1B1, hitsA2B2); + if ((hitsA2B1.size() > 0) || (hitsA1B2.size() > 0)) + found2 = FindHitsOnBothEnds(a, hitsA2B1, hitsA1B2); + } + else if (_searchType == "notboth") { + bool found1 = false; + bool found2 = false; + if ((hitsA1B1.size() > 0) || (hitsA2B2.size() > 0)) + found1 = FindHitsOnBothEnds(a, hitsA1B1, hitsA2B2); + if ((hitsA2B1.size() > 0) || (hitsA1B2.size() > 0)) + found2 = FindHitsOnBothEnds(a, hitsA2B1, hitsA1B2); + if (found1 == false && found2 == false) + _bedA->reportBedPENewLine(a); + } + else if (_searchType == "either") { + FindHitsOnEitherEnd(a, hitsA1B1, hitsA2B2); + FindHitsOnEitherEnd(a, hitsA2B1, hitsA1B2); + } +} + + +bool PairToPair::FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityHitsEnd1, + const vector<MATE> &qualityHitsEnd2) { + + map<unsigned int, vector<MATE>, less<int> > hitsMap; + + for (vector<MATE>::const_iterator h = qualityHitsEnd1.begin(); h != qualityHitsEnd1.end(); ++h) { + hitsMap[h->lineNum].push_back(*h); + } + for (vector<MATE>::const_iterator h = qualityHitsEnd2.begin(); h != qualityHitsEnd2.end(); ++h) { + hitsMap[h->lineNum].push_back(*h); + } + + + bool bothFound = false; + for (map<unsigned int, vector<MATE>, less<unsigned int> >::iterator m = hitsMap.begin(); m != hitsMap.end(); ++m) { + + // hits on both sides + if (m->second.size() >= 2) { + bothFound = true; + MATE b1 = m->second[0]; + MATE b2 = m->second[1]; + + if (_searchType == "both") { + _bedA->reportBedPETab(a); + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", b1.bed.chrom.c_str(), b1.bed.start, b1.bed.end, + b2.bed.chrom.c_str(), b2.bed.start, b2.bed.end, + b1.bed.name.c_str(), b1.bed.score.c_str(), + b1.bed.strand.c_str(), b2.bed.strand.c_str()); + for (size_t i = 0; i < b1.bed.otherFields.size(); ++i) + printf("\t%s", b1.bed.otherFields[i].c_str()); + printf("\n"); + } + } + } + return bothFound; +} + + +void PairToPair::FindHitsOnEitherEnd(const BEDPE &a, const vector<MATE> &qualityHitsEnd1, + const vector<MATE> &qualityHitsEnd2) { + + map<unsigned int, vector<MATE>, less<int> > hitsMap; + + for (vector<MATE>::const_iterator h = qualityHitsEnd1.begin(); h != qualityHitsEnd1.end(); ++h) { + hitsMap[h->lineNum].push_back(*h); + } + for (vector<MATE>::const_iterator h = qualityHitsEnd2.begin(); h != qualityHitsEnd2.end(); ++h) { + hitsMap[h->lineNum].push_back(*h); + } + + for (map<unsigned int, vector<MATE>, less<unsigned int> >::iterator m = hitsMap.begin(); m != hitsMap.end(); ++m) { + if (m->second.size() >= 1) { + + if ((m->second.size()) == 2) { + MATE b1 = m->second[0]; + MATE b2 = m->second[1]; + + _bedA->reportBedPETab(a); + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", b1.bed.chrom.c_str(), b1.bed.start, b1.bed.end, + b2.bed.chrom.c_str(), b2.bed.start, b2.bed.end, + b1.bed.name.c_str(), b1.bed.score.c_str(), + b1.bed.strand.c_str(), b2.bed.strand.c_str()); + for (size_t i = 0; i < b1.bed.otherFields.size(); ++i) + printf("\t%s", b1.bed.otherFields[i].c_str()); + printf("\n"); + } + else { + MATE b1 = m->second[0]; + + _bedA->reportBedPETab(a); + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", b1.bed.chrom.c_str(), b1.bed.start, b1.bed.end, + b1.mate->bed.chrom.c_str(), b1.mate->bed.start, b1.mate->bed.end, + b1.bed.name.c_str(), b1.bed.score.c_str(), + b1.bed.strand.c_str(), b1.mate->bed.strand.c_str()); + for (size_t i = 0; i < b1.bed.otherFields.size(); ++i) + printf("\t%s", b1.bed.otherFields[i].c_str()); + printf("\n"); + } + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToPair/pairToPair.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,76 @@ +/***************************************************************************** + pairToPair.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef PAIRTOPAIR_H +#define PAIRTOPAIR_H + +#include "bedFile.h" +#include "bedFilePE.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + + + +//************************************************ +// Class methods and elements +//************************************************ +class PairToPair { + +public: + + // constructor + PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction, + string searchType, bool ignoreStrand, bool reqDiffNames, int slop, bool strandedSlop); + + // destructor + ~PairToPair(void); + + void IntersectPairs(); + + +private: + + string _bedAFilePE; + string _bedBFilePE; + + float _overlapFraction; + string _searchType; + bool _ignoreStrand; + bool _reqDiffNames; + int _slop; + bool _strandedSlop; + + // instance of a paired-end bed file class. + BedFilePE *_bedA; + + // instance of a bed file class. + BedFilePE *_bedB; + + // methods + // void FindOverlaps(const BEDPE &a, vector<MATE> &hitsA1B1, vector<MATE> &hitsA1B2, + // vector<MATE> &hitsA2B1, vector<MATE> &hitsA2B2); + void FindOverlaps(const BEDPE &a); + + void FindQualityHitsBetweenEnds(CHRPOS start, CHRPOS end, + const vector<MATE> &hits, vector<MATE> &qualityHits, int &numOverlaps); + + bool FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityHitsEnd1, + const vector<MATE> &qualityHitsEnd2); + + void FindHitsOnEitherEnd(const BEDPE &a, const vector<MATE> &qualityHitsEnd1, + const vector<MATE> &qualityHitsEnd2); + +}; + +#endif /* PAIRTOPAIR_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/pairToPair/pairToPairMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,188 @@ +/***************************************************************************** + pairToPairMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "pairToPair.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "pairToPair" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + + // input arguments + float overlapFraction = 1E-9; + int slop = 0; + string searchType = "both"; + + // flags to track parameters + bool haveBedA = false; + bool haveBedB = false; + bool haveSearchType = false; + bool haveFraction = false; + bool ignoreStrand = false; + bool requireDifferentNames = false; + bool haveSlop = false; + bool strandedSlop = false; + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-type", 5, parameterLength)) { + if ((i+1) < argc) { + haveSearchType = true; + searchType = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-f", 2, parameterLength)) { + if ((i+1) < argc) { + haveFraction = true; + overlapFraction = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-slop", 5, parameterLength)) { + if ((i+1) < argc) { + haveSlop = true; + slop = atoi(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-ss", 3, parameterLength)) { + strandedSlop = true; + } + else if(PARAMETER_CHECK("-rdn", 4, parameterLength)) { + requireDifferentNames = true; + } + else if(PARAMETER_CHECK("-is", 3, parameterLength)) { + ignoreStrand = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (haveSearchType && (searchType != "neither") && (searchType != "both") && (searchType != "either") && (searchType != "notboth")) { + cerr << endl << "*****" << endl << "*****ERROR: Request \"both\",\"neither\",\"either\",or \"notboth\"" << endl << "*****" << endl; + showHelp = true; + } + + if (strandedSlop == true && haveSlop == false) { + cerr << endl << "*****" << endl << "*****ERROR: Need a -slop value if requesting -ss." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + + PairToPair *bi = new PairToPair(bedAFile, bedBFile, overlapFraction, searchType, + ignoreStrand, requireDifferentNames, slop, strandedSlop); + delete bi; + return 0; + } + else { + ShowHelp(); + } +} + + +void ShowHelp(void) { + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Report overlaps between two paired-end BED files (BEDPE)." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <BEDPE> -b <BEDPE>" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl; + cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl; + + cerr << "\t-type \t" << "Approach to reporting overlaps between A and B." << endl << endl; + cerr << "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl; + cerr << "\t\teither\tReport overlaps if either ends of A overlap B." << endl; + cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl; + cerr << "\t\tnotboth\tReport overlaps if one or neither of ends of A overlap B." << endl; + + cerr << "\t\t- Default = both." << endl << endl; + + cerr << "\t-slop \t" << "The amount of slop (in b.p.). to be added to each footprint." << endl; + cerr << "\t\t*Note*: Slop is subtracted from start1 and start2 and added to end1 and end2." << endl << endl; + + cerr << "\t-ss\t" << "Add slop based to each BEDPE footprint based on strand." << endl; + cerr << "\t\t- If strand is \"+\", slop is only added to the end coordinates." << endl; + cerr << "\t\t- If strand is \"-\", slop is only added to the start coordinates." << endl; + cerr << "\t\t- By default, slop is added in both directions." << endl << endl; + + cerr << "\t-is\t" << "Ignore strands when searching for overlaps." << endl; + cerr << "\t\t- By default, strands are enforced." << endl << endl; + + cerr << "\t-rdn\t" << "Require the hits to have different names (i.e. avoid self-hits)." << endl; + cerr << "\t\t- By default, same names are allowed." << endl << endl; + + + cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl; + + // end the program here + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/shuffleBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,50 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= shuffleBedMain.cpp shuffleBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= shuffleBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/shuffleBed/shuffleBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,244 @@ +/***************************************************************************** + shuffleBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "shuffleBed.h" + + +BedShuffle::BedShuffle(string &bedFile, string &genomeFile, string &excludeFile, string &includeFile, + bool haveSeed, bool haveExclude, bool haveInclude, bool sameChrom, + float overlapFraction, int seed) { + + _bedFile = bedFile; + _genomeFile = genomeFile; + _excludeFile = excludeFile; + _includeFile = includeFile; + _sameChrom = sameChrom; + _haveExclude = haveExclude; + _haveInclude = haveInclude; + _overlapFraction = overlapFraction; + _haveSeed = haveSeed; + + + // use the supplied seed for the random + // number generation if given. else, + // roll our own. + if (_haveSeed) { + _seed = seed; + srand(seed); + } + else { + // thanks to Rob Long for the tip. + _seed = (unsigned)time(0)+(unsigned)getpid(); + srand(_seed); + } + + _bed = new BedFile(bedFile); + _genome = new GenomeFile(genomeFile); + _chroms = _genome->getChromList(); + _numChroms = _genome->getNumberOfChroms(); + + if (_haveExclude) { + _exclude = new BedFile(excludeFile); + _exclude->loadBedFileIntoMap(); + } + + if (_haveInclude) { + _include = new BedFile(includeFile); + _include->loadBedFileIntoMapNoBin(); + + _numIncludeChroms = 0; + masterBedMapNoBin::const_iterator it = _include->bedMapNoBin.begin(); + masterBedMapNoBin::const_iterator itEnd = _include->bedMapNoBin.end(); + for(; it != itEnd; ++it) { + _includeChroms.push_back(it->first); + _numIncludeChroms++; + } + } + + if (_haveExclude == true && _haveInclude == false) + ShuffleWithExclusions(); + else if (_haveExclude == false && _haveInclude == true) + ShuffleWithInclusions(); + else + Shuffle(); +} + + +BedShuffle::~BedShuffle(void) { + +} + + +void BedShuffle::Shuffle() { + + int lineNum = 0; + BED bedEntry, nullBed; // used to store the current BED line from the BED file. + BedLineStatus bedStatus; + + _bed->Open(); + while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + ChooseLocus(bedEntry); + _bed->reportBedNewLine(bedEntry); + bedEntry = nullBed; + } + } + _bed->Close(); +} + + + +void BedShuffle::ShuffleWithExclusions() { + + int lineNum = 0; + BED bedEntry, nullBed; // used to store the current BED line from the BED file. + BedLineStatus bedStatus; + + _bed->Open(); + while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + // keep looking as long as the chosen + // locus happens to overlap with regions + // that the user wishes to exclude. + int tries = 0; + bool haveOverlap = false; + do + { + // choose a new locus + ChooseLocus(bedEntry); + haveOverlap = _exclude->FindOneOrMoreOverlapsPerBin(bedEntry.chrom, bedEntry.start, bedEntry.end, + bedEntry.strand, false, _overlapFraction); + tries++; + } while ((haveOverlap == true) && (tries <= MAX_TRIES)); + + + if (tries > MAX_TRIES) { + cerr << "Error, line " << lineNum << ": tried " << MAX_TRIES << " potential loci for entry, but could not avoid excluded regions. Ignoring entry and moving on." << endl; + } + else { + _bed->reportBedNewLine(bedEntry); + } + } + bedEntry = nullBed; + } + _bed->Close(); +} + + +void BedShuffle::ShuffleWithInclusions() { + + int lineNum = 0; + BED bedEntry, nullBed; // used to store the current BED line from the BED file. + BedLineStatus bedStatus; + + _bed->Open(); + while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + // choose a new locus + ChooseLocusFromInclusionFile(bedEntry); + _bed->reportBedNewLine(bedEntry); + } + bedEntry = nullBed; + } + _bed->Close(); +} + + +void BedShuffle::ChooseLocus(BED &bedEntry) { + + string chrom = bedEntry.chrom; + CHRPOS start = bedEntry.start; + CHRPOS end = bedEntry.end; + CHRPOS length = end - start; + + string randomChrom; + CHRPOS randomStart; + CHRPOS chromSize; + + if (_sameChrom == false) { + randomChrom = _chroms[rand() % _numChroms]; + chromSize = _genome->getChromSize(randomChrom); + randomStart = rand() % chromSize; + bedEntry.chrom = randomChrom; + bedEntry.start = randomStart; + bedEntry.end = randomStart + length; + } + else { + chromSize = _genome->getChromSize(chrom); + randomStart = rand() % chromSize; + bedEntry.start = randomStart; + bedEntry.end = randomStart + length; + } + + // ensure that the chosen location doesn't go past + // the length of the chromosome. if so, keep looking + // for a new spot. + while (bedEntry.end > chromSize) { + if (_sameChrom == false) { + randomChrom = _chroms[rand() % _numChroms]; + chromSize = _genome->getChromSize(randomChrom); + randomStart = rand() % chromSize; + bedEntry.chrom = randomChrom; + bedEntry.start = randomStart; + bedEntry.end = randomStart + length; + } + else { + chromSize = _genome->getChromSize(chrom); + randomStart = rand() % chromSize; + bedEntry.start = randomStart; + bedEntry.end = randomStart + length; + } + } +} + + +void BedShuffle::ChooseLocusFromInclusionFile(BED &bedEntry) { + + string chrom = bedEntry.chrom; + CHRPOS length = bedEntry.end - bedEntry.start; + + string randomChrom; + CHRPOS randomStart; + BED includeInterval; + + if (_sameChrom == false) { + + // grab a random chromosome from the inclusion file. + randomChrom = _includeChroms[rand() % _numIncludeChroms]; + // get the number of inclusion intervals for that chrom + size_t size = _include->bedMapNoBin[randomChrom].size(); + // grab a random interval on the chosen chromosome. + size_t interval = rand() % size; + // retreive a ranom -incl interval on the selected chrom + includeInterval = _include->bedMapNoBin[randomChrom][interval]; + + bedEntry.chrom = randomChrom; + } + else { + // get the number of inclusion intervals for the original chrom + size_t size = _include->bedMapNoBin[chrom].size(); + // grab a random interval on the chosen chromosome. + includeInterval = _include->bedMapNoBin[chrom][rand() % size]; + } + + randomStart = includeInterval.start + rand() % (includeInterval.size()); + bedEntry.start = randomStart; + bedEntry.end = randomStart + length; + + // use recursion to ensure that the chosen location + // doesn't go past the end of the chrom + if (bedEntry.end > ((size_t) _genome->getChromSize(chrom))) { + //bedEntry.end = _genome->getChromSize(chrom); + ChooseLocusFromInclusionFile(bedEntry); + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/shuffleBed/shuffleBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,76 @@ +/***************************************************************************** + shuffleBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" +#include "genomeFile.h" + +#include <vector> +#include <iostream> +#include <fstream> +#include <map> +#include <cstdlib> +#include <ctime> +#include <sys/time.h> +#include <unistd.h> +#include <sys/types.h> +using namespace std; + +const int MAX_TRIES = 1000000; + +//************************************************ +// Class methods and elements +//************************************************ +class BedShuffle { + +public: + + // constructor + BedShuffle(string &bedFile, string &genomeFile, string &excludeFile, string &includeFile, + bool haveSeed, bool haveExclude, bool haveInclude, bool sameChrom, + float overlapFraction, int seed); + + // destructor + ~BedShuffle(void); + +private: + + string _bedFile; + string _genomeFile; + string _excludeFile; + string _includeFile; + float _overlapFraction; + int _seed; + bool _sameChrom; + bool _haveExclude; + bool _haveInclude; + bool _haveSeed; + + + // The BED file from which to compute coverage. + BedFile *_bed; + BedFile *_exclude; + BedFile *_include; + + GenomeFile *_genome; + + vector<string> _chroms; + int _numChroms; + vector<string> _includeChroms; + int _numIncludeChroms; + + // methods + void Shuffle(); + void ShuffleWithExclusions(); + void ShuffleWithInclusions(); + + void ChooseLocus(BED &); + void ChooseLocusFromInclusionFile(BED &); +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/shuffleBed/shuffleBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,188 @@ +/***************************************************************************** + shuffleBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "shuffleBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "shuffleBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + string excludeFile; + string includeFile; + string genomeFile; + + bool haveBed = true; + bool haveGenome = false; + bool haveExclude = false; + bool haveInclude = false; + bool haveSeed = false; + float overlapFraction = 0.0; + int seed = -1; + bool sameChrom = false; + + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-excl", 5, parameterLength)) { + if ((i+1) < argc) { + haveExclude = true; + excludeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-incl", 5, parameterLength)) { + if ((i+1) < argc) { + haveInclude = true; + includeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-seed", 5, parameterLength)) { + if ((i+1) < argc) { + haveSeed = true; + seed = atoi(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-chrom", 6, parameterLength)) { + sameChrom = true; + } + else if(PARAMETER_CHECK("-f", 2, parameterLength)) { + if ((i+1) < argc) { + overlapFraction = atof(argv[i + 1]); + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed || !haveGenome) { + cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl; + showHelp = true; + } + + if (haveInclude && haveExclude) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot use -incl and -excl together." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedShuffle *bc = new BedShuffle(bedFile, genomeFile, excludeFile, includeFile, + haveSeed, haveExclude, haveInclude, sameChrom, + overlapFraction, seed); + delete bc; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Randomly permute the locations of a feature file among a genome." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-excl\t" << "A BED/GFF/VCF file of coordinates in which features in -i" << endl; + cerr << "\t\tshould not be placed (e.g. gaps.bed)." << endl << endl; + + cerr << "\t-incl\t" << "Instead of randomly placing features in a genome, the -incl" << endl; + cerr << "\t\toptions defines a BED/GFF/VCF file of coordinates in which " << endl; + cerr << "\t\tfeatures in -i should be randomly placed (e.g. genes.bed). " << endl << endl; + + cerr << "\t-chrom\t" << "Keep features in -i on the same chromosome."<< endl; + cerr << "\t\t- By default, the chrom and position are randomly chosen." << endl << endl; + + cerr << "\t-seed\t" << "Supply an integer seed for the shuffling." << endl; + cerr << "\t\t- By default, the seed is chosen automatically." << endl; + cerr << "\t\t- (INTEGER)" << endl << endl; + + cerr << "\t-f\t" << "Maximum overlap (as a fraction of the -i feature) with an -excl" << endl; + cerr << "\t\tfeature that is tolerated before searching for a new, " << endl; + cerr << "\t\trandomized locus. For example, -f 0.10 allows up to 10%" << endl; + cerr << "\t\tof a randomized feature to overlap with a given feature" << endl; + cerr << "\t\tin the -excl file. **Cannot be used with -incl file.**" << endl; + cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl; + cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl; + cerr << "\t <chromName><TAB><chromSize>" << endl << endl; + cerr << "\tFor example, Human (hg19):" << endl; + cerr << "\tchr1\t249250621" << endl; + cerr << "\tchr2\t243199373" << endl; + cerr << "\t..." << endl; + cerr << "\tchr18_gl000207_random\t4262" << endl << endl; + + + cerr << "Tips: " << endl; + cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl; + cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl; + cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl; + cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl; + + + // end the program here + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/slopBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,50 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= slopBedMain.cpp slopBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= slopBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/slopBed/slopBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,91 @@ +/***************************************************************************** + slopBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "slopBed.h" + + +BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional) { + + _bedFile = bedFile; + _genomeFile = genomeFile; + _forceStrand = forceStrand; + _leftSlop = leftSlop; + _rightSlop = rightSlop; + _fractional = fractional; + + _bed = new BedFile(bedFile); + _genome = new GenomeFile(genomeFile); + + // get going, slop it up. + SlopBed(); +} + + +BedSlop::~BedSlop(void) { + +} + + +void BedSlop::SlopBed() { + + int lineNum = 0; + BED bedEntry, nullBed; // used to store the current BED line from the BED file. + BedLineStatus bedStatus; + + _bed->Open(); + bedStatus = _bed->GetNextBed(bedEntry, lineNum); + while (bedStatus != BED_INVALID) { + if (bedStatus == BED_VALID) { + if (_fractional == false) { + AddSlop(bedEntry, (int) _leftSlop, (int) _rightSlop); + } + else { + int leftSlop = (int) (_leftSlop * bedEntry.size()); + int rightSlop = (int) (_rightSlop * bedEntry.size()); + AddSlop(bedEntry, leftSlop, rightSlop); + } + _bed->reportBedNewLine(bedEntry); + bedEntry = nullBed; + } + bedStatus = _bed->GetNextBed(bedEntry, lineNum); + } + _bed->Close(); +} + + +void BedSlop::AddSlop(BED &bed, int leftSlop, int rightSlop) { + + // special handling if the BED entry is on the negative + // strand and the user cares about strandedness. + CHRPOS chromSize = _genome->getChromSize(bed.chrom); + + if ( (_forceStrand) && (bed.strand == "-") ) { + // inspect the start + if ( (static_cast<int>(bed.start) - rightSlop) > 0 ) bed.start -= rightSlop; + else bed.start = 0; + + // inspect the start + if ( (static_cast<int>(bed.end) + leftSlop) <= static_cast<int>(chromSize)) bed.end += leftSlop; + else bed.end = chromSize; + } + else { + // inspect the start + if ( (static_cast<int>(bed.start) - leftSlop) > 0) bed.start -= leftSlop; + else bed.start = 0; + + // inspect the end + if ( (static_cast<int>(bed.end) + rightSlop) <= static_cast<int>(chromSize)) bed.end += rightSlop; + else bed.end = chromSize; + } +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/slopBed/slopBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,59 @@ +/***************************************************************************** + slopBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ + +#include "bedFile.h" +#include "genomeFile.h" + +#include <vector> +#include <iostream> +#include <fstream> +#include <map> +#include <cstdlib> +#include <ctime> +using namespace std; + + +//************************************************ +// Class methods and elements +//************************************************ +class BedSlop { + +public: + + // constructor + BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional); + + // destructor + ~BedSlop(void); + + + +private: + + string _bedFile; + string _genomeFile; + + bool _forceStrand; + float _leftSlop; + float _rightSlop; + bool _fractional; + + BedFile *_bed; + GenomeFile *_genome; + + // methods + + void SlopBed(); + + // method to add requested "slop" to a single BED entry + void AddSlop(BED &bed, int leftSlop, int rightSlop); +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/slopBed/slopBedMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,190 @@ +/***************************************************************************** + slopBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "slopBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "slopBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + string genomeFile; + + bool haveBed = true; + bool haveGenome = false; + bool haveLeft = false; + bool haveRight = false; + bool haveBoth = false; + + bool forceStrand = false; + float leftSlop = 0.0; + float rightSlop = 0.0; + bool fractional = false; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-l", 2, parameterLength)) { + if ((i+1) < argc) { + haveLeft = true; + leftSlop = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-r", 2, parameterLength)) { + if ((i+1) < argc) { + haveRight = true; + rightSlop = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBoth = true; + leftSlop = atof(argv[i + 1]); + rightSlop = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-s", 2, parameterLength)) { + forceStrand = true; + } + else if(PARAMETER_CHECK("-pct", 4, parameterLength)) { + fractional = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed || !haveGenome) { + cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl; + showHelp = true; + } + if (!haveLeft && !haveRight && !haveBoth) { + cerr << endl << "*****" << endl << "*****ERROR: Need -l and -r together or -b alone. " << endl << "*****" << endl; + showHelp = true; + } + if ((!haveLeft && haveRight) || (haveLeft && !haveRight)) { + cerr << endl << "*****" << endl << "*****ERROR: Need both -l and -r. " << endl << "*****" << endl; + showHelp = true; + } + if (forceStrand && (!(haveLeft) || !(haveRight))) { + cerr << endl << "*****" << endl << "*****ERROR: Must supply -l and -r with -s. " << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional); + delete bc; + + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Add requested base pairs of \"slop\" to each feature." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome> [-b <int> or (-l and -r)]" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-b\t" << "Increase the BED/GFF/VCF entry by -b base pairs in each direction." << endl; + cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl; + + cerr << "\t-l\t" << "The number of base pairs to subtract from the start coordinate." << endl; + cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl; + + cerr << "\t-r\t" << "The number of base pairs to add to the end coordinate." << endl; + cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl; + + cerr << "\t-s\t" << "Define -l and -r based on strand." << endl; + cerr << "\t\tE.g. if used, -l 500 for a negative-stranded feature, " << endl; + cerr << "\t\tit will add 500 bp downstream. Default = false." << endl << endl; + + cerr << "\t-pct\t" << "Define -l and -r as a fraction of the feature's length." << endl; + cerr << "\t\tE.g. if used on a 1000bp feature, -l 0.50, " << endl; + cerr << "\t\twill add 500 bp \"upstream\". Default = false." << endl << endl; + + cerr << "Notes: " << endl; + cerr << "\t(1) Starts will be set to 0 if options would force it below 0." << endl; + cerr << "\t(2) Ends will be set to the chromosome length if requested slop would" << endl; + cerr << "\tforce it above the max chrom length." << endl; + + cerr << "\t(3) The genome file should tab delimited and structured as follows:" << endl; + cerr << "\n\t<chromName><TAB><chromSize>" << endl << endl; + cerr << "\tFor example, Human (hg19):" << endl; + cerr << "\tchr1\t249250621" << endl; + cerr << "\tchr2\t243199373" << endl; + cerr << "\t..." << endl; + cerr << "\tchr18_gl000207_random\t4262" << endl << endl; + + + cerr << "Tips: " << endl; + cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl; + cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl; + cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl; + cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl; + + + // end the program here + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/sortBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,43 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= sortMain.cpp sortBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= sortBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/sortBed/sortBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,201 @@ +/***************************************************************************** + sortBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "sortBed.h" + +// +// Constructor +// +BedSort::BedSort(string &bedFile) { + _bedFile = bedFile; + _bed = new BedFile(bedFile); +} + +// +// Destructor +// +BedSort::~BedSort(void) { +} + + +void BedSort::SortBed() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + // loop through each chromosome and merge their BED entries + for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) { + + // bedList is already sorted by start position. + vector<BED> bedList = m->second; + + for (unsigned int i = 0; i < bedList.size(); ++i) { + _bed->reportBedNewLine(bedList[i]); + } + } +} + + +void BedSort::SortBedBySizeAsc() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + vector<BED> masterList; + masterList.reserve(1000000); + + // loop through each chromosome and merge their BED entries + for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) { + + // bedList is already sorted by start position. + vector<BED> bedList = m->second; + + // add the entries from this chromosome to the current list + for (unsigned int i = 0; i < m->second.size(); ++i) { + masterList.push_back(m->second[i]); + } + } + + // sort the master list by size (asc.) + sort(masterList.begin(), masterList.end(), sortBySizeAsc); + + // report the entries in ascending order + for (unsigned int i = 0; i < masterList.size(); ++i) { + _bed->reportBedNewLine(masterList[i]); + } +} + + +void BedSort::SortBedBySizeDesc() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + vector<BED> masterList; + masterList.reserve(1000000); + + // loop through each chromosome and merge their BED entries + for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) { + + // bedList is already sorted by start position. + vector<BED> bedList = m->second; + + // add the entries from this chromosome to the current list + for (unsigned int i = 0; i < m->second.size(); ++i) { + masterList.push_back(m->second[i]); + } + } + + // sort the master list by size (asc.) + sort(masterList.begin(), masterList.end(), sortBySizeDesc); + + // report the entries in ascending order + for (unsigned int i = 0; i < masterList.size(); ++i) { + _bed->reportBedNewLine(masterList[i]); + } +} + +void BedSort::SortBedByChromThenSizeAsc() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + // loop through each chromosome and merge their BED entries + for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) { + + // bedList is already sorted by start position. + vector<BED> bedList = m->second; + sort(bedList.begin(), bedList.end(), sortBySizeAsc); + + for (unsigned int i = 0; i < bedList.size(); ++i) { + _bed->reportBedNewLine(bedList[i]); + } + } +} + + +void BedSort::SortBedByChromThenSizeDesc() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + // loop through each chromosome and merge their BED entries + for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) { + + // bedList is already sorted by start position. + vector<BED> bedList = m->second; + + sort(bedList.begin(), bedList.end(), sortBySizeDesc); + + for (unsigned int i = 0; i < bedList.size(); ++i) { + _bed->reportBedNewLine(bedList[i]); + } + } +} + + +void BedSort::SortBedByChromThenScoreAsc() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + if (_bed->bedType >= 5) { + // loop through each chromosome and merge their BED entries + for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) { + + // bedList is already sorted by start position. + vector<BED> bedList = m->second; + sort(bedList.begin(), bedList.end(), sortByScoreAsc); + + for (unsigned int i = 0; i < bedList.size(); ++i) { + _bed->reportBedNewLine(bedList[i]); + } + } + } + else { + cerr << "Error: Requested a sort by score, but your BED file does not appear to be in BED 5 format or greater. Exiting." << endl; + exit(1); + } +} + + +void BedSort::SortBedByChromThenScoreDesc() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bed->loadBedFileIntoMapNoBin(); + + if (_bed->bedType >= 5) { + // loop through each chromosome and merge their BED entries + for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) { + + // bedList is already sorted by start position. + vector<BED> bedList = m->second; + sort(bedList.begin(), bedList.end(), sortByScoreDesc); + + for (unsigned int i = 0; i < bedList.size(); ++i) { + _bed->reportBedNewLine(bedList[i]); + } + } + } + else { + cerr << "Error: Requested a sort by score, but your BED file does not appear to be in BED 5 format or greater. Exiting." << endl; + exit(1); + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/sortBed/sortBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,50 @@ +/***************************************************************************** + sortBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" +#include <vector> +#include <algorithm> +#include <iostream> +#include <fstream> + +using namespace std; + + +//************************************************ +// Class methods and elements +//************************************************ +class BedSort { + +public: + + // constructor + BedSort(string &); + + // destructor + ~BedSort(void); + + void SortBed(); // the default. sorts by chrom (asc.) then by start (asc.) + void SortBedBySizeAsc(); + void SortBedBySizeDesc(); + void SortBedByChromThenSizeAsc(); + void SortBedByChromThenSizeDesc(); + void SortBedByChromThenScoreAsc(); + void SortBedByChromThenScoreDesc(); + +private: + string _bedFile; + + // instance of a bed file class. + BedFile *_bed; + + // methods + +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/sortBed/sortMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,157 @@ +/***************************************************************************** + sortBedMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "sortBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "sortBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedFile = "stdin"; + bool haveBed = true; + int sortChoices = 0; + + bool sortBySizeAsc = false; + bool sortBySizeDesc = false; + bool sortByChromThenSizeAsc = false; + bool sortByChromThenSizeDesc = false; + bool sortByChromThenScoreAsc = false; + bool sortByChromThenScoreDesc = false; + + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + bedFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-sizeA", 6, parameterLength)) { + sortBySizeAsc = true; + sortChoices++; + } + else if(PARAMETER_CHECK("-sizeD", 6, parameterLength)) { + sortBySizeDesc = true; + sortChoices++; + } + else if(PARAMETER_CHECK("-chrThenSizeA", 13, parameterLength)) { + sortByChromThenSizeAsc = true; + sortChoices++; + } + else if(PARAMETER_CHECK("-chrThenSizeD", 13, parameterLength)) { + sortByChromThenSizeDesc = true; + sortChoices++; + } + else if(PARAMETER_CHECK("-chrThenScoreA", 14, parameterLength)) { + sortByChromThenScoreAsc = true; + sortChoices++; + } + else if(PARAMETER_CHECK("-chrThenScoreD", 14, parameterLength)) { + sortByChromThenScoreDesc = true; + sortChoices++; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBed) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl; + showHelp = true; + } + if (sortChoices > 1) { + cerr << endl << "*****" << endl << "*****ERROR: Sorting options are mutually exclusive. Please choose just one. " << endl << "*****" << endl; + showHelp = true; + } + + + if (!showHelp) { + BedSort *bm = new BedSort(bedFile); + + if (sortBySizeAsc) { + bm->SortBedBySizeAsc(); + } + else if (sortBySizeDesc) { + bm->SortBedBySizeDesc(); + } + else if (sortByChromThenSizeAsc) { + bm->SortBedByChromThenSizeAsc(); + } + else if (sortByChromThenSizeDesc) { + bm->SortBedByChromThenSizeDesc(); + } + else if (sortByChromThenScoreAsc) { + bm->SortBedByChromThenScoreAsc(); + } + else if (sortByChromThenScoreDesc) { + bm->SortBedByChromThenScoreDesc(); + } + else { + bm->SortBed(); + } + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + cerr << "Summary: Sorts a feature file in various and useful ways." << endl << endl; + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t" << "-sizeA\t\t" << "Sort by feature size in ascending order." << endl; + cerr << "\t" << "-sizeD\t\t" << "Sort by feature size in descending order." << endl; + cerr << "\t" << "-chrThenSizeA\t" << "Sort by chrom (asc), then feature size (asc)." << endl; + cerr << "\t" << "-chrThenSizeD\t" << "Sort by chrom (asc), then feature size (desc)." << endl; + cerr << "\t" << "-chrThenScoreA\t" << "Sort by chrom (asc), then score (asc)." << endl; + cerr << "\t" << "-chrThenScoreD\t" << "Sort by chrom (asc), then score (desc)." << endl << endl; + + exit(1); + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/subtractBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,47 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= subtractMain.cpp subtractBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= subtractBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/subtractBed/subtractBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,178 @@ +/***************************************************************************** + subtractBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "subtractBed.h" + + +/* + Constructor +*/ +BedSubtract::BedSubtract(string &bedAFile, string &bedBFile, float overlapFraction, bool sameStrand, bool diffStrand) { + + _bedAFile = bedAFile; + _bedBFile = bedBFile; + _overlapFraction = overlapFraction; + _sameStrand = sameStrand; + _diffStrand = diffStrand; + + _bedA = new BedFile(bedAFile); + _bedB = new BedFile(bedBFile); + + SubtractBed(); +} + + +/* + Destructor +*/ +BedSubtract::~BedSubtract(void) { +} + + +void BedSubtract::FindAndSubtractOverlaps(BED &a, vector<BED> &hits) { + + // find all of the overlaps between a and B. + _bedB->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, _sameStrand, _diffStrand); + + // is A completely spanned by an entry in B? + // if so, A should not be reported. + int numConsumedByB = 0; + int numOverlaps = 0; + vector<BED> bOverlaps; // list of hits in B. Special processing if there are multiple. + + vector<BED>::const_iterator h = hits.begin(); + vector<BED>::const_iterator hitsEnd = hits.end(); + for (; h != hitsEnd; ++h) { + + int s = max(a.start, h->start); + int e = min(a.end, h->end); + int overlapBases = (e - s); // the number of overlapping bases b/w a and b + int aLength = (a.end - a.start); // the length of a in b.p. + + if (s < e) { + + // is there enough overlap (default ~ 1bp) + float overlap = ((float) overlapBases / (float) aLength); + + if (overlap >= 1.0) { + numOverlaps++; + numConsumedByB++; + } + else if ( overlap >= _overlapFraction ) { + numOverlaps++; + bOverlaps.push_back(*h); + } + } + } + + if (numOverlaps == 0) { + // no overlap found, so just report A as-is. + _bedA->reportBedNewLine(a); + } + else if (numOverlaps == 1) { + // one overlap found. only need to look at the single + // entry in bOverlaps. + + // if A was not "consumed" by any entry in B + if (numConsumedByB == 0) { + + BED theHit = bOverlaps[0]; + + // A ++++++++++++ + // B ---- + // Res. ==== ==== + if ( (theHit.start > a.start) && (theHit.end < a.end) ) { + _bedA->reportBedRangeNewLine(a,a.start,theHit.start); + _bedA->reportBedRangeNewLine(a,theHit.end,a.end); + } + // A ++++++++++++ + // B ---------- + // Res. == + else if (theHit.start == a.start) { + _bedA->reportBedRangeNewLine(a,theHit.end,a.end); + } + // A ++++++++++++ + // B ---------- + // Res. ==== + else if (theHit.start < a.start) { + _bedA->reportBedRangeNewLine(a,theHit.end,a.end); + } + // A ++++++++++++ + // B ---------- + // Res. ======= + else if (theHit.start > a.start) { + _bedA->reportBedRangeNewLine(a,a.start,theHit.start); + } + } + } + else if (numOverlaps > 1) { + // multiple overlapz found. look at all the hits + // and figure out which bases in A survived. then + // report the contigous intervals that survived. + + vector<bool> aKeep(a.end - a.start, true); + + if (numConsumedByB == 0) { + // track the number of hit starts and ends at each position in A + for (vector<BED>::iterator h = bOverlaps.begin(); h != bOverlaps.end(); ++h) { + int s = max(a.start, h->start); + int e = min(a.end, h->end); + + for (int i = s+1; i <= e; ++i) { + aKeep[i-a.start-1] = false; + } + } + // report the remaining blocks. + for (unsigned int i = 0; i < aKeep.size(); ++i) { + if (aKeep[i] == true) { + CHRPOS blockStart = i + a.start; + while ((aKeep[i] == true) && (i < aKeep.size())) { + i++; + } + CHRPOS blockEnd = i + a.start; + blockEnd = min(a.end, blockEnd); + _bedA->reportBedRangeNewLine(a,blockStart,blockEnd); + } + } + } + } +} + + + +void BedSubtract::SubtractBed() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedFileIntoMap(); + + BED a, nullBed; + BedLineStatus bedStatus; + int lineNum = 0; // current input line number + vector<BED> hits; // vector of potential hits + // reserve some space + hits.reserve(100); + + _bedA->Open(); + while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + FindAndSubtractOverlaps(a, hits); + hits.clear(); + a = nullBed; + } + } + _bedA->Close(); + +} +// END Intersect + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/subtractBed/subtractBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,53 @@ +/***************************************************************************** + subtractBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef SUBTRACTBED_H +#define SUBTRACTBED_H + +#include "bedFile.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class BedSubtract { + +public: + + // constructor + BedSubtract(string &bedAFile, string &bedBFile, float overlapFraction, bool sameStrand, bool diffStrand); + + // destructor + ~BedSubtract(void); + +private: + + // processing variables + string _bedAFile; + string _bedBFile; + float _overlapFraction; + bool _sameStrand; + bool _diffStrand; + + + // instances of bed file class. + BedFile *_bedA, *_bedB; + + // methods + void FindAndSubtractOverlaps(BED &a, vector<BED> &hits); + void SubtractBed(); +}; + +#endif /* SUBTRACTBED_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/subtractBed/subtractMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,145 @@ +/***************************************************************************** + subtractMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "subtractBed.h" +#include "version.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "subtractBed" + + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + + // input arguments + float overlapFraction = 1E-9; + + bool haveBedA = false; + bool haveBedB = false; + bool haveFraction = false; + bool sameStrand = false; + bool diffStrand = false; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-f", 2, parameterLength)) { + if ((i+1) < argc) { + haveFraction = true; + overlapFraction = atof(argv[i + 1]); + i++; + } + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + sameStrand = true; + } + else if (PARAMETER_CHECK("-S", 2, parameterLength)) { + diffStrand = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (sameStrand && diffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + + BedSubtract *bs = new BedSubtract(bedAFile, bedBFile, overlapFraction, sameStrand, diffStrand); + delete bs; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Removes the portion(s) of an interval that is overlapped" << endl; + cerr << "\t by another feature(s)." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl; + cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl; + cerr << "\t\t- (FLOAT) (e.g. 0.50)" << endl << endl; + + cerr << "\t-s\t" << "Require same strandedness. That is, only subtract hits in B that" << endl; + cerr << "\t\toverlap A on the _same_ strand." << endl; + cerr << "\t\t- By default, overlaps are subtracted without respect to strand." << endl << endl; + + cerr << "\t-S\t" << "Force strandedness. That is, only subtract hits in B that" << endl; + cerr << "\t\toverlap A on the _opposite_ strand." << endl; + cerr << "\t\t- By default, overlaps are subtracted without respect to strand." << endl << endl; + + // end the program here + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/tagBam/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,51 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= tagBamMain.cpp tagBam.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= tagBam + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/tagBam/tagBam.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,136 @@ +/***************************************************************************** + tagBam.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "tagBam.h" + +// build +TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames, + const vector<string> &annoLables, const string &tag, + bool useNames, bool useScores, bool sameStrand, bool diffStrand, float overlapFraction): + + _bamFile(bamFile), + _annoFileNames(annoFileNames), + _annoLabels(annoLables), + _tag(tag), + _useNames(useNames), + _useScores(useScores), + _sameStrand(sameStrand), + _diffStrand(diffStrand), + _overlapFraction(overlapFraction) +{} + + +// destroy and delete the open file pointers +TagBam::~TagBam(void) { + delete _bed; + CloseAnnoFiles(); +} + + +void TagBam::OpenAnnoFiles() { + for (size_t i=0; i < _annoFileNames.size(); ++i) { + BedFile *file = new BedFile(_annoFileNames[i]); + file->loadBedFileIntoMap(); + _annoFiles.push_back(file); + } +} + + +void TagBam::CloseAnnoFiles() { + for (size_t i=0; i < _annoFiles.size(); ++i) { + BedFile *file = _annoFiles[i]; + delete file; + _annoFiles[i] = NULL; + } +} + + +void TagBam::Tag() { + + // open the annotations files for processing; + OpenAnnoFiles(); + + // open the BAM file + BamReader reader; + BamWriter writer; + reader.Open(_bamFile); + // get header & reference information + string bamHeader = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // set compression mode + BamWriter::CompressionMode compressionMode = BamWriter::Compressed; +// if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed; + writer.SetCompressionMode(compressionMode); + // open our BAM writer + writer.Open("stdout", bamHeader, refs); + + // rip through the BAM file and test for overlaps with each annotation file. + BamAlignment al; + vector<BED> hits; + + while (reader.GetNextAlignment(al)) { + if (al.IsMapped() == true) { + BED a; + a.chrom = refs.at(al.RefID).RefName; + a.start = al.Position; + a.end = al.GetEndPosition(false, false); + a.strand = "+"; + if (al.IsReverseStrand()) a.strand = "-"; + + ostringstream annotations; + // annotate the BAM file based on overlaps with the annotation files. + for (size_t i = 0; i < _annoFiles.size(); ++i) + { + // grab the current annotation file. + BedFile *anno = _annoFiles[i]; + + if (!_useNames && !_useScores) { + // add the label for this annotation file to tag if there is overlap + if (anno->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _sameStrand, _diffStrand, _overlapFraction)) + { + annotations << _annoLabels[i] << ";"; + } + } + // use the score field + else if (!_useNames && _useScores) { + anno->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, _sameStrand, _diffStrand); + for (size_t i = 0; i < hits.size(); ++i) { + annotations << hits[i].score; + if (i < hits.size() - 1) annotations << ","; + } + if (hits.size() > 0) annotations << ";"; + hits.clear(); + } + // use the name field from the annotation files to populate tag + else if (_useNames && !_useScores) { + anno->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, _sameStrand, _diffStrand); + for (size_t i = 0; i < hits.size(); ++i) { + annotations << hits[i].name; + if (i < hits.size() - 1) annotations << ","; + } + if (hits.size() > 0) annotations << ";"; + hits.clear(); + } + } + // were there any overlaps with which to make a tag? + if (annotations.str().size() > 0) { + al.AddTag(_tag, "Z", annotations.str().substr(0, annotations.str().size() - 1)); // get rid of the last ";" + } + writer.SaveAlignment(al); + } + } + reader.Close(); + + // close the annotations files; + CloseAnnoFiles(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/tagBam/tagBam.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,83 @@ +/***************************************************************************** + tagBam.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef TAGBAM_H +#define TAGBAM_H + +#include "bedFile.h" + +#include "version.h" +#include "api/BamReader.h" +#include "api/BamWriter.h" +#include "api/BamAux.h" +#include "BamAncillary.h" +using namespace BamTools; + +#include "bedFile.h" +#include <vector> +#include <algorithm> +#include <iostream> +#include <iomanip> +#include <fstream> +#include <stdlib.h> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class TagBam { + +public: + + // constructor + TagBam(const string &bamFile, const vector<string> &annoFileNames, + const vector<string> &annoLabels, const string &tag, + bool useNames, bool useScores, bool sameStrand, + bool diffStrand, float overlapFraction); + + // destructor + ~TagBam(void); + + // annotate the BAM file with all of the annotation files. + void Tag(); + +private: + + // input files. + string _bamFile; + vector<string> _annoFileNames; + vector<string> _annoLabels; + + string _tag; + + // instance of a bed file class. + BedFile *_bed; + vector<BedFile*> _annoFiles; + + // should we use the name field from the annotation files? + bool _useNames; + bool _useScores; + + // do we care about strandedness when tagging? + bool _sameStrand; + bool _diffStrand; + float _overlapFraction; + + // private function for reporting coverage information + void ReportAnnotations(); + + void OpenAnnoFiles(); + + void CloseAnnoFiles(); + +}; +#endif /* TAGBAM_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/tagBam/tagBamMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,209 @@ +/***************************************************************************** + annotateMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "tagBam.h" +#include "version.h" + +using namespace std; + +// define the version +#define PROGRAM_NAME "tagBam" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input file + string bamFile; + float overlapFraction = 1E-9; + string tag = "YB"; + + // parm flags + bool haveTag = false; + bool haveFraction = false; + bool useNames = false; + bool useScores = false; + bool sameStrand = false; + bool diffStrand = false; + bool haveBam = false; + bool haveFiles = false; + bool haveLabels = false; + + + // list of annotation files / names + vector<string> inputFiles; + vector<string> inputLabels; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + haveBam = true; + bamFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-files", 6, parameterLength)) { + if ((i+1) < argc) { + haveFiles = true; + i = i+1; + string file = argv[i]; + while (file[0] != '-' && i < argc) { + inputFiles.push_back(file); + i++; + if (i < argc) + file = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-labels", 7, parameterLength)) { + if ((i+1) < argc) { + haveLabels = true; + i = i+1; + string label = argv[i]; + while (label[0] != '-' && i < argc) { + inputLabels.push_back(label); + i++; + if (i < argc) + label = argv[i]; + } + i--; + } + } + else if (PARAMETER_CHECK("-names", 6, parameterLength)) { + useNames = true; + } + else if (PARAMETER_CHECK("-scores", 7, parameterLength)) { + useScores = true; + } + else if (PARAMETER_CHECK("-s", 2, parameterLength)) { + sameStrand = true; + } + else if (PARAMETER_CHECK("-S", 2, parameterLength)) { + diffStrand = true; + } + else if(PARAMETER_CHECK("-f", 2, parameterLength)) { + if ((i+1) < argc) { + haveFraction = true; + overlapFraction = atof(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-tag", 4, parameterLength)) { + if ((i+1) < argc) { + haveTag = true; + tag = argv[i + 1]; + i++; + } + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBam || !haveFiles) { + cerr << endl << "*****" << endl << "*****ERROR: Need -i, -files" << endl << "*****" << endl; + showHelp = true; + } + if (!useNames && !haveLabels && !useScores) { + cerr << endl << "*****" << endl << "*****ERROR: Need -labels or -names or -scores" << endl << "*****" << endl; + showHelp = true; + } + if (sameStrand && diffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Use -s or -S, not both. " << endl << "*****" << endl; + showHelp = true; + } + if (haveLabels && useNames) { + cerr << endl << "*****" << endl << "*****ERROR: Use -labels or -names, not both. " << endl << "*****" << endl; + showHelp = true; + } + if (useScores && useNames) { + cerr << endl << "*****" << endl << "*****ERROR: Use -scores or -names, not both. " << endl << "*****" << endl; + showHelp = true; + } + if (haveTag && tag.size() > 2) { + cerr << endl << "*****" << endl << "*****ERROR: Custom tags should be at most two characters per the SAM specification. " << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, tag, useNames, useScores, sameStrand, diffStrand, overlapFraction); + ba->Tag(); + delete ba; + return 0; + } + else { + ShowHelp(); + } +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files" << endl; + cerr << "\t on the intervals in -i." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <BAM> -files FILE1 .. FILEn -labels LAB1 .. LABn" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-s\t" << "Require overlaps on the same strand. That is, only tag alignments that have the same" << endl; + cerr << "\t\tstrand as a feature in the annotation file(s)." << endl << endl; + + cerr << "\t-S\t" << "Require overlaps on the opposite strand. That is, only tag alignments that have the opposite" << endl; + cerr << "\t\tstrand as a feature in the annotation file(s)." << endl << endl; + + cerr << "\t-f\t" << "Minimum overlap required as a fraction of the alignment." << endl; + cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl; + cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl; + + cerr << "\t-tag\t" << "Dictate what the tag should be. Default is YB." << endl; + cerr << "\t\t- STRING (two characters, e.g., YK)" << endl << endl; + + cerr << "\t-names\t" << "Use the name field from the annotation files to populate tags." << endl; + cerr << "\t\tBy default, the -labels values are used." << endl << endl; + + cerr << "\t-scores\t" << "A list of 1-based columns for each annotation file" << endl; + cerr << "\t\tin which a color can be found." << endl << endl; + + + exit(1); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/unionBedGraphs/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,49 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedGraphFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= unionBedGraphs.cpp unionBedGraphsMain.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedGraphFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= unionBedGraphs + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedGraphFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/unionBedGraphs/intervalItem.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,62 @@ +/***************************************************************************** + intervalItem.h + + (c) 2010 - Assaf Gordon + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef INTERVALITEM_H +#define INTERVALITEM_H + +#include <string> +#include <queue> + +enum COORDINATE_TYPE { + START, + END +}; + +/* + An interval item in the priority queue. + + An IntervalItem can mark either a START position or an END position. + */ +class IntervalItem +{ +private: + IntervalItem(); + +public: + int source_index; // which source BedGraph file this came from + COORDINATE_TYPE coord_type; // is this the start or the end position? + CHRPOS coord; + std::string depth; + + IntervalItem(int _index, COORDINATE_TYPE _type, CHRPOS _coord, std::string _depth) : + source_index(_index), + coord_type(_type), + coord(_coord), + depth(_depth) + {} + + IntervalItem(const IntervalItem &other) : + source_index(other.source_index), + coord_type(other.coord_type), + coord(other.coord), + depth(other.depth) + {} + + bool operator< ( const IntervalItem& other ) const + { + return this->coord > other.coord; + } +}; + +// our priority queue +typedef std::priority_queue<IntervalItem> INTERVALS_PRIORITY_QUEUE; + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/unionBedGraphs/unionBedGraphs.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,255 @@ +/***************************************************************************** + unionBedGraphs.cpp + + (c) 2010 - Assaf Gordon, CSHL + - Aaron Quinlan, UVA + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include <cassert> +#include <cstring> +#include <cstdlib> +#include <iostream> +#include <algorithm> + +#include "bedGraphFile.h" +#include "unionBedGraphs.h" + +using namespace std; + + +UnionBedGraphs::UnionBedGraphs(std::ostream& _output, + const vector<string>& _filenames, + const vector<string>& _titles, + bool _print_empty_regions, + const std::string& _genome_size_filename, + const std::string& _no_coverage_value ) : + filenames(_filenames), + titles(_titles), + output(_output), + current_non_zero_inputs(0), + print_empty_regions(_print_empty_regions), + genome_sizes(NULL), + no_coverage_value(_no_coverage_value) +{ + if (print_empty_regions) { + assert(!_genome_size_filename.empty()); + + genome_sizes = new GenomeFile(_genome_size_filename); + } +} + + +UnionBedGraphs::~UnionBedGraphs() { + CloseBedgraphFiles(); + if (genome_sizes) { + delete genome_sizes; + genome_sizes = NULL ; + } +} + + +void UnionBedGraphs::Union() { + OpenBedgraphFiles(); + + // Add the first interval from each file + for(size_t i=0;i<bedgraph_files.size();++i) + LoadNextBedgraphItem(i); + + // Chromosome loop - once per chromosome + do { + // Find the first chromosome to use + current_chrom = DetermineNextChrom(); + + // Populate the queue with initial values from all files + // (if they belong to the correct chromosome) + for(size_t i=0;i<bedgraph_files.size();++i) + AddInterval(i); + + CHRPOS current_start = ConsumeNextCoordinate(); + + // User wanted empty regions, and the first coordinate is not 0 - print a dummy empty coverage + if (print_empty_regions && current_start > 0) + PrintEmptyCoverage(0,current_start); + + // Intervals loop - until all intervals (of current chromosome) from all files are used. + do { + CHRPOS current_end = queue.top().coord; + PrintCoverage(current_start, current_end); + current_start = ConsumeNextCoordinate(); + } while (!queue.empty()); + + // User wanted empty regions, and the last coordinate is not the last coordinate of the chromosome + // print a dummy empty coverage + if (print_empty_regions) { + CHRPOS chrom_size = genome_sizes->getChromSize(current_chrom); + if (current_start < chrom_size) + PrintEmptyCoverage(current_start, chrom_size); + } + + } while (!AllFilesDone()); +} + + +CHRPOS UnionBedGraphs::ConsumeNextCoordinate() { + assert(!queue.empty()); + + CHRPOS new_position = queue.top().coord; + do { + IntervalItem item = queue.top(); + UpdateInformation(item); + queue.pop(); + } while (!queue.empty() && queue.top().coord == new_position); + + return new_position; +} + + +void UnionBedGraphs::UpdateInformation(const IntervalItem &item) { + // Update the depth coverage for this file + + // Which coordinate is it - start or end? + switch (item.coord_type) + { + case START: + current_depth[item.source_index] = item.depth; + current_non_zero_inputs++; + break; + case END: + //Read the next interval from this file + AddInterval(item.source_index); + current_depth[item.source_index] = no_coverage_value; + current_non_zero_inputs--; + break; + default: + assert(0); + } +} + + +void UnionBedGraphs::PrintHeader() { + output << "chrom\tstart\tend" ; + for (size_t i=0;i<titles.size();++i) + output << "\t" <<titles[i]; + output << endl; +} + + +void UnionBedGraphs::PrintCoverage(CHRPOS start, CHRPOS end) { + if ( current_non_zero_inputs == 0 && ! print_empty_regions ) + return ; + + output << current_chrom << "\t" + << start << "\t" + << end; + + for (size_t i=0;i<current_depth.size();++i) + output << "\t" << current_depth[i] ; + + output << endl; +} + + +void UnionBedGraphs::PrintEmptyCoverage(CHRPOS start, CHRPOS end) { + output << current_chrom << "\t" + << start << "\t" + << end; + + for (size_t i=0;i<current_depth.size();++i) + output << "\t" << no_coverage_value ; + + output << endl; +} + + +void UnionBedGraphs::LoadNextBedgraphItem(int index) { + assert(static_cast<unsigned int>(index) < bedgraph_files.size()); + + current_bedgraph_item[index].chrom=""; + + BedGraphFile *file = bedgraph_files[index]; + BEDGRAPH_STR bg; + int lineNum = 0; + BedGraphLineStatus status; + + while ( (status = file->GetNextBedGraph(bg, lineNum)) != BEDGRAPH_INVALID ) { + if (status != BEDGRAPH_VALID) + continue; + + current_bedgraph_item[index] = bg ; + break; + } +} + + +bool UnionBedGraphs::AllFilesDone() { + for (size_t i=0;i<current_bedgraph_item.size();++i) + if (!current_bedgraph_item[i].chrom.empty()) + return false; + return true; +} + + +string UnionBedGraphs::DetermineNextChrom() { + string next_chrom; + for (size_t i=0;i<current_bedgraph_item.size();++i) { + if (current_bedgraph_item[i].chrom.empty()) + continue; + + if (next_chrom.empty()) + next_chrom = current_bedgraph_item[i].chrom; + else + if (current_bedgraph_item[i].chrom < next_chrom) + next_chrom = current_bedgraph_item[i].chrom ; + } + return next_chrom; +} + + +void UnionBedGraphs::AddInterval(int index) { + assert(static_cast<unsigned int>(index) < bedgraph_files.size()); + + //This file has no more intervals + if (current_bedgraph_item[index].chrom.empty()) + return ; + + //If the next interval belongs to a different chrom, don't add it + if (current_bedgraph_item[index].chrom!=current_chrom) + return ; + + const BEDGRAPH_STR &bg(current_bedgraph_item[index]); + + IntervalItem start_item(index, START, bg.start, bg.depth); + IntervalItem end_item(index, END, bg.end, bg.depth); + + queue.push(start_item); + queue.push(end_item); + + LoadNextBedgraphItem(index); +} + + +void UnionBedGraphs::OpenBedgraphFiles() { + for (size_t i=0;i<filenames.size();++i) { + BedGraphFile *file = new BedGraphFile(filenames[i]); + file->Open(); + bedgraph_files.push_back(file); + + current_depth.push_back(no_coverage_value); + } + current_bedgraph_item.resize(filenames.size()); +} + + +void UnionBedGraphs::CloseBedgraphFiles() { + for (size_t i=0;i<bedgraph_files.size();++i) { + BedGraphFile *file = bedgraph_files[i]; + delete file; + bedgraph_files[i] = NULL ; + } + bedgraph_files.clear(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/unionBedGraphs/unionBedGraphs.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,123 @@ +/***************************************************************************** + unionBedGraphs.h + + (c) 2010 - Assaf Gordon, CSHL + - Aaron Quinlan, UVA + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef UNIONBEDGRAPHS_H +#define UNIONBEDGRAPHS_H + +#include <vector> +#include <string> +#include "bedGraphFile.h" +#include "genomeFile.h" +#include "intervalItem.h" + +class UnionBedGraphs +{ +private: + typedef BEDGRAPH_STR BEDGRAPH_TYPE; + + vector<string> filenames; + vector<string> titles; + + vector<BedGraphFile*> bedgraph_files; + vector<BEDGRAPH_TYPE::DEPTH_TYPE> current_depth; + vector<BEDGRAPH_TYPE> current_bedgraph_item; + + std::ostream &output; + + INTERVALS_PRIORITY_QUEUE queue; + std::string current_chrom; + int current_non_zero_inputs; + bool print_empty_regions; + + GenomeFile* genome_sizes; + + std::string no_coverage_value; + +public: + UnionBedGraphs(std::ostream& _output, + const vector<string>& _filenames, + const vector<string>& _titles, + bool _print_empty_regions, + const std::string& _genomeFileName, + const std::string& _no_coverage_value); + + virtual ~UnionBedGraphs(); + + // Combines all bedgraph files + void Union(); + + // Print the header line: chrom/start/end + name of each bedgraph file. + void PrintHeader(); + + +private: + + // Open all BedGraph files, initialize "current_XXX" vectors + void OpenBedgraphFiles(); + + // Close the BedGraph files. + void CloseBedgraphFiles(); + + /* + Add an interval from BedGraph file 'index' into the queue. + will only be added if it belongs to the current chromosome. + + If the interval was added (=consumed), the next interval will be read from the file + using 'LoadNextBedgraphItem' + */ + void AddInterval(int index); + + /* + Loads the next interval from BedGraph file 'index'. + Stores it in 'current_bedgraph_item' vector. + */ + void LoadNextBedgraphItem(int index); + + /* + Scans the 'current_bedgraph_item' vector, + find the 'first' chromosome to use (different BedGraph files can start with different chromosomes). + */ + std::string DetermineNextChrom(); + + /* + Returns 'true' if ALL intervals from ALL BedGraph files were used + */ + bool AllFilesDone(); + + /* + Extract the next coordinate from the queue, and updates the current coverage information. + If multiple interval share the same coordinate values, all of them are handled. + If an END coordinate is consumed, the next interval (from the corresponding file) is read. + */ + CHRPOS ConsumeNextCoordinate(); + + /* + Updates the coverage information based on the given item. + Item can be a START coordinate or an END coordiante. + */ + void UpdateInformation(const IntervalItem &item); + + /* + prints chrom/start/end and the current depth coverage values of all the files. + */ + void PrintCoverage(CHRPOS start, CHRPOS end); + + /* + prints chrom/start/end and the ZERO depth coverage values of all the files. + */ + void PrintEmptyCoverage(CHRPOS start, CHRPOS end); + + void DebugPrintQueue(); +}; + + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/unionBedGraphs/unionBedGraphsMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,294 @@ +/***************************************************************************** + unionBedGraphsMain.cpp + + (c) 2010 - Assaf Gordon, CSHL + - Aaron Quinlan, UVA + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include <climits> +#include <cstring> +#include <cstdlib> +#include <vector> +#include <string> +#include <iostream> +#include <getopt.h> +#include <libgen.h> //for basename() +#include "version.h" + +#include "genomeFile.h" +#include "unionBedGraphs.h" + +using namespace std; + +// define our program name +#define PROGRAM_NAME "unionBedGraphs" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +//STLized version of basename() +// (because POSIX basename() modifies the input string pointer) +// Additionally: removes any extension the basename might have. +std::string stl_basename(const std::string& path); + +// function declarations +void ShowHelp(void); +void ShowExamples(void); + + +int main(int argc, char* argv[]) +{ + bool haveFiles = false; + bool haveTitles = false; + bool haveGenome = false; + bool haveFiller = true; + bool printHeader = false; + bool printEmptyRegions = false; + bool showHelp = false; + string genomeFile; + string basePath; + string noCoverageValue = "0"; + vector<string> inputFiles; + vector<string> inputTitles; + + //Parse command line options + if(argc <= 1) + ShowHelp(); + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp == true) { + ShowHelp(); + exit(1); + } + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-i", 2, parameterLength)) { + if ((i+1) < argc) { + haveFiles = true; + i = i+1; + string file = argv[i]; + while (file[0] != '-' && i < argc) { + inputFiles.push_back(file); + i++; + if (i < argc) + file = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-names", 6, parameterLength)) { + if ((i+1) < argc) { + haveTitles = true; + i = i+1; + string title = argv[i]; + while (title[0] != '-' && i < argc) { + inputTitles.push_back(title); + i++; + if (i < argc) + title = argv[i]; + } + i--; + } + } + else if(PARAMETER_CHECK("-g", 2, parameterLength)) { + if ((i+1) < argc) { + haveGenome = true; + genomeFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-filler", 7, parameterLength)) { + if ((i+1) < argc) { + haveFiller = true; + noCoverageValue = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-header", 7, parameterLength)) { + printHeader = true; + } + else if(PARAMETER_CHECK("-empty", 6, parameterLength)) { + printEmptyRegions = true; + } + else if(PARAMETER_CHECK("-examples", 9, parameterLength)) { + ShowHelp(); + ShowExamples(); + exit(1); + } + } + + //Sanity checks + if (inputFiles.empty() == true) { + cerr << "Error: missing BedGraph file names (-i) to combine." << endl; + exit(1); + } + if (inputFiles.size() == 1) { + cerr << "Error: Only a single BedGraph file was specified. Nothing to combine, exiting." << endl; + exit(1); + } + if (printEmptyRegions && (genomeFile.empty() == true)) { + cerr << "Error: when using -empty, the genome sizes file (-g) must be specified using '-g FILE'." << endl; + exit(1); + } + if ((haveTitles == true) && (inputFiles.size() != inputTitles.size())) { + cerr << "Error: The number of file titles (-names) does not match the number of files (-i)." << endl; + exit(1); + } + + UnionBedGraphs ubg(cout, inputFiles, inputTitles, printEmptyRegions, genomeFile, noCoverageValue); + if (printHeader) + ubg.PrintHeader(); + ubg.Union(); +} + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Authors: Assaf Gordon, CSHL" << endl; + cerr << " Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl; + + cerr << "Summary: Combines multiple BedGraph files into a single file," << endl; + cerr << "\t allowing coverage comparisons between them." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i FILE1 FILE2 .. FILEn" << endl; + cerr << "\t Assumes that each BedGraph file is sorted by chrom/start " << endl; + cerr << "\t and that the intervals in each are non-overlapping." << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-header\t\t" << "Print a header line." << endl; + cerr << "\t\t\t(chrom/start/end + names of each file)." << endl << endl; + + cerr << "\t-names\t\t" << "A list of names (one / file) to describe each file in -i." << endl; + cerr << "\t\t\tThese names will be printed in the header line." << endl << endl; + + cerr << "\t-g\t\t" << "Use genome file to calculate empty regions." << endl; + cerr << "\t\t\t- STRING." << endl << endl; + + cerr << "\t-empty\t\t" << "Report empty regions (i.e., start/end intervals w/o" << endl; + cerr << "\t\t\tvalues in all files)." << endl; + cerr << "\t\t\t- Requires the '-g FILE' parameter.\n" << endl; + + cerr << "\t-filler TEXT\t" << "Use TEXT when representing intervals having no value." << endl; + cerr << "\t\t\t- Default is '0', but you can use 'N/A' or any other text." << endl << endl; + + cerr << "\t-examples\t" << "Show detailed usage examples." << endl << endl; +} + + + +void ShowExamples() +{ + cerr << "Example usage:\n\n" \ +"== Input files: ==\n" \ +"\n" \ +" $ cat 1.bg\n" \ +" chr1 1000 1500 10\n" \ +" chr1 2000 2100 20\n" \ +"\n" \ +" $ cat 2.bg\n" \ +" chr1 900 1600 60\n" \ +" chr1 1700 2050 50\n" \ +"\n" \ +" $ cat 3.bg\n" \ +" chr1 1980 2070 80\n" \ +" chr1 2090 2100 20\n" \ +"\n" \ +" $ cat sizes.txt\n" \ +" chr1 5000\n" \ +"\n" \ +"== Union/combine the files: ==\n" \ +"\n" \ +" $ unionBedGraphs -i 1.bg 2.bg 3.bg\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +"\n" \ +"== Union/combine the files, with a header line (titles are the file names): ==\n" \ +"\n" \ +" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg\n" \ +" chrom start end 1 2 3\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +"\n" \ +"== Union/combine the files, with a header line and custom names: ==\n" \ +"\n" \ +" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg -names WT-1 WT-2 KO-1\n" \ +" chrom start end WT-1 WT-2 KO-1\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +"\n" \ +"== Union/combine, showing empty regions (note, requires -g): ==\n" \ +"\n" \ +" $ unionBedGraphs -header -empty -g sizes.TXT -i 1.bg 2.bg 3.bg\n" \ +" chrom start end 1 2 3\n" \ +" chr1 0 900 0 0 0\n" \ +" chr1 900 1000 0 60 0\n" \ +" chr1 1000 1500 10 60 0\n" \ +" chr1 1500 1600 0 60 0\n" \ +" chr1 1600 1700 0 0 0\n" \ +" chr1 1700 1980 0 50 0\n" \ +" chr1 1980 2000 0 50 80\n" \ +" chr1 2000 2050 20 50 80\n" \ +" chr1 2050 2070 20 0 80\n" \ +" chr1 2070 2090 20 0 0\n" \ +" chr1 2090 2100 20 0 20\n" \ +" chr1 2100 5000 0 0 0\n" \ +"\n" \ +; +} + +std::string stl_basename(const std::string& path) +{ + string result; + + char* path_dup = strdup(path.c_str()); + char* basename_part = basename(path_dup); + result = basename_part; + free(path_dup); + + size_t pos = result.find_last_of('.'); + if (pos != string::npos ) + result = result.substr(0,pos); + + return result; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools-Ancillary/BamAncillary.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,73 @@ +/***************************************************************************** + bamAncillary.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "BamAncillary.h" +using namespace std; + +// 10 15 20 25 30 4000 +// acccctttggacct---ataggga.................aaaa +// acccc---ggaccttttataggga.................aaaa +// 5M 3D 6M 2I 7M 20N 4M + +namespace BamTools { + void getBamBlocks(const BamAlignment &bam, const RefVector &refs, + vector<BED> &blocks, bool breakOnDeletionOps) { + + CHRPOS currPosition = bam.Position; + CHRPOS blockStart = bam.Position; + string chrom = refs.at(bam.RefID).RefName; + string name = bam.Name; + string strand = "+"; + string score = ToString(bam.MapQuality); + char prevOp = '\0'; + if (bam.IsReverseStrand()) strand = "-"; + bool blocksFound = false; + + vector<CigarOp>::const_iterator cigItr = bam.CigarData.begin(); + vector<CigarOp>::const_iterator cigEnd = bam.CigarData.end(); + for ( ; cigItr != cigEnd; ++cigItr ) { + if (cigItr->Type == 'M') { + currPosition += cigItr->Length; + // we only want to create a new block if the current M op + // was preceded by an N op or a D op (and we are breaking on D ops) + if ((prevOp == 'D' && breakOnDeletionOps == true) || (prevOp == 'N')) { + blocks.push_back( BED(chrom, blockStart, currPosition, name, score, strand) ); + blockStart = currPosition; + } + } + else if (cigItr->Type == 'D') { + if (breakOnDeletionOps == false) + currPosition += cigItr->Length; + else { + currPosition += cigItr->Length; + blockStart = currPosition; + } + } + else if (cigItr->Type == 'N') { + currPosition += cigItr->Length; + blockStart = currPosition; + } + else if (cigItr->Type == 'S' || cigItr->Type == 'H' || cigItr->Type == 'P' || cigItr->Type == 'I') { + // do nothing + } + else { + cerr << "Input error: invalid CIGAR type (" << cigItr->Type + << ") for: " << bam.Name << endl; + exit(1); + } + prevOp = cigItr->Type; + } + // if there were no splits, we just create a block representing the contiguous alignment. + if (blocksFound == false) { + blocks.push_back( BED(chrom, bam.Position, currPosition, name, score, strand) ); + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools-Ancillary/BamAncillary.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,19 @@ +/***************************************************************************** + bamAncillary.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" +#include "lineFileUtilities.h" +#include "api/BamAlignment.h" + +namespace BamTools { + void getBamBlocks(const BamAlignment &bam, const RefVector &refs, + vector<BED> &blocks, bool includeDeletions = true); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools-Ancillary/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,26 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../ + +INCLUDES = -I$(UTILITIES_DIR)/BamTools/include -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= BamAncillary.cpp +OBJECTS= $(SOURCES:.cpp=.o) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +all: $(BUILT_OBJECTS) + +.PHONY: all + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/LICENSE Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,22 @@ +The MIT License + +Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,61 @@ +# ------------------- +# define our includes +# ------------------- +OBJ_DIR = ../../../obj/ +INCLUDES = -Isrc/ -Iinclude/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- + +SOURCES= src/api/BamAlignment.cpp \ + src/api/BamMultiReader.cpp \ + src/api/BamReader.cpp \ + src/api/BamWriter.cpp \ + src/api/SamHeader.cpp \ + src/api/SamProgram.cpp \ + src/api/SamProgramChain.cpp \ + src/api/SamReadGroup.cpp \ + src/api/SamReadGroupDictionary.cpp \ + src/api/SamSequence.cpp \ + src/api/SamSequenceDictionary.cpp \ + src/api/internal/BamHeader_p.cpp \ + src/api/internal/BamIndexFactory_p.cpp \ + src/api/internal/BamMultiReader_p.cpp \ + src/api/internal/BamRandomAccessController_p.cpp \ + src/api/internal/BamReader_p.cpp \ + src/api/internal/BamStandardIndex_p.cpp \ + src/api/internal/BamToolsIndex_p.cpp \ + src/api/internal/BamWriter_p.cpp \ + src/api/internal/BgzfStream_p.cpp \ + src/api/internal/SamFormatParser_p.cpp \ + src/api/internal/SamFormatPrinter_p.cpp \ + src/api/internal/SamHeaderValidator_p.cpp + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +OBJECTS= $(SOURCES:.cpp=.o) +LIBRARY=libbamtools.a + +all: $(LIBRARY) + +.PHONY: all + +$(LIBRARY): $(OBJECTS) + [ -d lib ] || mkdir -p lib + [ -d include ] || mkdir -p include + [ -d include/api ] || mkdir -p include/api + [ -d include/shared ] || mkdir -p include/shared + + @cp src/api/*.h include/api + @cp src/shared/*.h include/shared + + + @echo " * linking $(LIBRARY)" + ar cr lib/$@ $^ + +$(OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -o $(*D)/$(*F).o + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamAlignment.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,2433 @@ +// *************************************************************************** +// BamAlignment.cpp (c) 2009 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 22 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the BamAlignment data structure +// *************************************************************************** + +#include <api/BamAlignment.h> +#include <api/BamConstants.h> +using namespace BamTools; + +#include <cctype> +#include <cstdio> +#include <cstdlib> +#include <cstring> +#include <exception> +#include <iostream> +#include <map> +#include <utility> +using namespace std; + +/*! \class BamTools::BamAlignment + \brief The main BAM alignment data structure. + + Provides methods to query/modify BAM alignment data fields. +*/ +/*! \var BamAlignment::Name + \brief read name +*/ +/*! \var BamAlignment::Length + \brief length of query sequence +*/ +/*! \var BamAlignment::QueryBases + \brief 'original' sequence (as reported from sequencing machine) +*/ +/*! \var BamAlignment::AlignedBases + \brief 'aligned' sequence (includes any indels, padding, clipping) +*/ +/*! \var BamAlignment::Qualities + \brief FASTQ qualities (ASCII characters, not numeric values) +*/ +/*! \var BamAlignment::TagData + \brief tag data (use the provided methods to query/modify) +*/ +/*! \var BamAlignment::RefID + \brief ID number for reference sequence +*/ +/*! \var BamAlignment::Position + \brief position (0-based) where alignment starts +*/ +/*! \var BamAlignment::Bin + \brief BAM (standard) index bin number for this alignment +*/ +/*! \var BamAlignment::MapQuality + \brief mapping quality score +*/ +/*! \var BamAlignment::AlignmentFlag + \brief alignment bit-flag (use the provided methods to query/modify) +*/ +/*! \var BamAlignment::CigarData + \brief CIGAR operations for this alignment +*/ +/*! \var BamAlignment::MateRefID + \brief ID number for reference sequence where alignment's mate was aligned +*/ +/*! \var BamAlignment::MatePosition + \brief position (0-based) where alignment's mate starts +*/ +/*! \var BamAlignment::InsertSize + \brief mate-pair insert size +*/ +/*! \var BamAlignment::Filename + \brief name of BAM file which this alignment comes from +*/ + +/*! \fn BamAlignment::BamAlignment(void) + \brief constructor +*/ +BamAlignment::BamAlignment(void) + : RefID(-1) + , Position(-1) + , MateRefID(-1) + , MatePosition(-1) + , InsertSize(0) +{ } + +/*! \fn BamAlignment::BamAlignment(const BamAlignment& other) + \brief copy constructor +*/ +BamAlignment::BamAlignment(const BamAlignment& other) + : Name(other.Name) + , Length(other.Length) + , QueryBases(other.QueryBases) + , AlignedBases(other.AlignedBases) + , Qualities(other.Qualities) + , TagData(other.TagData) + , RefID(other.RefID) + , Position(other.Position) + , Bin(other.Bin) + , MapQuality(other.MapQuality) + , AlignmentFlag(other.AlignmentFlag) + , CigarData(other.CigarData) + , MateRefID(other.MateRefID) + , MatePosition(other.MatePosition) + , InsertSize(other.InsertSize) + , Filename(other.Filename) + , SupportData(other.SupportData) +{ } + +/*! \fn BamAlignment::~BamAlignment(void) + \brief destructor +*/ +BamAlignment::~BamAlignment(void) { } + +/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const std::string& value) + \brief Adds a field with string data to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param type 1-character tag type (must be "Z" or "H") + \param value string data to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const std::string& value) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // validate tag/type size & that type is OK for string value + if ( !IsValidSize(tag, type) ) return false; + if ( type.at(0) != Constants::BAM_TAG_TYPE_STRING && + type.at(0) != Constants::BAM_TAG_TYPE_HEX + ) + { + return false; + } + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // otherwise, copy tag data to temp buffer + string newTag = tag + type + value; + const int newTagDataLength = tagDataLength + newTag.size() + 1; // leave room for null-term + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term + + // append newTag + strcat(originalTagData + tagDataLength, newTag.data()); // removes original null-term, appends newTag + null-term + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const uint32_t& value) + \brief Adds a field with unsigned integer data to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") + \param value unsigned int data to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const uint32_t& value) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // validate tag/type size & that type is OK for uint32_t value + if ( !IsValidSize(tag, type) ) return false; + if ( type.at(0) == Constants::BAM_TAG_TYPE_FLOAT || + type.at(0) == Constants::BAM_TAG_TYPE_STRING || + type.at(0) == Constants::BAM_TAG_TYPE_HEX || + type.at(0) == Constants::BAM_TAG_TYPE_ARRAY + ) + { + return false; + } + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // otherwise, convert value to string + union { uint32_t value; char valueBuffer[sizeof(uint32_t)]; } un; + un.value = value; + + // copy original tag data to temp buffer + string newTag = tag + type; + const int newTagDataLength = tagDataLength + newTag.size() + 4; // leave room for new integer + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term + + // append newTag + strcat(originalTagData + tagDataLength, newTag.data()); + memcpy(originalTagData + tagDataLength + newTag.size(), un.valueBuffer, sizeof(uint32_t)); + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const int32_t& value) + \brief Adds a field with signed integer data to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") + \param value signed int data to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const int32_t& value) { + return AddTag(tag, type, (const uint32_t&)value); +} + +/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const float& value) + \brief Adds a field with floating-point data to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param type 1-character tag type (must NOT be "Z", "H", or "B") + \param value float data to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const float& value) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // validate tag/type size & that type is OK for float value + if ( !IsValidSize(tag, type) ) return false; + if ( type.at(0) == Constants::BAM_TAG_TYPE_STRING || + type.at(0) == Constants::BAM_TAG_TYPE_HEX || + type.at(0) == Constants::BAM_TAG_TYPE_ARRAY + ) + { + return false; + } + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // otherwise, convert value to string + union { float value; char valueBuffer[sizeof(float)]; } un; + un.value = value; + + // copy original tag data to temp buffer + string newTag = tag + type; + const int newTagDataLength = tagDataLength + newTag.size() + 4; // leave room for new float + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term + + // append newTag + strcat(originalTagData + tagDataLength, newTag.data()); + memcpy(originalTagData + tagDataLength + newTag.size(), un.valueBuffer, sizeof(float)); + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool AddTag(const std::string& tag, const std::vector<uint8_t>& values); + \brief Adds a numeric array field to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param values vector of uint8_t values to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::vector<uint8_t>& values) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // check for valid tag length + if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // build new tag's base information + char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; + memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); + newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; + newTagBase[3] = Constants::BAM_TAG_TYPE_UINT8; + + // add number of array elements to newTagBase + const int32_t numElements = values.size(); + memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); + + // copy current TagData string to temp buffer, leaving room for new tag's contents + const int newTagDataLength = tagDataLength + + Constants::BAM_TAG_ARRAYBASE_SIZE + + numElements*sizeof(uint8_t); + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term + + // write newTagBase (removes old null term) + strcat(originalTagData + tagDataLength, (const char*)newTagBase); + + // add vector elements to tag + int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; + for ( int i = 0 ; i < numElements; ++i ) { + const uint8_t value = values.at(i); + memcpy(originalTagData + elementsBeginOffset + i*sizeof(uint8_t), + &value, sizeof(uint8_t)); + } + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool AddTag(const std::string& tag, const std::vector<int8_t>& values); + \brief Adds a numeric array field to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param values vector of int8_t values to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::vector<int8_t>& values) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // check for valid tag length + if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // build new tag's base information + char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; + memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); + newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; + newTagBase[3] = Constants::BAM_TAG_TYPE_INT8; + + // add number of array elements to newTagBase + const int32_t numElements = values.size(); + memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); + + // copy current TagData string to temp buffer, leaving room for new tag's contents + const int newTagDataLength = tagDataLength + + Constants::BAM_TAG_ARRAYBASE_SIZE + + numElements*sizeof(int8_t); + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term + + // write newTagBase (removes old null term) + strcat(originalTagData + tagDataLength, (const char*)newTagBase); + + // add vector elements to tag + int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; + for ( int i = 0 ; i < numElements; ++i ) { + const int8_t value = values.at(i); + memcpy(originalTagData + elementsBeginOffset + i*sizeof(int8_t), + &value, sizeof(int8_t)); + } + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool AddTag(const std::string& tag, const std::vector<uint16_t>& values); + \brief Adds a numeric array field to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param values vector of uint16_t values to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::vector<uint16_t>& values) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // check for valid tag length + if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // build new tag's base information + char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; + memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); + newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; + newTagBase[3] = Constants::BAM_TAG_TYPE_UINT16; + + // add number of array elements to newTagBase + const int32_t numElements = values.size(); + memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); + + // copy current TagData string to temp buffer, leaving room for new tag's contents + const int newTagDataLength = tagDataLength + + Constants::BAM_TAG_ARRAYBASE_SIZE + + numElements*sizeof(uint16_t); + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term + + // write newTagBase (removes old null term) + strcat(originalTagData + tagDataLength, (const char*)newTagBase); + + // add vector elements to tag + int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; + for ( int i = 0 ; i < numElements; ++i ) { + const uint16_t value = values.at(i); + memcpy(originalTagData + elementsBeginOffset + i*sizeof(uint16_t), + &value, sizeof(uint16_t)); + } + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool AddTag(const std::string& tag, const std::vector<int16_t>& values); + \brief Adds a numeric array field to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param values vector of int16_t values to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::vector<int16_t>& values) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // check for valid tag length + if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // build new tag's base information + char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; + memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); + newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; + newTagBase[3] = Constants::BAM_TAG_TYPE_INT16; + + // add number of array elements to newTagBase + const int32_t numElements = values.size(); + memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); + + // copy current TagData string to temp buffer, leaving room for new tag's contents + const int newTagDataLength = tagDataLength + + Constants::BAM_TAG_ARRAYBASE_SIZE + + numElements*sizeof(int16_t); + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term + + // write newTagBase (removes old null term) + strcat(originalTagData + tagDataLength, (const char*)newTagBase); + + // add vector elements to tag + int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; + for ( int i = 0 ; i < numElements; ++i ) { + const int16_t value = values.at(i); + memcpy(originalTagData + elementsBeginOffset + i*sizeof(int16_t), + &value, sizeof(int16_t)); + } + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool AddTag(const std::string& tag, const std::vector<uint32_t>& values); + \brief Adds a numeric array field to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param values vector of uint32_t values to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::vector<uint32_t>& values) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // check for valid tag length + if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // build new tag's base information + char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; + memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); + newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; + newTagBase[3] = Constants::BAM_TAG_TYPE_UINT32; + + // add number of array elements to newTagBase + const int32_t numElements = values.size(); + memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); + + // copy current TagData string to temp buffer, leaving room for new tag's contents + const int newTagDataLength = tagDataLength + + Constants::BAM_TAG_ARRAYBASE_SIZE + + numElements*sizeof(uint32_t); + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term + + // write newTagBase (removes old null term) + strcat(originalTagData + tagDataLength, (const char*)newTagBase); + + // add vector elements to tag + int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; + for ( int i = 0 ; i < numElements; ++i ) { + const uint32_t value = values.at(i); + memcpy(originalTagData + elementsBeginOffset + i*sizeof(uint32_t), + &value, sizeof(uint32_t)); + } + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool AddTag(const std::string& tag, const std::vector<int32_t>& values); + \brief Adds a numeric array field to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param values vector of int32_t values to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::vector<int32_t>& values) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // check for valid tag length + if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // build new tag's base information + char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; + memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); + newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; + newTagBase[3] = Constants::BAM_TAG_TYPE_INT32; + + // add number of array elements to newTagBase + const int32_t numElements = values.size(); + memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); + + // copy current TagData string to temp buffer, leaving room for new tag's contents + const int newTagDataLength = tagDataLength + + Constants::BAM_TAG_ARRAYBASE_SIZE + + numElements*sizeof(int32_t); + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term + + // write newTagBase (removes old null term) + strcat(originalTagData + tagDataLength, (const char*)newTagBase); + + // add vector elements to tag + int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; + for ( int i = 0 ; i < numElements; ++i ) { + const int32_t value = values.at(i); + memcpy(originalTagData + elementsBeginOffset + i*sizeof(int32_t), + &value, sizeof(int32_t)); + } + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool AddTag(const std::string& tag, const std::vector<float>& values); + \brief Adds a numeric array field to the BAM tags. + + Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. + + \param tag 2-character tag name + \param values vector of float values to store + + \return \c true if the \b new tag was added successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::AddTag(const std::string& tag, const std::vector<float>& values) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // check for valid tag length + if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag already exists, return false + // use EditTag explicitly instead + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // build new tag's base information + char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; + memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); + newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; + newTagBase[3] = Constants::BAM_TAG_TYPE_FLOAT; + + // add number of array elements to newTagBase + const int32_t numElements = values.size(); + memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); + + // copy current TagData string to temp buffer, leaving room for new tag's contents + const int newTagDataLength = tagDataLength + + Constants::BAM_TAG_ARRAYBASE_SIZE + + numElements*sizeof(float); + char* originalTagData = new char[newTagDataLength]; + memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term + + // write newTagBase (removes old null term) + strcat(originalTagData + tagDataLength, (const char*)newTagBase); + + // add vector elements to tag + int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; + for ( int i = 0 ; i < numElements; ++i ) { + const float value = values.at(i); + memcpy(originalTagData + elementsBeginOffset + i*sizeof(float), + &value, sizeof(float)); + } + + // store temp buffer back in TagData + const char* newTagData = (const char*)originalTagData; + TagData.assign(newTagData, newTagDataLength); + + delete[] originalTagData; + + // return success + return true; +} + +/*! \fn bool BamAlignment::BuildCharData(void) + \brief Populates alignment string fields (read name, bases, qualities, tag data). + + An alignment retrieved using BamReader::GetNextAlignmentCore() lacks this data. + Using that method makes parsing much quicker when only positional data is required. + + However, if you later want to access the character data fields from such an alignment, + use this method to populate those fields. Provides ability to do 'lazy evaluation' of + alignment parsing. + + \return \c true if character data populated successfully (or was already available to begin with) +*/ +bool BamAlignment::BuildCharData(void) { + + // skip if char data already parsed + if ( !SupportData.HasCoreOnly ) + return true; + + // check system endianness + bool IsBigEndian = BamTools::SystemIsBigEndian(); + + // calculate character lengths/offsets + const unsigned int dataLength = SupportData.BlockLength - Constants::BAM_CORE_SIZE; + const unsigned int seqDataOffset = SupportData.QueryNameLength + (SupportData.NumCigarOperations * 4); + const unsigned int qualDataOffset = seqDataOffset + (SupportData.QuerySequenceLength+1)/2; + const unsigned int tagDataOffset = qualDataOffset + SupportData.QuerySequenceLength; + const unsigned int tagDataLength = dataLength - tagDataOffset; + + // check offsets to see what char data exists + const bool hasSeqData = ( seqDataOffset < dataLength ); + const bool hasQualData = ( qualDataOffset < dataLength ); + const bool hasTagData = ( tagDataOffset < dataLength ); + + // set up char buffers + const char* allCharData = SupportData.AllCharData.data(); + const char* seqData = ( hasSeqData ? (((const char*)allCharData) + seqDataOffset) : (const char*)0 ); + const char* qualData = ( hasQualData ? (((const char*)allCharData) + qualDataOffset) : (const char*)0 ); + char* tagData = ( hasTagData ? (((char*)allCharData) + tagDataOffset) : (char*)0 ); + + // store alignment name (relies on null char in name as terminator) + Name.assign((const char*)(allCharData)); + + // save query sequence + QueryBases.clear(); + if ( hasSeqData ) { + QueryBases.reserve(SupportData.QuerySequenceLength); + for (unsigned int i = 0; i < SupportData.QuerySequenceLength; ++i) { + char singleBase = Constants::BAM_DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ]; + QueryBases.append(1, singleBase); + } + } + + // save qualities, converting from numeric QV to 'FASTQ-style' ASCII character + Qualities.clear(); + if ( hasQualData ) { + Qualities.reserve(SupportData.QuerySequenceLength); + for (unsigned int i = 0; i < SupportData.QuerySequenceLength; ++i) { + char singleQuality = (char)(qualData[i]+33); + Qualities.append(1, singleQuality); + } + } + + // clear previous AlignedBases + AlignedBases.clear(); + + // if QueryBases has data, build AlignedBases using CIGAR data + // otherwise, AlignedBases will remain empty (this case IS allowed) + if ( !QueryBases.empty() ) { + + // resize AlignedBases + AlignedBases.reserve(SupportData.QuerySequenceLength); + + // iterate over CigarOps + int k = 0; + vector<CigarOp>::const_iterator cigarIter = CigarData.begin(); + vector<CigarOp>::const_iterator cigarEnd = CigarData.end(); + for ( ; cigarIter != cigarEnd; ++cigarIter ) { + const CigarOp& op = (*cigarIter); + + switch (op.Type) { + + // for 'M', 'I', '=', 'X' - write bases + case (Constants::BAM_CIGAR_MATCH_CHAR) : + case (Constants::BAM_CIGAR_INS_CHAR) : + case (Constants::BAM_CIGAR_SEQMATCH_CHAR) : + case (Constants::BAM_CIGAR_MISMATCH_CHAR) : + AlignedBases.append(QueryBases.substr(k, op.Length)); + // fall through + + // for 'S' - soft clip, do not write bases + // but increment placeholder 'k' + case (Constants::BAM_CIGAR_SOFTCLIP_CHAR) : + k += op.Length; + break; + + // for 'D' - write gap character + case (Constants::BAM_CIGAR_DEL_CHAR) : + AlignedBases.append(op.Length, Constants::BAM_DNA_DEL); + break; + + // for 'P' - write padding character + case (Constants::BAM_CIGAR_PAD_CHAR) : + AlignedBases.append( op.Length, Constants::BAM_DNA_PAD ); + break; + + // for 'N' - write N's, skip bases in original query sequence + case (Constants::BAM_CIGAR_REFSKIP_CHAR) : + AlignedBases.append( op.Length, Constants::BAM_DNA_N ); + break; + + // for 'H' - hard clip, do nothing to AlignedBases, move to next op + case (Constants::BAM_CIGAR_HARDCLIP_CHAR) : + break; + + // shouldn't get here + default: + cerr << "BamAlignment ERROR: invalid CIGAR operation type: " + << op.Type << endl; + exit(1); + } + } + } + + // save tag data + TagData.clear(); + if ( hasTagData ) { + if ( IsBigEndian ) { + int i = 0; + while ( (unsigned int)i < tagDataLength ) { + + i += Constants::BAM_TAG_TAGSIZE; // skip tag chars (e.g. "RG", "NM", etc.) + const char type = tagData[i]; // get tag type at position i + ++i; // move i past tag type + + switch (type) { + + case(Constants::BAM_TAG_TYPE_ASCII) : + case(Constants::BAM_TAG_TYPE_INT8) : + case(Constants::BAM_TAG_TYPE_UINT8) : + // no endian swapping necessary for single-byte data + ++i; + break; + + case(Constants::BAM_TAG_TYPE_INT16) : + case(Constants::BAM_TAG_TYPE_UINT16) : + BamTools::SwapEndian_16p(&tagData[i]); + i += sizeof(uint16_t); + break; + + case(Constants::BAM_TAG_TYPE_FLOAT) : + case(Constants::BAM_TAG_TYPE_INT32) : + case(Constants::BAM_TAG_TYPE_UINT32) : + BamTools::SwapEndian_32p(&tagData[i]); + i += sizeof(uint32_t); + break; + + case(Constants::BAM_TAG_TYPE_HEX) : + case(Constants::BAM_TAG_TYPE_STRING) : + // no endian swapping necessary for hex-string/string data + while ( tagData[i] ) + ++i; + // increment one more for null terminator + ++i; + break; + + case(Constants::BAM_TAG_TYPE_ARRAY) : + + { + // read array type + const char arrayType = tagData[i]; + ++i; + + // swap endian-ness of number of elements in place, then retrieve for loop + BamTools::SwapEndian_32p(&tagData[i]); + int32_t numElements; + memcpy(&numElements, &tagData[i], sizeof(uint32_t)); + i += sizeof(uint32_t); + + // swap endian-ness of array elements + for ( int j = 0; j < numElements; ++j ) { + switch (arrayType) { + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + // no endian-swapping necessary + ++i; + break; + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + BamTools::SwapEndian_16p(&tagData[i]); + i += sizeof(uint16_t); + break; + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + BamTools::SwapEndian_32p(&tagData[i]); + i += sizeof(uint32_t); + break; + default: + // error case + cerr << "BamAlignment ERROR: unknown binary array type encountered: " + << arrayType << endl; + return false; + } + } + + break; + } + + // shouldn't get here + default : + cerr << "BamAlignment ERROR: invalid tag value type: " + << type << endl; + exit(1); + } + } + } + + // store tagData in alignment + TagData.resize(tagDataLength); + memcpy((char*)TagData.data(), tagData, tagDataLength); + } + + // clear the core-only flag + SupportData.HasCoreOnly = false; + + // return success + return true; +} + +/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const std::string& value) + \brief Edits a BAM tag field containing string data. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param type 1-character tag type (must be "Z" or "H") + \param value string data to store + + \return \c true if the tag was modified/created successfully + + \sa BamAlignment::RemoveTag() + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const std::string& value) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // validate tag/type size & that type is OK for string value + if ( !IsValidSize(tag, type) ) return false; + if ( type.at(0) != Constants::BAM_TAG_TYPE_STRING && + type.at(0) != Constants::BAM_TAG_TYPE_HEX ) + return false; + + // localize the tag data + char* pOriginalTagData = (char*)TagData.data(); + char* pTagData = pOriginalTagData; + const unsigned int originalTagDataLength = TagData.size(); + + unsigned int newTagDataLength = 0; + unsigned int numBytesParsed = 0; + + // if tag found + if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { + + // make sure array is more than big enough + char* newTagData = new char[originalTagDataLength + value.size()]; + + // copy original tag data up til desired tag + const unsigned int beginningTagDataLength = numBytesParsed; + newTagDataLength += beginningTagDataLength; + memcpy(newTagData, pOriginalTagData, numBytesParsed); + + // copy new @value in place of current tag data + const unsigned int dataLength = strlen(value.c_str()); + memcpy(newTagData + beginningTagDataLength, (char*)value.c_str(), dataLength+1 ); + + // skip to next tag (if tag for removal is last, return true) + const char* pTagStorageType = pTagData - 1; + if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) + return true; + + // copy everything from current tag (the next one after tag for removal) to end + const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); + const unsigned int endTagOffset = beginningTagDataLength + dataLength + 1; + const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; + memcpy(newTagData + endTagOffset, pTagData, endTagDataLength); + + // ensure null-terminator + newTagData[ endTagOffset + endTagDataLength + 1 ] = 0; + + // save new tag data + TagData.assign(newTagData, endTagOffset + endTagDataLength); + + delete[] newTagData; + + return true; + } + + // tag not found, attempt AddTag + else return AddTag(tag, type, value); +} + +/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const uint32_t& value) + \brief Edits a BAM tag field containing unsigned integer data. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") + \param value unsigned integer data to store + + \return \c true if the tag was modified/created successfully + + \sa BamAlignment::RemoveTag() + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const uint32_t& value) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // validate tag/type size & that type is OK for uint32_t value + if ( !IsValidSize(tag, type) ) return false; + if ( type.at(0) == Constants::BAM_TAG_TYPE_FLOAT || + type.at(0) == Constants::BAM_TAG_TYPE_STRING || + type.at(0) == Constants::BAM_TAG_TYPE_HEX || + type.at(0) == Constants::BAM_TAG_TYPE_ARRAY + ) + { + return false; + } + + // localize the tag data + char* pOriginalTagData = (char*)TagData.data(); + char* pTagData = pOriginalTagData; + const unsigned int originalTagDataLength = TagData.size(); + + unsigned int newTagDataLength = 0; + unsigned int numBytesParsed = 0; + + // if tag found + if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { + + // make sure array is more than big enough + char* newTagData = new char[originalTagDataLength + sizeof(value)]; + + // copy original tag data up til desired tag + const unsigned int beginningTagDataLength = numBytesParsed; + newTagDataLength += beginningTagDataLength; + memcpy(newTagData, pOriginalTagData, numBytesParsed); + + // copy new @value in place of current tag data + union { uint32_t value; char valueBuffer[sizeof(uint32_t)]; } un; + un.value = value; + memcpy(newTagData + beginningTagDataLength, un.valueBuffer, sizeof(uint32_t)); + + // skip to next tag (if tag for removal is last, return true) + const char* pTagStorageType = pTagData - 1; + if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) + return true; + + // copy everything from current tag (the next one after tag for removal) to end + const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); + const unsigned int endTagOffset = beginningTagDataLength + sizeof(uint32_t); + const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; + memcpy(newTagData + endTagOffset, pTagData, endTagDataLength); + + // ensure null-terminator + newTagData[ endTagOffset + endTagDataLength + 1 ] = 0; + + // save new tag data + TagData.assign(newTagData, endTagOffset + endTagDataLength); + + delete[] newTagData; + + return true; + } + + // tag not found, attempt AddTag + else return AddTag(tag, type, value); +} + +/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const int32_t& value) + \brief Edits a BAM tag field containing signed integer data. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") + \param value signed integer data to store + + \return \c true if the tag was modified/created successfully + + \sa BamAlignment::RemoveTag() + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const int32_t& value) { + return EditTag(tag, type, (const uint32_t&)value); +} + +/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const float& value) + \brief Edits a BAM tag field containing floating-point data. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param type 1-character tag type (must NOT be "Z", "H", or "B") + \param value float data to store + + \return \c true if the tag was modified/created successfully + + \sa BamAlignment::RemoveTag() + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const float& value) { + + // skip if core data not parsed + if ( SupportData.HasCoreOnly ) return false; + + // validate tag/type size & that type is OK for float value + if ( !IsValidSize(tag, type) ) return false; + if ( type.at(0) == Constants::BAM_TAG_TYPE_STRING || + type.at(0) == Constants::BAM_TAG_TYPE_HEX || + type.at(0) == Constants::BAM_TAG_TYPE_ARRAY + ) + { + return false; + } + + // localize the tag data + char* pOriginalTagData = (char*)TagData.data(); + char* pTagData = pOriginalTagData; + const unsigned int originalTagDataLength = TagData.size(); + + unsigned int newTagDataLength = 0; + unsigned int numBytesParsed = 0; + + // if tag found + if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { + + // make sure array is more than big enough + char* newTagData = new char[originalTagDataLength + sizeof(value)]; + + // copy original tag data up til desired tag + const unsigned int beginningTagDataLength = numBytesParsed; + newTagDataLength += beginningTagDataLength; + memcpy(newTagData, pOriginalTagData, numBytesParsed); + + // copy new @value in place of current tag data + union { float value; char valueBuffer[sizeof(float)]; } un; + un.value = value; + memcpy(newTagData + beginningTagDataLength, un.valueBuffer, sizeof(float)); + + // skip to next tag (if tag for removal is last, return true) + const char* pTagStorageType = pTagData - 1; + if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) + return true; + + // copy everything from current tag (the next one after tag for removal) to end + const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); + const unsigned int endTagOffset = beginningTagDataLength + sizeof(float); + const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; + memcpy(newTagData + endTagOffset, pTagData, endTagDataLength); + + // ensure null-terminator + newTagData[ endTagOffset + endTagDataLength + 1 ] = 0; + + // save new tag data + TagData.assign(newTagData, endTagOffset + endTagDataLength); + + delete[] newTagData; + + return true; + } + + // tag not found, attempt AddTag + else return AddTag(tag, type, value); +} + +/*! \fn bool EditTag(const std::string& tag, const std::vector<uint8_t>& values); + \brief Edits a BAM tag field containing a numeric array. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param value vector of uint8_t values to store + + \return \c true if the tag was modified/created successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::vector<uint8_t>& values) { + + // can't do anything if TagData not parsed + if ( SupportData.HasCoreOnly ) + return false; + + // remove existing tag if present + if ( HasTag(tag) ) + RemoveTag(tag); + + // add tag record with new values + return AddTag(tag, values); +} + +/*! \fn bool EditTag(const std::string& tag, const std::vector<int8_t>& values); + \brief Edits a BAM tag field containing a numeric array. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param value vector of int8_t values to store + + \return \c true if the tag was modified/created successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::vector<int8_t>& values) { + + // can't do anything if TagData not parsed + if ( SupportData.HasCoreOnly ) + return false; + + // remove existing tag if present + if ( HasTag(tag) ) + RemoveTag(tag); + + // add tag record with new values + return AddTag(tag, values); +} + +/*! \fn bool EditTag(const std::string& tag, const std::vector<uint16_t>& values); + \brief Edits a BAM tag field containing a numeric array. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param value vector of uint16_t values to store + + \return \c true if the tag was modified/created successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::vector<uint16_t>& values) { + + // can't do anything if TagData not parsed + if ( SupportData.HasCoreOnly ) + return false; + + // remove existing tag if present + if ( HasTag(tag) ) + RemoveTag(tag); + + // add tag record with new values + return AddTag(tag, values); +} + +/*! \fn bool EditTag(const std::string& tag, const std::vector<int16_t>& values); + \brief Edits a BAM tag field containing a numeric array. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param value vector of int16_t values to store + + \return \c true if the tag was modified/created successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::vector<int16_t>& values) { + + // can't do anything if TagData not parsed + if ( SupportData.HasCoreOnly ) + return false; + + // remove existing tag if present + if ( HasTag(tag) ) + RemoveTag(tag); + + // add tag record with new values + return AddTag(tag, values); +} + +/*! \fn bool EditTag(const std::string& tag, const std::vector<uint32_t>& values); + \brief Edits a BAM tag field containing a numeric array. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param value vector of uint32_t values to store + + \return \c true if the tag was modified/created successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::vector<uint32_t>& values) { + + // can't do anything if TagData not parsed + if ( SupportData.HasCoreOnly ) + return false; + + // remove existing tag if present + if ( HasTag(tag) ) + RemoveTag(tag); + + // add tag record with new values + return AddTag(tag, values); +} + +/*! \fn bool EditTag(const std::string& tag, const std::vector<int32_t>& values); + \brief Edits a BAM tag field containing a numeric array. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param value vector of int32_t values to store + + \return \c true if the tag was modified/created successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::vector<int32_t>& values) { + + // can't do anything if TagData not parsed + if ( SupportData.HasCoreOnly ) + return false; + + // remove existing tag if present + if ( HasTag(tag) ) + RemoveTag(tag); + + // add tag record with new values + return AddTag(tag, values); +} + +/*! \fn bool EditTag(const std::string& tag, const std::vector<float>& values); + \brief Edits a BAM tag field containing a numeric array. + + If \a tag does not exist, a new entry is created. + + \param tag 2-character tag name + \param value vector of float values to store + + \return \c true if the tag was modified/created successfully + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::EditTag(const std::string& tag, const std::vector<float>& values) { + + // can't do anything if TagData not parsed + if ( SupportData.HasCoreOnly ) + return false; + + // remove existing tag if present + if ( HasTag(tag) ) + RemoveTag(tag); + + // add tag record with new values + return AddTag(tag, values); +} + +/*! \fn bool BamAlignment::FindTag(const std::string& tag, char*& pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed) + \internal + + Searches for requested tag in BAM tag data. + + \param tag requested 2-character tag name + \param pTagData pointer to current position in BamAlignment::TagData + \param tagDataLength length of BamAlignment::TagData + \param numBytesParsed number of bytes parsed so far + + \return \c true if found + + \post If \a tag is found, \a pTagData will point to the byte where the tag data begins. + \a numBytesParsed will correspond to the position in the full TagData string. + +*/ +bool BamAlignment::FindTag(const std::string& tag, + char*& pTagData, + const unsigned int& tagDataLength, + unsigned int& numBytesParsed) const +{ + + while ( numBytesParsed < tagDataLength ) { + + const char* pTagType = pTagData; + const char* pTagStorageType = pTagData + 2; + pTagData += 3; + numBytesParsed += 3; + + // check the current tag, return true on match + if ( strncmp(pTagType, tag.c_str(), 2) == 0 ) + return true; + + // get the storage class and find the next tag + if ( *pTagStorageType == '\0' ) return false; + if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return false; + if ( *pTagData == '\0' ) return false; + } + + // checked all tags, none match + return false; +} + +/*! \fn bool BamAlignment::GetEditDistance(uint32_t& editDistance) const + \brief Retrieves value of edit distance tag ("NM"). + + \deprecated Instead use BamAlignment::GetTag() + \code + BamAlignment::GetTag("NM", editDistance); + \endcode + + \param editDistance destination for retrieved value + + \return \c true if found +*/ +bool BamAlignment::GetEditDistance(uint32_t& editDistance) const { + return GetTag("NM", (uint32_t&)editDistance); +} + +/*! \fn int BamAlignment::GetEndPosition(bool usePadded = false, bool zeroBased = true) const + \brief Calculates alignment end position, based on starting position and CIGAR data. + + \param usePadded Inserted bases affect reported position. Default is false, so that reported + position stays 'sync-ed' with reference coordinates. + \param zeroBased Return (BAM standard) 0-based coordinate. Setting this to false can be useful + when using BAM data with half-open formats (e.g. BED). + + \return alignment end position +*/ +int BamAlignment::GetEndPosition(bool usePadded, bool zeroBased) const { + + // initialize alignment end to starting position + int alignEnd = Position; + + // iterate over cigar operations + vector<CigarOp>::const_iterator cigarIter = CigarData.begin(); + vector<CigarOp>::const_iterator cigarEnd = CigarData.end(); + for ( ; cigarIter != cigarEnd; ++cigarIter) { + const char cigarType = (*cigarIter).Type; + const uint32_t& cigarLength = (*cigarIter).Length; + + if ( cigarType == Constants::BAM_CIGAR_MATCH_CHAR || + cigarType == Constants::BAM_CIGAR_DEL_CHAR || + cigarType == Constants::BAM_CIGAR_REFSKIP_CHAR ) + alignEnd += cigarLength; + else if ( usePadded && cigarType == Constants::BAM_CIGAR_INS_CHAR ) + alignEnd += cigarLength; + } + + // adjust for zero-based coordinates, if requested + if ( zeroBased ) alignEnd -= 1; + + // return result + return alignEnd; +} + +/*! \fn bool BamAlignment::GetReadGroup(std::string& readGroup) const + \brief Retrieves value of read group tag ("RG"). + + \deprecated Instead use BamAlignment::GetTag() + \code + BamAlignment::GetTag("RG", readGroup); + \endcode + + \param readGroup destination for retrieved value + + \return \c true if found +*/ +bool BamAlignment::GetReadGroup(std::string& readGroup) const { + return GetTag("RG", readGroup); +} + +/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::string& destination) const + \brief Retrieves the string value associated with a BAM tag. + + \param tag 2-character tag name + \param destination destination for retrieved value + + \return \c true if found +*/ +bool BamAlignment::GetTag(const std::string& tag, std::string& destination) const { + + // make sure tag data exists + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag found + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { + const unsigned int dataLength = strlen(pTagData); + destination.clear(); + destination.resize(dataLength); + memcpy( (char*)destination.data(), pTagData, dataLength ); + return true; + } + + // tag not found, return failure + return false; +} + +/*! \fn bool BamAlignment::GetTag(const std::string& tag, uint32_t& destination) const + \brief Retrieves the unsigned integer value associated with a BAM tag. + + \param tag 2-character tag name + \param destination destination for retrieved value + + \return \c true if found +*/ +bool BamAlignment::GetTag(const std::string& tag, uint32_t& destination) const { + + // make sure tag data exists + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag found + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { + + // determine data byte-length + const char type = *(pTagData - 1); + int destinationLength = 0; + switch (type) { + + // 1 byte data + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + destinationLength = 1; + break; + + // 2 byte data + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + destinationLength = 2; + break; + + // 4 byte data + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + destinationLength = 4; + break; + + // unsupported type for integer destination (float or var-length strings) + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_STRING) : + case (Constants::BAM_TAG_TYPE_HEX) : + case (Constants::BAM_TAG_TYPE_ARRAY) : + cerr << "BamAlignment ERROR: cannot store tag of type " << type + << " in integer destination" << endl; + return false; + + // unknown tag type + default: + cerr << "BamAlignment ERROR: unknown tag type encountered: " + << type << endl; + return false; + } + + // store in destination + destination = 0; + memcpy(&destination, pTagData, destinationLength); + return true; + } + + // tag not found, return failure + return false; +} + +/*! \fn bool BamAlignment::GetTag(const std::string& tag, int32_t& destination) const + \brief Retrieves the signed integer value associated with a BAM tag. + + \param tag 2-character tag name + \param destination destination for retrieved value + + \return \c true if found +*/ +bool BamAlignment::GetTag(const std::string& tag, int32_t& destination) const { + return GetTag(tag, (uint32_t&)destination); +} + +/*! \fn bool BamAlignment::GetTag(const std::string& tag, float& destination) const + \brief Retrieves the floating-point value associated with a BAM tag. + + \param tag 2-character tag name + \param destination destination for retrieved value + + \return \c true if found +*/ +bool BamAlignment::GetTag(const std::string& tag, float& destination) const { + + // make sure tag data exists + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if tag found + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { + + // determine data byte-length + const char type = *(pTagData - 1); + int destinationLength = 0; + switch (type) { + + // 1 byte data + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + destinationLength = 1; + break; + + // 2 byte data + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + destinationLength = 2; + break; + + // 4 byte data + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + destinationLength = 4; + break; + + // unsupported type (var-length strings) + case (Constants::BAM_TAG_TYPE_STRING) : + case (Constants::BAM_TAG_TYPE_HEX) : + case (Constants::BAM_TAG_TYPE_ARRAY) : + cerr << "BamAlignment ERROR: cannot store tag of type " << type + << " in float destination" << endl; + return false; + + // unknown tag type + default: + cerr << "BamAlignment ERROR: unknown tag type encountered: " + << type << endl; + return false; + } + + // store in destination + destination = 0.0; + memcpy(&destination, pTagData, destinationLength); + return true; + } + + // tag not found, return failure + return false; +} + +/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector<uint32_t>& destination) const + \brief Retrieves the numeric array data associated with a BAM tag + + \param tag 2-character tag name + \param destination destination for retrieved data + + \return \c true if found +*/ +bool BamAlignment::GetTag(const std::string& tag, std::vector<uint32_t>& destination) const { + + // make sure tag data exists + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // return false if tag not found + if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // check that tag is array type + const char tagType = *(pTagData - 1); + if ( tagType != Constants::BAM_TAG_TYPE_ARRAY ) { + cerr << "BamAlignment ERROR: Cannot store non-array data from tag: " + << tag << " in array destination" << endl; + return false; + } + + // calculate length of each element in tag's array + const char elementType = *pTagData; + ++pTagData; + int elementLength = 0; + switch ( elementType ) { + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + elementLength = sizeof(uint8_t); + break; + + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + elementLength = sizeof(uint16_t); + break; + + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + elementLength = sizeof(uint32_t); + break; + + // unsupported type for integer destination (float or var-length data) + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_STRING) : + case (Constants::BAM_TAG_TYPE_HEX) : + case (Constants::BAM_TAG_TYPE_ARRAY) : + cerr << "BamAlignment ERROR: array element type: " << elementType + << " cannot be stored in integer value" << endl; + return false; + + // unknown tag type + default: + cerr << "BamAlignment ERROR: unknown element type encountered: " + << elementType << endl; + return false; + } + + // get number of elements + int32_t numElements; + memcpy(&numElements, pTagData, sizeof(int32_t)); + pTagData += 4; + destination.clear(); + destination.reserve(numElements); + + // read in elements + uint32_t value; + for ( int i = 0 ; i < numElements; ++i ) { + memcpy(&value, pTagData, sizeof(uint32_t)); + pTagData += sizeof(uint32_t); + destination.push_back(value); + } + + // return success + return false; +} + +/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector<int32_t>& destination) const + \brief Retrieves the numeric array data associated with a BAM tag + + \param tag 2-character tag name + \param destination destination for retrieved data + + \return \c true if found +*/ +bool BamAlignment::GetTag(const std::string& tag, std::vector<int32_t>& destination) const { + + // make sure tag data exists + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // return false if tag not found + if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // check that tag is array type + const char tagType = *(pTagData - 1); + if ( tagType != Constants::BAM_TAG_TYPE_ARRAY ) { + cerr << "BamAlignment ERROR: Cannot store non-array data from tag: " + << tag << " in array destination" << endl; + return false; + } + + // calculate length of each element in tag's array + const char elementType = *pTagData; + ++pTagData; + int elementLength = 0; + switch ( elementType ) { + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + elementLength = sizeof(uint8_t); + break; + + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + elementLength = sizeof(uint16_t); + break; + + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + elementLength = sizeof(uint32_t); + break; + + // unsupported type for integer destination (float or var-length data) + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_STRING) : + case (Constants::BAM_TAG_TYPE_HEX) : + case (Constants::BAM_TAG_TYPE_ARRAY) : + cerr << "BamAlignment ERROR: array element type: " << elementType + << " cannot be stored in integer value" << endl; + return false; + + // unknown tag type + default: + cerr << "BamAlignment ERROR: unknown element type encountered: " + << elementType << endl; + return false; + } + + // get number of elements + int32_t numElements; + memcpy(&numElements, pTagData, sizeof(int32_t)); + pTagData += 4; + destination.clear(); + destination.reserve(numElements); + + // read in elements + int32_t value; + for ( int i = 0 ; i < numElements; ++i ) { + memcpy(&value, pTagData, sizeof(int32_t)); + pTagData += sizeof(int32_t); + destination.push_back(value); + } + + // return success + return false; + +} + +/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector<float>& destination) const + \brief Retrieves the numeric array data associated with a BAM tag + + \param tag 2-character tag name + \param destination destination for retrieved data + + \return \c true if found +*/ +bool BamAlignment::GetTag(const std::string& tag, std::vector<float>& destination) const { + + // make sure tag data exists + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // return false if tag not found + if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) + return false; + + // check that tag is array type + const char tagType = *(pTagData - 1); + if ( tagType != Constants::BAM_TAG_TYPE_ARRAY ) { + cerr << "BamAlignment ERROR: Cannot store non-array data from tag: " + << tag << " in array destination" << endl; + return false; + } + + // calculate length of each element in tag's array + const char elementType = *pTagData; + ++pTagData; + int elementLength = 0; + switch ( elementType ) { + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + elementLength = sizeof(uint8_t); + break; + + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + elementLength = sizeof(uint16_t); + break; + + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + case (Constants::BAM_TAG_TYPE_FLOAT) : + elementLength = sizeof(uint32_t); + break; + + // unsupported type for float destination (var-length data) + case (Constants::BAM_TAG_TYPE_STRING) : + case (Constants::BAM_TAG_TYPE_HEX) : + case (Constants::BAM_TAG_TYPE_ARRAY) : + cerr << "BamAlignment ERROR: array element type: " << elementType + << " cannot be stored in float value" << endl; + return false; + + // unknown tag type + default: + cerr << "BamAlignment ERROR: unknown element type encountered: " + << elementType << endl; + return false; + } + + // get number of elements + int32_t numElements; + memcpy(&numElements, pTagData, sizeof(int32_t)); + pTagData += 4; + destination.clear(); + destination.reserve(numElements); + + // read in elements + float value; + for ( int i = 0 ; i < numElements; ++i ) { + memcpy(&value, pTagData, sizeof(float)); + pTagData += sizeof(float); + destination.push_back(value); + } + + // return success + return false; +} + +/*! \fn bool BamAlignment::GetTagType(const std::string& tag, char& type) const + \brief Retrieves the BAM tag type-code associated with requested tag name. + + \param tag 2-character tag name + \param type destination for the retrieved (1-character) tag type + + \return \c true if found + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +*/ +bool BamAlignment::GetTagType(const std::string& tag, char& type) const { + + // make sure tag data exists + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // lookup tag + if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { + + // retrieve tag type code + type = *(pTagData - 1); + + // validate that type is a proper BAM tag type + switch (type) { + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_STRING) : + case (Constants::BAM_TAG_TYPE_HEX) : + case (Constants::BAM_TAG_TYPE_ARRAY) : + return true; + + // unknown tag type + default: + cerr << "BamAlignment ERROR: unknown tag type encountered: " + << type << endl; + return false; + } + } + + // tag not found, return failure + return false; +} + +/*! \fn bool BamAlignment::HasTag(const std::string& tag) const + \brief Returns true if alignment has a record for requested tag. + \param tag 2-character tag name + \return \c true if alignment has a record for tag +*/ +bool BamAlignment::HasTag(const std::string& tag) const { + + // return false if no tag data present + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data for lookup + char* pTagData = (char*)TagData.data(); + const unsigned int tagDataLength = TagData.size(); + unsigned int numBytesParsed = 0; + + // if result of tag lookup + return FindTag(tag, pTagData, tagDataLength, numBytesParsed); +} + +/*! \fn bool BamAlignment::IsDuplicate(void) const + \return \c true if this read is a PCR duplicate +*/ +bool BamAlignment::IsDuplicate(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_DUPLICATE) != 0 ); +} + +/*! \fn bool BamAlignment::IsFailedQC(void) const + \return \c true if this read failed quality control +*/ +bool BamAlignment::IsFailedQC(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_QC_FAILED) != 0 ); +} + +/*! \fn bool BamAlignment::IsFirstMate(void) const + \return \c true if alignment is first mate on paired-end read +*/ +bool BamAlignment::IsFirstMate(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_READ_1) != 0 ); +} + +/*! \fn bool BamAlignment::IsMapped(void) const + \return \c true if alignment is mapped +*/ +bool BamAlignment::IsMapped(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_UNMAPPED) == 0 ); +} + +/*! \fn bool BamAlignment::IsMateMapped(void) const + \return \c true if alignment's mate is mapped +*/ +bool BamAlignment::IsMateMapped(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_MATE_UNMAPPED) == 0 ); +} + +/*! \fn bool BamAlignment::IsMateReverseStrand(void) const + \return \c true if alignment's mate mapped to reverse strand +*/ +bool BamAlignment::IsMateReverseStrand(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND) != 0 ); +} + +/*! \fn bool BamAlignment::IsPaired(void) const + \return \c true if alignment part of paired-end read +*/ +bool BamAlignment::IsPaired(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_PAIRED) != 0 ); +} + +/*! \fn bool BamAlignment::IsPrimaryAlignment(void) const + \return \c true if reported position is primary alignment +*/ +bool BamAlignment::IsPrimaryAlignment(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_SECONDARY) == 0 ); +} + +/*! \fn bool BamAlignment::IsProperPair(void) const + \return \c true if alignment is part of read that satisfied paired-end resolution +*/ +bool BamAlignment::IsProperPair(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_PROPER_PAIR) != 0 ); +} + +/*! \fn bool BamAlignment::IsReverseStrand(void) const + \return \c true if alignment mapped to reverse strand +*/ +bool BamAlignment::IsReverseStrand(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_REVERSE_STRAND) != 0 ); +} + +/*! \fn bool BamAlignment::IsSecondMate(void) const + \return \c true if alignment is second mate on read +*/ +bool BamAlignment::IsSecondMate(void) const { + return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_READ_2) != 0 ); +} + +/*! \fn bool BamAlignment::IsValidSize(const string& tag, const string& type) const + \internal + + Checks that tag name & type strings are expected sizes. + \a tag should have length + \a type should have length 1 + + \param tag BAM tag name + \param type BAM tag type-code + + \return \c true if both \a tag and \a type are correct sizes +*/ +bool BamAlignment::IsValidSize(const string& tag, const string& type) const { + return (tag.size() == Constants::BAM_TAG_TAGSIZE) && + (type.size() == Constants::BAM_TAG_TYPESIZE); +} + +/*! \fn bool BamAlignment::RemoveTag(const std::string& tag) + \brief Removes field from BAM tags. + + \return \c true if tag was removed successfully (or didn't exist before) +*/ +bool BamAlignment::RemoveTag(const std::string& tag) { + + // skip if no tag data available + if ( SupportData.HasCoreOnly || TagData.empty() ) + return false; + + // localize the tag data + char* pOriginalTagData = (char*)TagData.data(); + char* pTagData = pOriginalTagData; + const unsigned int originalTagDataLength = TagData.size(); + unsigned int newTagDataLength = 0; + unsigned int numBytesParsed = 0; + + // if tag found + if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { + + char* newTagData = new char[originalTagDataLength]; + + // copy original tag data up til desired tag + pTagData -= 3; + numBytesParsed -= 3; + const unsigned int beginningTagDataLength = numBytesParsed; + newTagDataLength += beginningTagDataLength; + memcpy(newTagData, pOriginalTagData, numBytesParsed); + + // skip to next tag (if tag for removal is last, return true) + const char* pTagStorageType = pTagData + 2; + pTagData += 3; + numBytesParsed += 3; + if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) + return true; + + // copy everything from current tag (the next one after tag for removal) to end + const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); + const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; + memcpy(newTagData + beginningTagDataLength, pTagData, endTagDataLength ); + + // save new tag data + TagData.assign(newTagData, beginningTagDataLength + endTagDataLength); + + delete[] newTagData; + + return true; + } + + // tag not found, no removal - return failure + return false; +} + +/*! \fn void BamAlignment::SetIsDuplicate(bool ok) + \brief Sets value of "PCR duplicate" flag to \a ok. +*/ +void BamAlignment::SetIsDuplicate(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_DUPLICATE; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_DUPLICATE; +} + +/*! \fn void BamAlignment::SetIsFailedQC(bool ok) + \brief Sets "failed quality control" flag to \a ok. +*/ +void BamAlignment::SetIsFailedQC(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_QC_FAILED; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_QC_FAILED; +} + +/*! \fn void BamAlignment::SetIsFirstMate(bool ok) + \brief Sets "alignment is first mate" flag to \a ok. +*/ +void BamAlignment::SetIsFirstMate(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_READ_1; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_READ_1; +} + +/*! \fn void BamAlignment::SetIsMapped(bool ok) + \brief Sets "alignment is mapped" flag to \a ok. +*/ +void BamAlignment::SetIsMapped(bool ok) { + if (ok) AlignmentFlag &= ~Constants::BAM_ALIGNMENT_UNMAPPED; + else AlignmentFlag |= Constants::BAM_ALIGNMENT_UNMAPPED; +} + +/*! \fn void BamAlignment::SetIsMateMapped(bool ok) + \brief Sets "alignment's mate is mapped" flag to \a ok. +*/ +void BamAlignment::SetIsMateMapped(bool ok) { + if (ok) AlignmentFlag &= ~Constants::BAM_ALIGNMENT_MATE_UNMAPPED; + else AlignmentFlag |= Constants::BAM_ALIGNMENT_MATE_UNMAPPED; +} + +/*! \fn void BamAlignment::SetIsMateUnmapped(bool ok) + \brief Complement of using SetIsMateMapped(). + \deprecated For sake of symmetry with the query methods + \sa IsMateMapped(), SetIsMateMapped() +*/ +void BamAlignment::SetIsMateUnmapped(bool ok) { + SetIsMateMapped(!ok); +} + +/*! \fn void BamAlignment::SetIsMateReverseStrand(bool ok) + \brief Sets "alignment's mate mapped to reverse strand" flag to \a ok. +*/ +void BamAlignment::SetIsMateReverseStrand(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND; +} + +/*! \fn void BamAlignment::SetIsPaired(bool ok) + \brief Sets "alignment part of paired-end read" flag to \a ok. +*/ +void BamAlignment::SetIsPaired(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_PAIRED; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_PAIRED; +} + +/*! \fn void BamAlignment::SetIsPrimaryAlignment(bool ok) + \brief Sets "position is primary alignment" flag to \a ok. +*/ +void BamAlignment::SetIsPrimaryAlignment(bool ok) { + if (ok) AlignmentFlag &= ~Constants::BAM_ALIGNMENT_SECONDARY; + else AlignmentFlag |= Constants::BAM_ALIGNMENT_SECONDARY; +} + +/*! \fn void BamAlignment::SetIsProperPair(bool ok) + \brief Sets "alignment is part of read that satisfied paired-end resolution" flag to \a ok. +*/ +void BamAlignment::SetIsProperPair(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_PROPER_PAIR; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_PROPER_PAIR; +} + +/*! \fn void BamAlignment::SetIsReverseStrand(bool ok) + \brief Sets "alignment mapped to reverse strand" flag to \a ok. +*/ +void BamAlignment::SetIsReverseStrand(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_REVERSE_STRAND; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_REVERSE_STRAND; +} + +/*! \fn void BamAlignment::SetIsSecondaryAlignment(bool ok) + \brief Complement of using SetIsPrimaryAlignment(). + \deprecated For sake of symmetry with the query methods + \sa IsPrimaryAlignment(), SetIsPrimaryAlignment() +*/ +void BamAlignment::SetIsSecondaryAlignment(bool ok) { + SetIsPrimaryAlignment(!ok); +} + +/*! \fn void BamAlignment::SetIsSecondMate(bool ok) + \brief Sets "alignment is second mate on read" flag to \a ok. +*/ +void BamAlignment::SetIsSecondMate(bool ok) { + if (ok) AlignmentFlag |= Constants::BAM_ALIGNMENT_READ_2; + else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_READ_2; +} + +/*! \fn void BamAlignment::SetIsUnmapped(bool ok) + \brief Complement of using SetIsMapped(). + \deprecated For sake of symmetry with the query methods + \sa IsMapped(), SetIsMapped() +*/ +void BamAlignment::SetIsUnmapped(bool ok) { + SetIsMapped(!ok); +} + +/*! \fn bool BamAlignment::SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed) + \internal + + Moves to next available tag in tag data string + + \param storageType BAM tag type-code that determines how far to move cursor + \param pTagData pointer to current position (cursor) in tag string + \param numBytesParsed report of how many bytes were parsed (cumulatively) + + \return \c if storageType was a recognized BAM tag type + \post \a pTagData will point to the byte where the next tag data begins. + \a numBytesParsed will correspond to the cursor's position in the full TagData string. +*/ +bool BamAlignment::SkipToNextTag(const char storageType, + char*& pTagData, + unsigned int& numBytesParsed) const +{ + switch (storageType) { + + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + ++numBytesParsed; + ++pTagData; + break; + + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + numBytesParsed += sizeof(uint16_t); + pTagData += sizeof(uint16_t); + break; + + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + numBytesParsed += sizeof(uint32_t); + pTagData += sizeof(uint32_t); + break; + + case (Constants::BAM_TAG_TYPE_STRING) : + case (Constants::BAM_TAG_TYPE_HEX) : + while( *pTagData ) { + ++numBytesParsed; + ++pTagData; + } + // increment for null-terminator + ++numBytesParsed; + ++pTagData; + break; + + case (Constants::BAM_TAG_TYPE_ARRAY) : + + { + // read array type + const char arrayType = *pTagData; + ++numBytesParsed; + ++pTagData; + + // read number of elements + int32_t numElements; + memcpy(&numElements, pTagData, sizeof(uint32_t)); // already endian-swapped if necessary + numBytesParsed += sizeof(uint32_t); + pTagData += sizeof(uint32_t); + + // calculate number of bytes to skip + int bytesToSkip = 0; + switch (arrayType) { + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + bytesToSkip = numElements; + break; + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + bytesToSkip = numElements*sizeof(uint16_t); + break; + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + bytesToSkip = numElements*sizeof(uint32_t); + break; + default: + cerr << "BamAlignment ERROR: unknown binary array type encountered: " + << arrayType << endl; + return false; + } + + // skip binary array contents + numBytesParsed += bytesToSkip; + pTagData += bytesToSkip; + break; + } + + default: + cerr << "BamAlignment ERROR: unknown tag type encountered" + << storageType << endl; + return false; + } + + // return success + return true; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamAlignment.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,207 @@ +// *************************************************************************** +// BamAlignment.h (c) 2009 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 22 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the BamAlignment data structure +// *************************************************************************** + +#ifndef BAMALIGNMENT_H +#define BAMALIGNMENT_H + +#include <api/api_global.h> +#include <api/BamAux.h> +#include <string> +#include <vector> + +namespace BamTools { + +// forward declaration of BamAlignment's friend classes +namespace Internal { + class BamReaderPrivate; + class BamWriterPrivate; +} // namespace Internal + +// BamAlignment data structure +struct API_EXPORT BamAlignment { + + // constructors & destructor + public: + BamAlignment(void); + BamAlignment(const BamAlignment& other); + ~BamAlignment(void); + + // queries against alignment flags + public: + bool IsDuplicate(void) const; // returns true if this read is a PCR duplicate + bool IsFailedQC(void) const; // returns true if this read failed quality control + bool IsFirstMate(void) const; // returns true if alignment is first mate on read + bool IsMapped(void) const; // returns true if alignment is mapped + bool IsMateMapped(void) const; // returns true if alignment's mate is mapped + bool IsMateReverseStrand(void) const; // returns true if alignment's mate mapped to reverse strand + bool IsPaired(void) const; // returns true if alignment part of paired-end read + bool IsPrimaryAlignment(void) const; // returns true if reported position is primary alignment + bool IsProperPair(void) const; // returns true if alignment is part of read that satisfied paired-end resolution + bool IsReverseStrand(void) const; // returns true if alignment mapped to reverse strand + bool IsSecondMate(void) const; // returns true if alignment is second mate on read + + // manipulate alignment flags + public: + void SetIsDuplicate(bool ok); // sets value of "PCR duplicate" flag + void SetIsFailedQC(bool ok); // sets value of "failed quality control" flag + void SetIsFirstMate(bool ok); // sets value of "alignment is first mate" flag + void SetIsMapped(bool ok); // sets value of "alignment is mapped" flag + void SetIsMateMapped(bool ok); // sets value of "alignment's mate is mapped" flag + void SetIsMateReverseStrand(bool ok); // sets value of "alignment's mate mapped to reverse strand" flag + void SetIsPaired(bool ok); // sets value of "alignment part of paired-end read" flag + void SetIsPrimaryAlignment(bool ok); // sets value of "position is primary alignment" flag + void SetIsProperPair(bool ok); // sets value of "alignment is part of read that satisfied paired-end resolution" flag + void SetIsReverseStrand(bool ok); // sets value of "alignment mapped to reverse strand" flag + void SetIsSecondMate(bool ok); // sets value of "alignment is second mate on read" flag + + // legacy methods (consider deprecated, but still available) + void SetIsMateUnmapped(bool ok); // complement of using SetIsMateMapped() + void SetIsSecondaryAlignment(bool ok); // complement of using SetIsPrimaryAlignment() + void SetIsUnmapped(bool ok); // complement of using SetIsMapped() + + // tag data access methods + public: + + // ------------------------------------------------------------------------------------- + // N.B. - The following tag access methods may not be used on BamAlignments fetched + // using BamReader::GetNextAlignmentCore(). Attempting to use them will not result in + // error message (to keep output clean) but will ALWAYS return false. Only user-created + // BamAlignments or those retrieved using BamReader::GetNextAlignment() are valid here. + // + // You can call BuildCharData() on such an alignment retrieved by GetNextAlignmentCore(). + // This populates all the character data, and will enable subsequent queries on tag data. + // ------------------------------------------------------------------------------------- + + // adds a tag + bool AddTag(const std::string& tag, const std::string& type, const std::string& value); + bool AddTag(const std::string& tag, const std::string& type, const uint32_t& value); + bool AddTag(const std::string& tag, const std::string& type, const int32_t& value); + bool AddTag(const std::string& tag, const std::string& type, const float& value); + + // adds a "binary array" tag + bool AddTag(const std::string& tag, const std::vector<uint8_t>& values); + bool AddTag(const std::string& tag, const std::vector<int8_t>& values); + bool AddTag(const std::string& tag, const std::vector<uint16_t>& values); + bool AddTag(const std::string& tag, const std::vector<int16_t>& values); + bool AddTag(const std::string& tag, const std::vector<uint32_t>& values); + bool AddTag(const std::string& tag, const std::vector<int32_t>& values); + bool AddTag(const std::string& tag, const std::vector<float>& values); + + // edits a tag + bool EditTag(const std::string& tag, const std::string& type, const std::string& value); + bool EditTag(const std::string& tag, const std::string& type, const uint32_t& value); + bool EditTag(const std::string& tag, const std::string& type, const int32_t& value); + bool EditTag(const std::string& tag, const std::string& type, const float& value); + + // edits a "binary array" tag + bool EditTag(const std::string& tag, const std::vector<uint8_t>& values); + bool EditTag(const std::string& tag, const std::vector<int8_t>& values); + bool EditTag(const std::string& tag, const std::vector<uint16_t>& values); + bool EditTag(const std::string& tag, const std::vector<int16_t>& values); + bool EditTag(const std::string& tag, const std::vector<uint32_t>& values); + bool EditTag(const std::string& tag, const std::vector<int32_t>& values); + bool EditTag(const std::string& tag, const std::vector<float>& values); + + // retrieves data for a tag + bool GetTag(const std::string& tag, std::string& destination) const; + bool GetTag(const std::string& tag, uint32_t& destination) const; + bool GetTag(const std::string& tag, int32_t& destination) const; + bool GetTag(const std::string& tag, float& destination) const; + + // retrieves data for a "binary array" tag + bool GetTag(const std::string& tag, std::vector<uint32_t>& destination) const; + bool GetTag(const std::string& tag, std::vector<int32_t>& destination) const; + bool GetTag(const std::string& tag, std::vector<float>& destination) const; + + // retrieves the BAM tag-type character for a tag + bool GetTagType(const std::string& tag, char& type) const; + + // legacy methods (consider deprecated, but still available) + bool GetEditDistance(uint32_t& editDistance) const; // retrieves value of "NM" tag + bool GetReadGroup(std::string& readGroup) const; // retrieves value of "RG" tag + + // returns true if alignment has a record for this tag name + bool HasTag(const std::string& tag) const; + + // removes a tag + bool RemoveTag(const std::string& tag); + + // additional methods + public: + // populates alignment string fields + bool BuildCharData(void); + // calculates alignment end position + int GetEndPosition(bool usePadded = false, bool zeroBased = true) const; + + // public data fields + public: + std::string Name; // read name + int32_t Length; // length of query sequence + std::string QueryBases; // 'original' sequence (as reported from sequencing machine) + std::string AlignedBases; // 'aligned' sequence (includes any indels, padding, clipping) + std::string Qualities; // FASTQ qualities (ASCII characters, not numeric values) + std::string TagData; // tag data (use provided methods to query/modify) + int32_t RefID; // ID number for reference sequence + int32_t Position; // position (0-based) where alignment starts + uint16_t Bin; // BAM (standard) index bin number for this alignment + uint16_t MapQuality; // mapping quality score + uint32_t AlignmentFlag; // alignment bit-flag (use provided methods to query/modify) + std::vector<CigarOp> CigarData; // CIGAR operations for this alignment + int32_t MateRefID; // ID number for reference sequence where alignment's mate was aligned + int32_t MatePosition; // position (0-based) where alignment's mate starts + int32_t InsertSize; // mate-pair insert size + std::string Filename; // name of BAM file which this alignment comes from + + //! \cond + // internal utility methods + private: + bool FindTag(const std::string& tag, + char*& pTagData, + const unsigned int& tagDataLength, + unsigned int& numBytesParsed) const; + bool IsValidSize(const std::string& tag, + const std::string& type) const; + bool SkipToNextTag(const char storageType, + char*& pTagData, + unsigned int& numBytesParsed) const; + + // internal data + private: + + struct BamAlignmentSupportData { + + // data members + std::string AllCharData; + uint32_t BlockLength; + uint32_t NumCigarOperations; + uint32_t QueryNameLength; + uint32_t QuerySequenceLength; + bool HasCoreOnly; + + // constructor + BamAlignmentSupportData(void) + : BlockLength(0) + , NumCigarOperations(0) + , QueryNameLength(0) + , QuerySequenceLength(0) + , HasCoreOnly(false) + { } + }; + BamAlignmentSupportData SupportData; + friend class Internal::BamReaderPrivate; + friend class Internal::BamWriterPrivate; + //! \endcond +}; + +typedef std::vector<BamAlignment> BamAlignmentVector; + +} // namespace BamTools + +#endif // BAMALIGNMENT_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamAux.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,457 @@ +// *************************************************************************** +// BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 4 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides data structures & utility methods that are used throughout the API. +// *************************************************************************** + +#ifndef BAMAUX_H +#define BAMAUX_H + +#include <api/api_global.h> +#include <fstream> +#include <iostream> +#include <string> +#include <vector> + +/*! \file BamAux.h + + Provides data structures & utility methods that are used throughout the API. +*/ +/*! \namespace BamTools + \brief Contains all BamTools classes & methods. + + The BamTools API contained in this namespace contains classes and methods + for reading, writing, and manipulating BAM alignment files. +*/ +namespace BamTools { + +// ---------------------------------------------------------------- +// CigarOp + +/*! \struct BamTools::CigarOp + \brief Represents a CIGAR alignment operation. + + \sa http://samtools.sourceforge.net/SAM-1.3.pdf for more details on using CIGAR operations. +*/ +struct API_EXPORT CigarOp { + + char Type; //!< CIGAR operation type (MIDNSHP) + uint32_t Length; //!< CIGAR operation length (number of bases) + + //! constructor + CigarOp(const char type = '\0', + const uint32_t& length = 0) + : Type(type) + , Length(length) + { } +}; + +// ---------------------------------------------------------------- +// RefData + +/*! \struct BamTools::RefData + \brief Represents a reference sequence entry +*/ +struct API_EXPORT RefData { + + std::string RefName; //!< name of reference sequence + int32_t RefLength; //!< length of reference sequence + + //! constructor + RefData(const std::string& name = "", + const int32_t& length = 0) + : RefName(name) + , RefLength(length) + { } +}; + +//! convenience typedef for vector of RefData entries +typedef std::vector<RefData> RefVector; + +// ---------------------------------------------------------------- +// BamRegion + +/*! \struct BamTools::BamRegion + \brief Represents a sequential genomic region + + Allowed to span multiple (sequential) references. +*/ +struct API_EXPORT BamRegion { + + int LeftRefID; //!< reference ID for region's left boundary + int LeftPosition; //!< position for region's left boundary + int RightRefID; //!< reference ID for region's right boundary + int RightPosition; //!< position for region's right boundary + + //! constructor + BamRegion(const int& leftID = -1, + const int& leftPos = -1, + const int& rightID = -1, + const int& rightPos = -1) + : LeftRefID(leftID) + , LeftPosition(leftPos) + , RightRefID(rightID) + , RightPosition(rightPos) + { } + + //! copy constructor + BamRegion(const BamRegion& other) + : LeftRefID(other.LeftRefID) + , LeftPosition(other.LeftPosition) + , RightRefID(other.RightRefID) + , RightPosition(other.RightPosition) + { } + + //! Clears region boundaries + void clear(void) { + LeftRefID = -1; LeftPosition = -1; + RightRefID = -1; RightPosition = -1; + } + + //! Returns true if region has a left boundary + bool isLeftBoundSpecified(void) const { + return ( LeftRefID >= 0 && LeftPosition >= 0 ); + } + + //! Returns true if region boundaries are not defined + bool isNull(void) const { + return ( !isLeftBoundSpecified() && !isRightBoundSpecified() ); + } + + //! Returns true if region has a right boundary + bool isRightBoundSpecified(void) const { + return ( RightRefID >= 0 && RightPosition >= 0 ); + } +}; + +// ---------------------------------------------------------------- +// General utility methods + +/*! \fn bool FileExists(const std::string& filename) + \brief checks if file exists + + Attempts to open file in a read-only mode. + + \return \c true if file can be opened successfully +*/ +API_EXPORT inline bool FileExists(const std::string& filename) { + std::ifstream f(filename.c_str(), std::ifstream::in); + return !f.fail(); +} + +/*! \fn void SwapEndian_16(int16_t& x) + \brief swaps endianness of signed 16-bit integer, in place + + Swaps endian representation of value in \a x. +*/ +API_EXPORT inline void SwapEndian_16(int16_t& x) { + x = ((x >> 8) | (x << 8)); +} + +/*! \fn void SwapEndian_16(uint16_t& x) + \brief swaps endianness of unsigned 16-bit integer, in place + + Swaps endian representation of value in \a x. +*/ +API_EXPORT inline void SwapEndian_16(uint16_t& x) { + x = ((x >> 8) | (x << 8)); +} + +/*! \fn void SwapEndian_32(int32_t& x) + \brief swaps endianness of signed 32-bit integer, in place + + Swaps endian representation of value in \a x. +*/ +API_EXPORT inline void SwapEndian_32(int32_t& x) { + x = ( (x >> 24) | + ((x << 8) & 0x00FF0000) | + ((x >> 8) & 0x0000FF00) | + (x << 24) + ); +} + +/*! \fn void SwapEndian_32(uint32_t& x) + \brief swaps endianness of unsigned 32-bit integer, in place + + Swaps endian representation of value in \a x. +*/ +API_EXPORT inline void SwapEndian_32(uint32_t& x) { + x = ( (x >> 24) | + ((x << 8) & 0x00FF0000) | + ((x >> 8) & 0x0000FF00) | + (x << 24) + ); +} + +/*! \fn void SwapEndian_64(int64_t& x) + \brief swaps endianness of signed 64-bit integer, in place + + Swaps endian representation of value in \a x. +*/ +API_EXPORT inline void SwapEndian_64(int64_t& x) { + x = ( (x >> 56) | + ((x << 40) & 0x00FF000000000000ll) | + ((x << 24) & 0x0000FF0000000000ll) | + ((x << 8) & 0x000000FF00000000ll) | + ((x >> 8) & 0x00000000FF000000ll) | + ((x >> 24) & 0x0000000000FF0000ll) | + ((x >> 40) & 0x000000000000FF00ll) | + (x << 56) + ); +} + +/*! \fn void SwapEndian_64(uint64_t& x) + \brief swaps endianness of unsigned 64-bit integer, in place + + Swaps endian representation of value in \a x. +*/ +API_EXPORT inline void SwapEndian_64(uint64_t& x) { + x = ( (x >> 56) | + ((x << 40) & 0x00FF000000000000ll) | + ((x << 24) & 0x0000FF0000000000ll) | + ((x << 8) & 0x000000FF00000000ll) | + ((x >> 8) & 0x00000000FF000000ll) | + ((x >> 24) & 0x0000000000FF0000ll) | + ((x >> 40) & 0x000000000000FF00ll) | + (x << 56) + ); +} + +/*! \fn void SwapEndian_16p(char* data) + \brief swaps endianness of the next 2 bytes in a buffer, in place + + Swaps endian representation the next 2 bytes in \a data. +*/ +API_EXPORT inline void SwapEndian_16p(char* data) { + uint16_t& value = (uint16_t&)*data; + SwapEndian_16(value); +} + +/*! \fn void SwapEndian_32p(char* data) + \brief swaps endianness of the next 4 bytes in a buffer, in place + + Swaps endian representation the next 4 bytes in \a data. +*/ +API_EXPORT inline void SwapEndian_32p(char* data) { + uint32_t& value = (uint32_t&)*data; + SwapEndian_32(value); +} + +/*! \fn void SwapEndian_64p(char* data) + \brief swaps endianness of the next 8 bytes in a buffer, in place + + Swaps endian representation the next 8 bytes in \a data. +*/ +API_EXPORT inline void SwapEndian_64p(char* data) { + uint64_t& value = (uint64_t&)*data; + SwapEndian_64(value); +} + +/*! \fn bool SystemIsBigEndian(void) + \brief checks host architecture's byte order + \return \c true if system uses big-endian ordering +*/ +API_EXPORT inline bool SystemIsBigEndian(void) { + const uint16_t one = 0x0001; + return ((*(char*) &one) == 0 ); +} + +/*! \fn void PackUnsignedInt(char* buffer, unsigned int value) + \brief stores unsigned integer value in a byte buffer + + \param buffer destination buffer + \param value unsigned integer to 'pack' in buffer +*/ +API_EXPORT inline void PackUnsignedInt(char* buffer, unsigned int value) { + buffer[0] = (char)value; + buffer[1] = (char)(value >> 8); + buffer[2] = (char)(value >> 16); + buffer[3] = (char)(value >> 24); +} + +/*! \fn void PackUnsignedShort(char* buffer, unsigned short value) + \brief stores unsigned short integer value in a byte buffer + + \param buffer destination buffer + \param value unsigned short integer to 'pack' in buffer +*/ +API_EXPORT inline void PackUnsignedShort(char* buffer, unsigned short value) { + buffer[0] = (char)value; + buffer[1] = (char)(value >> 8); +} + +/*! \fn double UnpackDouble(const char* buffer) + \brief reads a double value from byte buffer + + \param buffer source byte buffer + \return the (double) value read from the buffer +*/ +API_EXPORT inline double UnpackDouble(const char* buffer) { + union { double value; unsigned char valueBuffer[sizeof(double)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + un.valueBuffer[2] = buffer[2]; + un.valueBuffer[3] = buffer[3]; + un.valueBuffer[4] = buffer[4]; + un.valueBuffer[5] = buffer[5]; + un.valueBuffer[6] = buffer[6]; + un.valueBuffer[7] = buffer[7]; + return un.value; +} + +/*! \fn double UnpackDouble(char* buffer) + \brief reads a double value from byte buffer + + This is an overloaded function. + + \param buffer source byte buffer + \return the (double) value read from the buffer +*/ +API_EXPORT inline double UnpackDouble(char* buffer) { + return UnpackDouble( (const char*)buffer ); +} + +/*! \fn double UnpackFloat(const char* buffer) + \brief reads a float value from byte buffer + + \param buffer source byte buffer + \return the (float) value read from the buffer +*/ +API_EXPORT inline float UnpackFloat(const char* buffer) { + union { float value; unsigned char valueBuffer[sizeof(float)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + un.valueBuffer[2] = buffer[2]; + un.valueBuffer[3] = buffer[3]; + return un.value; +} + +/*! \fn double UnpackFloat(char* buffer) + \brief reads a float value from byte buffer + + This is an overloaded function. + + \param buffer source byte buffer + \return the (float) value read from the buffer +*/ +API_EXPORT inline float UnpackFloat(char* buffer) { + return UnpackFloat( (const char*)buffer ); +} + +/*! \fn signed int UnpackSignedInt(const char* buffer) + \brief reads a signed integer value from byte buffer + + \param buffer source byte buffer + \return the (signed int) value read from the buffer +*/ +API_EXPORT inline signed int UnpackSignedInt(const char* buffer) { + union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + un.valueBuffer[2] = buffer[2]; + un.valueBuffer[3] = buffer[3]; + return un.value; +} + +/*! \fn signed int UnpackSignedInt(char* buffer) + \brief reads a signed integer value from byte buffer + + This is an overloaded function. + + \param buffer source byte buffer + \return the (signed int) value read from the buffer +*/ +API_EXPORT inline signed int UnpackSignedInt(char* buffer) { + return UnpackSignedInt( (const char*) buffer ); +} + +/*! \fn signed short UnpackSignedShort(const char* buffer) + \brief reads a signed short integer value from byte buffer + + \param buffer source byte buffer + \return the (signed short) value read from the buffer +*/ +API_EXPORT inline signed short UnpackSignedShort(const char* buffer) { + union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + return un.value; +} + +/*! \fn signed short UnpackSignedShort(char* buffer) + \brief reads a signed short integer value from byte buffer + + This is an overloaded function. + + \param buffer source byte buffer + \return the (signed short) value read from the buffer +*/ +API_EXPORT inline signed short UnpackSignedShort(char* buffer) { + return UnpackSignedShort( (const char*)buffer ); +} + +/*! \fn unsigned int UnpackUnsignedInt(const char* buffer) + \brief reads an unsigned integer value from byte buffer + + \param buffer source byte buffer + \return the (unsigned int) value read from the buffer +*/ +API_EXPORT inline unsigned int UnpackUnsignedInt(const char* buffer) { + union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + un.valueBuffer[2] = buffer[2]; + un.valueBuffer[3] = buffer[3]; + return un.value; +} + +/*! \fn unsigned int UnpackUnsignedInt(char* buffer) + \brief reads an unsigned integer value from byte buffer + + This is an overloaded function. + + \param buffer source byte buffer + \return the (unsigned int) value read from the buffer +*/ +API_EXPORT inline unsigned int UnpackUnsignedInt(char* buffer) { + return UnpackUnsignedInt( (const char*)buffer ); +} + +/*! \fn unsigned short UnpackUnsignedShort(const char* buffer) + \brief reads an unsigned short integer value from byte buffer + + \param buffer source byte buffer + \return the (unsigned short) value read from the buffer +*/ +API_EXPORT inline unsigned short UnpackUnsignedShort(const char* buffer) { + union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + return un.value; +} + +/*! \fn unsigned short UnpackUnsignedShort(char* buffer) + \brief reads an unsigned short integer value from byte buffer + + This is an overloaded function. + + \param buffer source byte buffer + \return the (unsigned short) value read from the buffer +*/ +API_EXPORT inline unsigned short UnpackUnsignedShort(char* buffer) { + return UnpackUnsignedShort( (const char*)buffer ); +} + +} // namespace BamTools + +#endif // BAMAUX_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamConstants.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,128 @@ +// *************************************************************************** +// BamConstants.h (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides basic constants for handling BAM files. +// *************************************************************************** + +#ifndef BAM_CONSTANTS_H +#define BAM_CONSTANTS_H + +#include <string> + +/*! \namespace BamTools::Constants + \brief Provides basic constants for handling BAM files. +*/ + +namespace BamTools { +namespace Constants { + +const int BAM_SIZEOF_INT = 4; + +// header magic number +const char* const BAM_HEADER_MAGIC = "BAM\1"; +const unsigned int BAM_HEADER_MAGIC_LENGTH = 4; + +// BAM alignment core size +const int BAM_CORE_SIZE = 32; +const int BAM_CORE_BUFFER_SIZE = 8; + +// BAM alignment flags +const int BAM_ALIGNMENT_PAIRED = 0x0001; +const int BAM_ALIGNMENT_PROPER_PAIR = 0x0002; +const int BAM_ALIGNMENT_UNMAPPED = 0x0004; +const int BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008; +const int BAM_ALIGNMENT_REVERSE_STRAND = 0x0010; +const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020; +const int BAM_ALIGNMENT_READ_1 = 0x0040; +const int BAM_ALIGNMENT_READ_2 = 0x0080; +const int BAM_ALIGNMENT_SECONDARY = 0x0100; +const int BAM_ALIGNMENT_QC_FAILED = 0x0200; +const int BAM_ALIGNMENT_DUPLICATE = 0x0400; + +// CIGAR constants +const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X"; +const int BAM_CIGAR_MATCH = 0; +const int BAM_CIGAR_INS = 1; +const int BAM_CIGAR_DEL = 2; +const int BAM_CIGAR_REFSKIP = 3; +const int BAM_CIGAR_SOFTCLIP = 4; +const int BAM_CIGAR_HARDCLIP = 5; +const int BAM_CIGAR_PAD = 6; +const int BAM_CIGAR_SEQMATCH = 7; +const int BAM_CIGAR_MISMATCH = 8; + +const char BAM_CIGAR_MATCH_CHAR = 'M'; +const char BAM_CIGAR_INS_CHAR = 'I'; +const char BAM_CIGAR_DEL_CHAR = 'D'; +const char BAM_CIGAR_REFSKIP_CHAR = 'N'; +const char BAM_CIGAR_SOFTCLIP_CHAR = 'S'; +const char BAM_CIGAR_HARDCLIP_CHAR = 'H'; +const char BAM_CIGAR_PAD_CHAR = 'P'; +const char BAM_CIGAR_SEQMATCH_CHAR = '='; +const char BAM_CIGAR_MISMATCH_CHAR = 'X'; + +const int BAM_CIGAR_SHIFT = 4; +const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1); + +// BAM tag types +const char BAM_TAG_TYPE_ASCII = 'A'; +const char BAM_TAG_TYPE_UINT8 = 'c'; +const char BAM_TAG_TYPE_INT8 = 'C'; +const char BAM_TAG_TYPE_UINT16 = 's'; +const char BAM_TAG_TYPE_INT16 = 'S'; +const char BAM_TAG_TYPE_UINT32 = 'i'; +const char BAM_TAG_TYPE_INT32 = 'I'; +const char BAM_TAG_TYPE_FLOAT = 'f'; +const char BAM_TAG_TYPE_STRING = 'Z'; +const char BAM_TAG_TYPE_HEX = 'H'; +const char BAM_TAG_TYPE_ARRAY = 'B'; + +const size_t BAM_TAG_TAGSIZE = 2; +const size_t BAM_TAG_TYPESIZE = 1; +const int BAM_TAG_ARRAYBASE_SIZE = 8; + +// DNA bases +const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN"; +const unsigned char BAM_BASECODE_EQUAL = 0; +const unsigned char BAM_BASECODE_A = 1; +const unsigned char BAM_BASECODE_C = 2; +const unsigned char BAM_BASECODE_G = 4; +const unsigned char BAM_BASECODE_T = 8; +const unsigned char BAM_BASECODE_N = 15; + +const char BAM_DNA_EQUAL = '='; +const char BAM_DNA_A = 'A'; +const char BAM_DNA_C = 'C'; +const char BAM_DNA_G = 'G'; +const char BAM_DNA_T = 'T'; +const char BAM_DNA_N = 'N'; +const char BAM_DNA_DEL = '-'; +const char BAM_DNA_PAD = '*'; + +// zlib constants +const int GZIP_ID1 = 31; +const int GZIP_ID2 = 139; +const int CM_DEFLATE = 8; +const int FLG_FEXTRA = 4; +const int OS_UNKNOWN = 255; +const int BGZF_XLEN = 6; +const int BGZF_ID1 = 66; +const int BGZF_ID2 = 67; +const int BGZF_LEN = 2; +const int GZIP_WINDOW_BITS = -15; +const int Z_DEFAULT_MEM_LEVEL = 8; + +// BZGF constants +const int BGZF_BLOCK_HEADER_LENGTH = 18; +const int BGZF_BLOCK_FOOTER_LENGTH = 8; +const int BGZF_MAX_BLOCK_SIZE = 65536; +const int BGZF_DEFAULT_BLOCK_SIZE = 65536; + +} // namespace Constants +} // namespace BamTools + +#endif // BAM_CONSTANTS_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamIndex.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,80 @@ +// *************************************************************************** +// BamIndex.h (c) 2009 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides basic BAM index interface +// *************************************************************************** + +#ifndef BAM_INDEX_H +#define BAM_INDEX_H + +#include <api/api_global.h> +#include <api/BamAux.h> +#include <string> + +namespace BamTools { + +namespace Internal { + class BamReaderPrivate; +} // namespace Internal + +/*! \class BamTools::BamIndex + \brief Provides methods for generating & loading BAM index files. + + This class straddles the line between public API and internal + implementation detail. Most client code should never have to use this + class directly. + + It is exposed to the public API to allow advanced users to implement + their own custom indexing schemes. + + More documentation on methods & enums coming soon. +*/ + +class API_EXPORT BamIndex { + + // enums + public: + // specify index-caching behavior + enum IndexCacheMode { FullIndexCaching = 0 // store entire index file contents in memory + , LimitedIndexCaching // store only index data for current reference + , NoIndexCaching // do not store any index data between jumps + }; + + // list of supported BamIndex types + enum IndexType { BAMTOOLS = 0 + , STANDARD + }; + + // ctor & dtor + public: + BamIndex(Internal::BamReaderPrivate* reader) : m_reader(reader) { } + virtual ~BamIndex(void) { } + + // index interface + public: + // builds index from associated BAM file & writes out to index file + virtual bool Create(void) =0; // creates index file from BAM file + // returns whether reference has alignments or no + virtual bool HasAlignments(const int& referenceID) const =0; + // attempts to use index data to jump to @region, returns success/fail + // a "successful" jump indicates no error, but not whether this region has data + // * thus, the method sets a flag to indicate whether there are alignments + // available after the jump position + virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0; + // loads existing data from file into memory + virtual bool Load(const std::string& filename) =0; + // change the index caching behavior + virtual void SetCacheMode(const BamIndex::IndexCacheMode& mode) =0; + + // data members + protected: + Internal::BamReaderPrivate* m_reader; // copy, not ownedprivate: +}; + +} // namespace BamTools + +#endif // BAM_INDEX_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamMultiReader.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,396 @@ +// *************************************************************************** +// BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 15 March 2011 (DB) +// --------------------------------------------------------------------------- +// Convenience class for reading multiple BAM files. +// +// This functionality allows applications to work on very large sets of files +// without requiring intermediate merge, sort, and index steps for each file +// subset. It also improves the performance of our merge system as it +// precludes the need to sort merged files. +// *************************************************************************** + +#include <api/BamMultiReader.h> +#include <api/internal/BamMultiReader_p.h> +using namespace BamTools; + +#include <string> +#include <vector> +using namespace std; + +/*! \class BamTools::BamReader + \brief Convenience class for reading multiple BAM files. +*/ + +/*! \fn BamMultiReader::BamMultiReader(void) + \brief constructor +*/ +BamMultiReader::BamMultiReader(void) + : d(new Internal::BamMultiReaderPrivate) +{ } + +/*! \fn BamMultiReader::~BamMultiReader(void) + \brief destructor +*/ +BamMultiReader::~BamMultiReader(void) { + delete d; + d = 0; +} + +/*! \fn void BamMultiReader::Close(void) + \brief Closes all open BAM files. + + Also clears out all header and reference data. + + \sa CloseFile(), IsOpen(), Open(), BamReader::Close() +*/ +void BamMultiReader::Close(void) { + d->Close(); +} + +/*! \fn void BamMultiReader::CloseFile(const std::string& filename) + \brief Closes requested BAM file. + + Leaves any other file(s) open, along with header and reference data. + + \sa Close(), IsOpen(), Open(), BamReader::Close() +*/ +void BamMultiReader::CloseFile(const std::string& filename) { + d->CloseFile(filename); +} + +/*! \fn bool BamMultiReader::CreateIndexes(const BamIndex::IndexType& type) + \brief Creates index files for the current BAM files. + + \param type file format to create, see BamIndex::IndexType for available formats + \return \c true if index files created OK + \sa LocateIndexes(), OpenIndexes(), BamReader::CreateIndex() +*/ +bool BamMultiReader::CreateIndexes(const BamIndex::IndexType& type) { + return d->CreateIndexes(type); +} + +/*! \fn const std::vector<std::string> BamMultiReader::Filenames(void) const + \brief Returns list of filenames for all open BAM files. + + Retrieved filenames will contain whatever was passed via Open(). + If you need full directory paths here, be sure to include them + when you open the BAM files. + + \returns names of open BAM files. If no files are open, returns an empty vector. + \sa IsOpen(), BamReader::GetFilename() +*/ +const std::vector<std::string> BamMultiReader::Filenames(void) const { + return d->Filenames(); +} + +/*! \fn SamHeader BamMultiReader::GetHeader(void) const + \brief Returns unified SAM-format header for all files + + N.B. - Modifying the retrieved text does NOT affect the current + BAM files. Thesse file have been opened in a read-only mode. However, + your modified header text can be used in conjunction with BamWriter + to generate a new BAM file with the appropriate header information. + + \returns header data wrapped in SamHeader object + \sa GetHeaderText(), BamReader::GetHeader() +*/ +SamHeader BamMultiReader::GetHeader(void) const { + return d->GetHeader(); +} + +/*! \fn std::string BamMultiReader::GetHeaderText(void) const + \brief Returns unified SAM-format header text for all files + + N.B. - Modifying the retrieved text does NOT affect the current + BAM files. Thesse file have been opened in a read-only mode. However, + your modified header text can be used in conjunction with BamWriter + to generate a new BAM file with the appropriate header information. + + \returns SAM-formatted header text + \sa GetHeader(), BamReader::GetHeaderText() +*/ +std::string BamMultiReader::GetHeaderText(void) const { + return d->GetHeaderText(); +} + +/*! \fn bool BamMultiReader::GetNextAlignment(BamAlignment& alignment) + \brief Retrieves next available alignment. + + Equivalent to BamReader::GetNextAlignment() with respect to what is a valid + overlapping alignment and what data gets populated. + + This method takes care of determining which alignment actually is 'next' + across multiple files, depending on current SortOrder. + + \param alignment destination for alignment record data + \returns \c true if a valid alignment was found + \sa GetNextAlignmentCore(), SetRegion(), SetSortOrder(), BamReader::GetNextAlignment() +*/ +bool BamMultiReader::GetNextAlignment(BamAlignment& nextAlignment) { + return d->GetNextAlignment(nextAlignment); +} + +/*! \fn bool BamMultiReader::GetNextAlignmentCore(BamAlignment& alignment) + \brief Retrieves next available alignment. + + Equivalent to BamReader::GetNextAlignmentCore() with respect to what is a valid + overlapping alignment and what data gets populated. + + This method takes care of determining which alignment actually is 'next' + across multiple files, depending on current SortOrder. + + \param alignment destination for alignment record data + \returns \c true if a valid alignment was found + \sa GetNextAlignment(), SetRegion(), SetSortOrder(), BamReader::GetNextAlignmentCore() +*/ +bool BamMultiReader::GetNextAlignmentCore(BamAlignment& nextAlignment) { + return d->GetNextAlignmentCore(nextAlignment); +} + +/*! \fn int BamMultiReader::GetReferenceCount(void) const + \brief Returns number of reference sequences. + \sa BamReader::GetReferenceCount() +*/ +int BamMultiReader::GetReferenceCount(void) const { + return d->GetReferenceCount(); +} + +/*! \fn const RefVector& BamMultiReader::GetReferenceData(void) const + \brief Returns all reference sequence entries. + \sa RefData, BamReader::GetReferenceData() +*/ +const BamTools::RefVector BamMultiReader::GetReferenceData(void) const { + return d->GetReferenceData(); +} + +/*! \fn int BamMultiReader::GetReferenceID(const std::string& refName) const + \brief Returns the ID of the reference with this name. + + If \a refName is not found, returns -1. + + \sa BamReader::GetReferenceID() +*/ +int BamMultiReader::GetReferenceID(const std::string& refName) const { + return d->GetReferenceID(refName); +} + +/*! \fn bool BamMultiReader::HasIndexes(void) const + \brief Returns \c true if all BAM files have index data available. + \sa BamReader::HasIndex() +*/ +bool BamMultiReader::HasIndexes(void) const { + return d->HasIndexes(); +} + +/*! \fn bool BamMultiReader::HasOpenReaders(void) const + \brief Returns \c true if there are any open BAM files. +*/ +bool BamMultiReader::HasOpenReaders(void) const { + return d->HasOpenReaders(); +} + +/*! \fn bool BamMultiReader::IsIndexLoaded(void) const + \brief Returns \c true if all BAM files have index data available. + + \deprecated Instead use HasIndexes() + \cond + See explanation in BamReader.cpp for more details on the deprecation decision. + \endcond +*/ + +bool BamMultiReader::IsIndexLoaded(void) const { + return d->HasIndexes(); +} + +/*! \fn bool BamMultiReader::Jump(int refID, int position) + \brief Performs a random-access jump within current BAM files. + + This is a convenience method, equivalent to calling SetRegion() + with only a left boundary specified. + + \returns \c true if jump was successful + \sa HasIndex(), BamReader::Jump() +*/ + +bool BamMultiReader::Jump(int refID, int position) { + return d->Jump(refID, position); +} + +/*! \fn bool BamMultiReader::LocateIndexes(const BamIndex::IndexType& preferredType) + \brief Looks for index files that match current BAM files. + + Use this function when you need index files, and perhaps have a + preferred index format, but do not depend heavily on which indexes + actually get loaded at runtime. + + For each BAM file, this function will defer to your \a preferredType + whenever possible. However, if an index file of \a preferredType can + not be found, then it will look for any other index file that matches + that BAM file. + + An example case would look this: + \code + + BamMultiReader reader; + // do setup + + // ensure that all files have an index + if ( !reader.LocateIndexes() ) // opens any existing index files that match our BAM files + reader.CreateIndexes(); // creates index files for BAM files that still lack one + + // do interesting stuff + // ... + + \endcode + + If you want precise control over which index files are loaded, use OpenIndexes() + with the desired index filenames. If that function returns false, you can use + CreateIndexes() to then build index files of the exact requested format. + + \param preferredType desired index file format, see BamIndex::IndexType for available formats + \returns \c true if index files could be found for \b ALL open BAM files + \sa BamReader::LocateIndex() +*/ +bool BamMultiReader::LocateIndexes(const BamIndex::IndexType& preferredType) { + return d->LocateIndexes(preferredType); +} + +/*! \fn bool BamMultiReader::Open(const std::vector<std::string>& filenames) + \brief Opens BAM files. + + N.B. - Opening BAM files will invalidate any current region set on the multireader. + All file pointers will be returned to the beginning of the alignment data. + Follow this with Jump() or SetRegion() to establish a region of interest. + + \param filenames list of BAM filenames to open + \returns \c true if BAM files were opened successfully + \sa Close(), HasOpenReaders(), OpenFile(), OpenIndexes(), BamReader::Open() +*/ +bool BamMultiReader::Open(const std::vector<std::string>& filenames) { + return d->Open(filenames); +} + +/*! \fn bool BamMultiReader::OpenFile(const std::string& filename) + \brief Opens a single BAM file. + + Adds another BAM file to multireader "on-the-fly". + + N.B. - Opening a BAM file invalidates any current region set on the multireader. + All file pointers will be returned to the beginning of the alignment data. + Follow this with Jump() or SetRegion() to establish a region of interest. + + \param filename BAM filename to open + \returns \c true if BAM file was opened successfully + \sa Close(), HasOpenReaders(), Open(), OpenIndexes(), BamReader::Open() +*/ +bool BamMultiReader::OpenFile(const std::string& filename) { + return d->OpenFile(filename); +} + +/*! \fn bool BamMultiReader::OpenIndexes(const std::vector<std::string>& indexFilenames) + \brief Opens index files for current BAM files. + + N.B. - Currently assumes that index filenames match the order (and number) of + BAM files passed to Open(). + + \param indexFilenames list of BAM index file names + \returns \c true if BAM index file was opened & data loaded successfully + \sa LocateIndex(), Open(), SetIndex(), BamReader::OpenIndex() +*/ +bool BamMultiReader::OpenIndexes(const std::vector<std::string>& indexFilenames) { + return d->OpenIndexes(indexFilenames); +} + +/*! \fn void BamMultiReader::PrintFilenames(void) const + \brief Convenience method for printing filenames to stdout. + \deprecated Doesn't really belong as an API function. Clients should + determine how the data is reported. + \sa Filenames(), BamReader::GetFilename() +*/ +void BamMultiReader::PrintFilenames(void) const { + d->PrintFilenames(); +} + +/*! \fn bool BamMultiReader::Rewind(void) + \brief Returns the internal file pointers to the beginning of alignment records. + + Useful for performing multiple sequential passes through BAM files. + Calling this function clears any prior region that may have been set. + + \returns \c true if rewind operation was successful + \sa Jump(), SetRegion(), BamReader::Rewind() +*/ +bool BamMultiReader::Rewind(void) { + return d->Rewind(); +} + +/*! \fn void BamMultiReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) + \brief Changes the caching behavior of the index data. + + Default mode is BamIndex::LimitedIndexCaching. + + \param mode desired cache mode for index, see BamIndex::IndexCacheMode for + description of the available cache modes + \sa HasIndex(), BamReader::SetIndexCacheMode() +*/ +void BamMultiReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) { + d->SetIndexCacheMode(mode); +} + +/*! \fn bool BamMultiReader::SetRegion(const BamRegion& region) + \brief Sets a target region of interest + + Equivalent to calling BamReader::SetRegion() on all open BAM files. + + \param region desired region-of-interest to activate + \returns \c true if ALL readers set the region successfully + \sa HasIndexes(), Jump(), BamReader::SetRegion() +*/ +bool BamMultiReader::SetRegion(const BamRegion& region) { + return d->SetRegion(region); +} + +/*! \fn bool BamMultiReader::SetRegion(const int& leftRefID, + const int& leftPosition, + const int& rightRefID, + const int& rightPosition) + \brief Sets a target region of interest + + This is an overloaded function. + + Equivalent to calling BamReader::SetRegion() on all open BAM files. + + \param leftRefID referenceID of region's left boundary + \param leftPosition position of region's left boundary + \param rightRefID reference ID of region's right boundary + \param rightPosition position of region's right boundary + + \returns \c true if ALL readers set the region successfully + \sa HasIndexes(), Jump(), BamReader::SetRegion() +*/ +bool BamMultiReader::SetRegion(const int& leftRefID, + const int& leftPosition, + const int& rightRefID, + const int& rightPosition) +{ + BamRegion region(leftRefID, leftPosition, rightRefID, rightPosition); + return d->SetRegion(region); +} + +/*! \fn void BamMultiReader::SetSortOrder(const SortOrder& order) + \brief Sets the expected sorting order for reading across multiple BAM files. + + Default is BamMultiReader::SortedByPosition. + + The SortOrder determines how the reader determines which alignment is "next" + from among its open readers. + + \param order expected sort order +*/ +void BamMultiReader::SetSortOrder(const SortOrder& order) { + d->SetSortOrder(order); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamMultiReader.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,127 @@ +// *************************************************************************** +// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 15 March 2011 (DB) +// --------------------------------------------------------------------------- +// Convenience class for reading multiple BAM files. +// *************************************************************************** + +#ifndef BAMMULTIREADER_H +#define BAMMULTIREADER_H + +#include <api/api_global.h> +#include <api/BamReader.h> +#include <map> +#include <sstream> +#include <string> +#include <utility> + +namespace BamTools { + +namespace Internal { + class BamMultiReaderPrivate; +} // namespace Internal + +class API_EXPORT BamMultiReader { + + public: + enum SortOrder { SortedByPosition = 0 + , SortedByReadName + , Unsorted + }; + + // constructor / destructor + public: + BamMultiReader(void); + ~BamMultiReader(void); + + // public interface + public: + + // ---------------------- + // BAM file operations + // ---------------------- + + // closes all open BAM files + void Close(void); + // close only the requested BAM file + void CloseFile(const std::string& filename); + // returns list of filenames for all open BAM files + const std::vector<std::string> Filenames(void) const; + // returns true if multireader has any open BAM files + bool HasOpenReaders(void) const; + // performs random-access jump within current BAM files + bool Jump(int refID, int position = 0); + // opens BAM files + bool Open(const std::vector<std::string>& filenames); + // opens a single BAM file, adding to any other current BAM files + bool OpenFile(const std::string& filename); + // returns file pointers to beginning of alignments + bool Rewind(void); + // sets the target region of interest + bool SetRegion(const BamRegion& region); + // sets the target region of interest + bool SetRegion(const int& leftRefID, + const int& leftPosition, + const int& rightRefID, + const int& rightPosition); + + // ---------------------- + // access alignment data + // ---------------------- + + // retrieves next available alignment + bool GetNextAlignment(BamAlignment& alignment); + // retrieves next available alignmnet (without populating the alignment's string data fields) + bool GetNextAlignmentCore(BamAlignment& alignment); + + // sets the expected sorting order for reading across multiple BAM files + void SetSortOrder(const SortOrder& order); + + // ---------------------- + // access auxiliary data + // ---------------------- + + // returns unified SAM header for all files + SamHeader GetHeader(void) const; + // returns unified SAM header text for all files + std::string GetHeaderText(void) const; + // returns number of reference sequences + int GetReferenceCount(void) const; + // returns all reference sequence entries. + const BamTools::RefVector GetReferenceData(void) const; + // returns the ID of the reference with this name. + int GetReferenceID(const std::string& refName) const; + + // ---------------------- + // BAM index operations + // ---------------------- + + // creates index files for current BAM files + bool CreateIndexes(const BamIndex::IndexType& type = BamIndex::STANDARD); + // returns true if all BAM files have index data available + bool HasIndexes(void) const; + // looks for index files that match current BAM files + bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD); + // opens index files for current BAM files. + bool OpenIndexes(const std::vector<std::string>& indexFilenames); + // changes the caching behavior of the index data + void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode); + + // deprecated methods + public: + // returns \c true if all BAM files have index data available. + bool IsIndexLoaded(void) const; + // convenience method for printing filenames to stdout + void PrintFilenames(void) const; + + // private implementation + private: + Internal::BamMultiReaderPrivate* d; +}; + +} // namespace BamTools + +#endif // BAMMULTIREADER_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamReader.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,370 @@ +// *************************************************************************** +// BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 4 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides read access to BAM files. +// *************************************************************************** + +#include <api/BamReader.h> +#include <api/internal/BamReader_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <algorithm> +#include <iostream> +#include <iterator> +#include <string> +#include <vector> +using namespace std; + +/*! \class BamTools::BamReader + \brief Provides read access to BAM files. +*/ + +/*! \fn BamReader::BamReader(void) + \brief constructor +*/ +BamReader::BamReader(void) + : d(new BamReaderPrivate(this)) +{ } + +/*! \fn BamReader::~BamReader(void) + \brief destructor +*/ +BamReader::~BamReader(void) { + delete d; + d = 0; +} + +/*! \fn void BamReader::Close(void) + \brief Closes the current BAM file. + + Also clears out all header and reference data. + + \sa IsOpen(), Open() +*/ +void BamReader::Close(void) { + d->Close(); +} + +/*! \fn bool BamReader::CreateIndex(const BamIndex::IndexType& type) + \brief Creates an index file for current BAM file. + + \param type file format to create, see BamIndex::IndexType for available formats + \return \c true if index created OK + \sa LocateIndex(), OpenIndex() +*/ +bool BamReader::CreateIndex(const BamIndex::IndexType& type) { + return d->CreateIndex(type); +} + +/*! \fn const std::string BamReader::GetFilename(void) const + \brief Returns name of current BAM file. + + Retrieved filename will contain whatever was passed via Open(). + If you need full directory paths here, be sure to include them + when you open the BAM file. + + \returns name of open BAM file. If no file is open, returns an empty string. + \sa IsOpen() +*/ +const std::string BamReader::GetFilename(void) const { + return d->Filename(); +} + +/*! \fn SamHeader BamReader::GetHeader(void) const + \brief Returns SAM header data. + + Header data is wrapped in a SamHeader object that can be conveniently queried & modified. + + N.B. - Modifying the retrieved SamHeader object does NOT affect the + current BAM file. This file has been opened in a read-only mode. + However, your modified SamHeader object can be used in conjunction with + BamWriter to generate a new BAM file with the appropriate header information. + + \returns header data object + \sa GetHeaderText() +*/ +SamHeader BamReader::GetHeader(void) const { + return d->GetSamHeader(); +} + +/*! \fn std::string BamReader::GetHeaderText(void) const + \brief Returns SAM header data, as SAM-formatted text. + + N.B. - Modifying the retrieved text does NOT affect the current + BAM file. This file has been opened in a read-only mode. However, + your modified header text can be used in conjunction with BamWriter + to generate a new BAM file with the appropriate header information. + + \returns SAM-formatted header text + \sa GetHeader() +*/ +std::string BamReader::GetHeaderText(void) const { + return d->GetHeaderText(); +} + +/*! \fn bool BamReader::GetNextAlignment(BamAlignment& alignment) + \brief Retrieves next available alignment. + + Attempts to read the next alignment record from BAM file, and checks to see + if it overlaps the current region. If no region is currently set, then the + next alignment available is always considered valid. + + If a region has been set, via Jump() or SetRegion(), an alignment is only + considered valid if it overlaps the region. If the actual 'next' alignment record + in the BAM file does not overlap this region, then this function will read sequentially + through the file until the next alignment that overlaps this region is found. + Once the region has been exhausted (i.e. the next alignment loaded is beyond the region), + the function aborts and returns \c false. In this case, there is no point to continue + reading, assuming properly sorted alignments. + + This function fully populates all of the alignment's available data fields, + including the string data fields (read name, bases, qualities, tags, filename). + If only positional data (refID, position, CIGAR ops, alignment flags, etc.) + are required, consider using GetNextAlignmentCore() for a significant + performance boost. + + \param alignment destination for alignment record data + \returns \c true if a valid alignment was found +*/ +bool BamReader::GetNextAlignment(BamAlignment& alignment) { + return d->GetNextAlignment(alignment); +} + +/*! \fn bool BamReader::GetNextAlignmentCore(BamAlignment& alignment) + \brief Retrieves next available alignment, without populating the alignment's string data fields. + + Equivalent to GetNextAlignment() with respect to what is a valid overlapping alignment. + + However, this method does NOT populate the alignment's string data fields + (read name, bases, qualities, tags, filename). This provides a boost in speed + when these fields are not required for every alignment. These fields can be + populated 'lazily' (as needed) by calling BamAlignment::BuildCharData() later. + + \param alignment destination for alignment record data + \returns \c true if a valid alignment was found + \sa SetRegion() +*/ +bool BamReader::GetNextAlignmentCore(BamAlignment& alignment) { + return d->GetNextAlignmentCore(alignment); +} + +/*! \fn int BamReader::GetReferenceCount(void) const + \brief Returns number of reference sequences. +*/ +int BamReader::GetReferenceCount(void) const { + return d->GetReferenceCount(); +} + +/*! \fn const RefVector& BamReader::GetReferenceData(void) const + \brief Returns all reference sequence entries. + \sa RefData +*/ +const RefVector& BamReader::GetReferenceData(void) const { + return d->GetReferenceData(); +} + +/*! \fn int BamReader::GetReferenceID(const std::string& refName) const + \brief Returns the ID of the reference with this name. + + If \a refName is not found, returns -1. +*/ +int BamReader::GetReferenceID(const std::string& refName) const { + return d->GetReferenceID(refName); +} + +/*! \fn bool BamReader::HasIndex(void) const + \brief Returns \c true if index data is available. +*/ +bool BamReader::HasIndex(void) const { + return d->HasIndex(); +} + +/*! \fn bool BamReader::IsIndexLoaded(void) const + \brief Returns \c true if index data is available. + + \deprecated Instead use HasIndex() + \cond + Deprecated purely for API semantic clarity - HasIndex() should be clearer + than IsIndexLoaded() in light of the new caching modes that may clear the + index data from memory, but leave the index file open for later random access + seeks. + + For example, what would (IsIndexLoaded() == true) mean when cacheMode has been + explicitly set to NoIndexCaching? This is confusing at best, misleading about + current memory behavior at worst. + \endcond +*/ +bool BamReader::IsIndexLoaded(void) const { + return d->HasIndex(); +} + +/*! \fn bool BamReader::IsOpen(void) const + \brief Returns \c true if a BAM file is open for reading. +*/ +bool BamReader::IsOpen(void) const { + return d->IsOpen(); +} + +/*! \fn bool BamReader::Jump(int refID, int position) + \brief Performs a random-access jump within BAM file. + + This is a convenience method, equivalent to calling SetRegion() + with only a left boundary specified. + + \returns \c true if jump was successful + \sa HasIndex() +*/ +bool BamReader::Jump(int refID, int position) { + return d->SetRegion( BamRegion(refID, position) ); +} + +/*! \fn bool BamReader::LocateIndex(const BamIndex::IndexType& preferredType) + \brief Looks in BAM file's directory for a matching index file. + + Use this function when you need an index file, and perhaps have a + preferred index format, but do not depend heavily on which format + actually gets loaded at runtime. + + This function will defer to your \a preferredType whenever possible. + However, if an index file of \a preferredType can not be found, then + it will look for any other index file that corresponds to this BAM file. + + If you want precise control over which index file is loaded, use OpenIndex() + with the desired index filename. If that function returns false, you can use + CreateIndex() to then build an index of the exact requested format. + + \param preferredType desired index file format, see BamIndex::IndexType for available formats + \returns \c true if (any) index file could be found +*/ +bool BamReader::LocateIndex(const BamIndex::IndexType& preferredType) { + return d->LocateIndex(preferredType); +} + +/*! \fn bool BamReader::Open(const std::string& filename) + \brief Opens a BAM file. + + If BamReader is already opened on another file, this function closes + that file, then attempts to open requested \a filename. + + \param filename name of BAM file to open + \returns \c true if BAM file was opened successfully + \sa Close(), IsOpen(), OpenIndex() +*/ +bool BamReader::Open(const std::string& filename) { + return d->Open(filename); +} + +/*! \fn bool BamReader::OpenIndex(const std::string& indexFilename) + \brief Opens a BAM index file. + + \param indexFilename name of BAM index file + + \returns \c true if BAM index file was opened & data loaded successfully + \sa LocateIndex(), Open(), SetIndex() +*/ +bool BamReader::OpenIndex(const std::string& indexFilename) { + return d->OpenIndex(indexFilename); +} + +/*! \fn bool BamReader::Rewind(void) + \brief Returns the internal file pointer to the first alignment record. + + Useful for performing multiple sequential passes through a BAM file. + Calling this function clears any prior region that may have been set. + + N.B. - Note that this function sets the file pointer to first alignment record + in the BAM file, NOT the beginning of the file. + + \returns \c true if rewind operation was successful + \sa Jump(), SetRegion() +*/ +bool BamReader::Rewind(void) { + return d->Rewind(); +} + +/*! \fn void BamReader::SetIndex(BamIndex* index) + \brief Sets a custom BamIndex on this reader. + + Only necessary for custom BamIndex subclasses. Most clients should + never have to use this function. + + Example: + \code + BamReader reader; + reader.SetIndex(new MyCustomBamIndex); + \endcode + + N.B. - BamReader takes ownership of \a index - i.e. BamReader will + take care of deleting the pointer when the reader is destructed, + when the current BAM file is closed, or when a new index is requested. + + \param index custom BamIndex subclass created by client + \sa CreateIndex(), LocateIndex(), OpenIndex() +*/ +void BamReader::SetIndex(BamIndex* index) { + d->SetIndex(index); +} + +/*! \fn void BamReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) + \brief Changes the caching behavior of the index data. + + Default mode is BamIndex::LimitedIndexCaching. + + \param mode desired cache mode for index, see BamIndex::IndexCacheMode for + description of the available cache modes + \sa HasIndex() +*/ +void BamReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) { + d->SetIndexCacheMode(mode); +} + +/*! \fn bool BamReader::SetRegion(const BamRegion& region) + \brief Sets a target region of interest + + Requires that index data be available. Attempts a random-access + jump in the BAM file, near \a region left boundary position. + + Subsequent calls to GetNextAlignment() or GetNextAlignmentCore() + will only return \c true when alignments can be found that overlap + this \a region. + + A \a region with no right boundary is considered open-ended, meaning + that all alignments that lie downstream of the left boundary are + considered valid, continuing to the end of the BAM file. + + \param region desired region-of-interest to activate + \returns \c true if reader was able to jump successfully to the region's left boundary + \sa HasIndex(), Jump() +*/ +bool BamReader::SetRegion(const BamRegion& region) { + return d->SetRegion(region); +} + +/*! \fn bool BamReader::SetRegion(const int& leftRefID, + const int& leftPosition, + const int& rightRefID, + const int& rightPosition) + \brief Sets a target region of interest. + + This is an overloaded function. + + \param leftRefID referenceID of region's left boundary + \param leftPosition position of region's left boundary + \param rightRefID reference ID of region's right boundary + \param rightPosition position of region's right boundary + + \returns \c true if reader was able to jump successfully to the region's left boundary + \sa HasIndex(), Jump() +*/ +bool BamReader::SetRegion(const int& leftRefID, + const int& leftBound, + const int& rightRefID, + const int& rightBound) +{ + return d->SetRegion( BamRegion(leftRefID, leftBound, rightRefID, rightBound) ); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamReader.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,118 @@ +// *************************************************************************** +// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 4 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides read access to BAM files. +// *************************************************************************** + +#ifndef BAMREADER_H +#define BAMREADER_H + +#include <api/api_global.h> +#include <api/BamAlignment.h> +#include <api/BamIndex.h> +#include <api/SamHeader.h> +#include <string> + +namespace BamTools { + +namespace Internal { + class BamReaderPrivate; +} // namespace Internal + +class API_EXPORT BamReader { + + // constructor / destructor + public: + BamReader(void); + ~BamReader(void); + + // public interface + public: + + // ---------------------- + // BAM file operations + // ---------------------- + + // closes the current BAM file + void Close(void); + // returns filename of current BAM file + const std::string GetFilename(void) const; + // returns true if a BAM file is open for reading + bool IsOpen(void) const; + // performs random-access jump within BAM file + bool Jump(int refID, int position = 0); + // opens a BAM file + bool Open(const std::string& filename); + // returns internal file pointer to beginning of alignment data + bool Rewind(void); + // sets the target region of interest + bool SetRegion(const BamRegion& region); + // sets the target region of interest + bool SetRegion(const int& leftRefID, + const int& leftPosition, + const int& rightRefID, + const int& rightPosition); + + // ---------------------- + // access alignment data + // ---------------------- + + // retrieves next available alignment + bool GetNextAlignment(BamAlignment& alignment); + // retrieves next available alignmnet (without populating the alignment's string data fields) + bool GetNextAlignmentCore(BamAlignment& alignment); + + // ---------------------- + // access header data + // ---------------------- + + // returns SAM header data + SamHeader GetHeader(void) const; + // returns SAM header data, as SAM-formatted text + std::string GetHeaderText(void) const; + + // ---------------------- + // access reference data + // ---------------------- + + // returns the number of reference sequences + int GetReferenceCount(void) const; + // returns all reference sequence entries + const RefVector& GetReferenceData(void) const; + // returns the ID of the reference with this name + int GetReferenceID(const std::string& refName) const; + + // ---------------------- + // BAM index operations + // ---------------------- + + // creates an index file for current BAM file, using the requested index type + bool CreateIndex(const BamIndex::IndexType& type = BamIndex::STANDARD); + // returns true if index data is available + bool HasIndex(void) const; + // looks in BAM file's directory for a matching index file + bool LocateIndex(const BamIndex::IndexType& preferredType = BamIndex::STANDARD); + // opens a BAM index file + bool OpenIndex(const std::string& indexFilename); + // sets a custom BamIndex on this reader + void SetIndex(BamIndex* index); + // changes the caching behavior of the index data + void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode); + + // deprecated methods + public: + // returns true if index data is available + bool IsIndexLoaded(void) const; + + // private implementation + private: + Internal::BamReaderPrivate* d; +}; + +} // namespace BamTools + +#endif // BAMREADER_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamWriter.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,143 @@ +// *************************************************************************** +// BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 4 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for producing BAM files +// *************************************************************************** + +#include <api/BamAlignment.h> +#include <api/BamWriter.h> +#include <api/SamHeader.h> +#include <api/internal/BamWriter_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <iostream> +using namespace std; + +/*! \class BamTools::BamWriter + \brief Provides write access for generating BAM files. +*/ +/*! \enum BamTools::BamWriter::CompressionMode + \brief This enum describes the compression behaviors for output BAM files. +*/ +/*! \var BamWriter::CompressionMode BamWriter::Compressed + \brief Use normal BAM compression +*/ +/*! \var BamWriter::CompressionMode BamWriter::Uncompressed + \brief Disable BAM compression + + Useful in situations where the BAM data is streamed (e.g. piping). + It would be wasteful to compress, and then immediately decompress + the data. +*/ + +/*! \fn BamWriter::BamWriter(void) + \brief constructor +*/ +BamWriter::BamWriter(void) + : d(new BamWriterPrivate) +{ } + +/*! \fn BamWriter::~BamWriter(void) + \brief destructor +*/ +BamWriter::~BamWriter(void) { + delete d; + d = 0; +} + +/*! \fn BamWriter::Close(void) + \brief Closes the current BAM file. + \sa Open() +*/ +void BamWriter::Close(void) { + d->Close(); +} + +/*! \fn bool BamWriter::IsOpen(void) const + \brief Returns \c true if BAM file is open for writing. + \sa Open() +*/ +bool BamWriter::IsOpen(void) const { + return d->IsOpen(); +} + +/*! \fn bool BamWriter::Open(const std::string& filename, + const std::string& samHeaderText, + const RefVector& referenceSequences) + \brief Opens a BAM file for writing. + + Will overwrite the BAM file if it already exists. + + \param filename name of output BAM file + \param samHeaderText header data, as SAM-formatted string + \param referenceSequences list of reference entries + + \return \c true if opened successfully + \sa Close(), IsOpen(), BamReader::GetHeaderText(), BamReader::GetReferenceData() +*/ +bool BamWriter::Open(const std::string& filename, + const std::string& samHeaderText, + const RefVector& referenceSequences) +{ + return d->Open(filename, samHeaderText, referenceSequences); +} + +/*! \fn bool BamWriter::Open(const std::string& filename, + const SamHeader& samHeader, + const RefVector& referenceSequences) + \brief Opens a BAM file for writing. + + This is an overloaded function. + + Will overwrite the BAM file if it already exists. + + \param filename name of output BAM file + \param samHeader header data, wrapped in SamHeader object + \param referenceSequences list of reference entries + + \return \c true if opened successfully + \sa Close(), IsOpen(), BamReader::GetHeader(), BamReader::GetReferenceData() +*/ +bool BamWriter::Open(const std::string& filename, + const SamHeader& samHeader, + const RefVector& referenceSequences) +{ + return d->Open(filename, samHeader.ToString(), referenceSequences); +} + +/*! \fn void BamWriter::SaveAlignment(const BamAlignment& alignment) + \brief Saves an alignment to the BAM file. + + \param alignment BamAlignment record to save + \sa BamReader::GetNextAlignment(), BamReader::GetNextAlignmentCore() +*/ +void BamWriter::SaveAlignment(const BamAlignment& alignment) { + d->SaveAlignment(alignment); +} + +/*! \fn void BamWriter::SetCompressionMode(const CompressionMode& compressionMode) + \brief Sets the output compression mode. + + Default mode is BamWriter::Compressed. + + N.B. - Changing the compression mode is disabled on open files (i.e. the request will be ignored). + Be sure to call this function before opening the BAM file. + + \code + BamWriter writer; + writer.SetCompressionMode(BamWriter::Uncompressed); + writer.Open( ... ); + // ... + \endcode + + \param compressionMode desired output compression behavior + \sa IsOpen(), Open() +*/ +void BamWriter::SetCompressionMode(const CompressionMode& compressionMode) { + d->SetWriteCompressed( compressionMode == BamWriter::Compressed ); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/BamWriter.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,64 @@ +// *************************************************************************** +// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 4 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for producing BAM files +// *************************************************************************** + +#ifndef BAMWRITER_H +#define BAMWRITER_H + +#include <api/api_global.h> +#include <api/BamAux.h> +#include <string> + +namespace BamTools { + +class BamAlignment; +class SamHeader; + +namespace Internal { + class BamWriterPrivate; +} // namespace Internal + +class API_EXPORT BamWriter { + + public: enum CompressionMode { Compressed = 0 + , Uncompressed + }; + + // ctor & dtor + public: + BamWriter(void); + ~BamWriter(void); + + // public interface + public: + // closes the current BAM file + void Close(void); + // returns true if BAM file is open for writing + bool IsOpen(void) const; + // opens a BAM file for writing + bool Open(const std::string& filename, + const std::string& samHeaderText, + const RefVector& referenceSequences); + // opens a BAM file for writing + bool Open(const std::string& filename, + const SamHeader& samHeader, + const RefVector& referenceSequences); + // saves the alignment to the alignment archive + void SaveAlignment(const BamAlignment& alignment); + // sets the output compression mode + void SetCompressionMode(const CompressionMode& compressionMode); + + // private implementation + private: + Internal::BamWriterPrivate* d; +}; + +} // namespace BamTools + +#endif // BAMWRITER_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/CMakeLists.txt Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,78 @@ +# ========================== +# BamTools CMakeLists.txt +# (c) 2010 Derek Barnett +# +# src/api/ +# ========================== + +# list include paths +include_directories( ${BamTools_SOURCE_DIR}/src ) + +# add compiler definitions +add_definitions( -DBAMTOOLS_API_LIBRARY ) # (for proper exporting of library symbols) +add_definitions( -fPIC ) # (attempt to force PIC compiling on some archs) + +# list of all BamTools API source (.cpp) files +set( BamToolsAPISources + BamAlignment.cpp + BamMultiReader.cpp + BamReader.cpp + BamWriter.cpp + SamHeader.cpp + SamProgram.cpp + SamProgramChain.cpp + SamReadGroup.cpp + SamReadGroupDictionary.cpp + SamSequence.cpp + SamSequenceDictionary.cpp + internal/BamHeader_p.cpp + internal/BamIndexFactory_p.cpp + internal/BamMultiReader_p.cpp + internal/BamRandomAccessController_p.cpp + internal/BamReader_p.cpp + internal/BamStandardIndex_p.cpp + internal/BamToolsIndex_p.cpp + internal/BamWriter_p.cpp + internal/BgzfStream_p.cpp + internal/SamFormatParser_p.cpp + internal/SamFormatPrinter_p.cpp + internal/SamHeaderValidator_p.cpp +) + +# create main BamTools API shared library +add_library( BamTools SHARED ${BamToolsAPISources} ) +set_target_properties( BamTools PROPERTIES SOVERSION "1.0.2" ) +set_target_properties( BamTools PROPERTIES OUTPUT_NAME "bamtools" ) + +# create main BamTools API static library +add_library( BamTools-static STATIC ${BamToolsAPISources} ) +set_target_properties( BamTools-static PROPERTIES OUTPUT_NAME "bamtools" ) +set_target_properties( BamTools-static PROPERTIES PREFIX "lib" ) + +# link libraries with zlib automatically +target_link_libraries( BamTools z ) +target_link_libraries( BamTools-static z ) + +# set library install destinations +install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools") +install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") + +# export API headers +include(../ExportHeader.cmake) +set(ApiIncludeDir "api") +ExportHeader(APIHeaders api_global.h ${ApiIncludeDir}) +ExportHeader(APIHeaders BamAlignment.h ${ApiIncludeDir}) +ExportHeader(APIHeaders BamAux.h ${ApiIncludeDir}) +ExportHeader(APIHeaders BamConstants.h ${ApiIncludeDir}) +ExportHeader(APIHeaders BamIndex.h ${ApiIncludeDir}) +ExportHeader(APIHeaders BamMultiReader.h ${ApiIncludeDir}) +ExportHeader(APIHeaders BamReader.h ${ApiIncludeDir}) +ExportHeader(APIHeaders BamWriter.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamConstants.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamHeader.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamProgram.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamProgramChain.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamReadGroup.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamReadGroupDictionary.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamSequence.h ${ApiIncludeDir}) +ExportHeader(APIHeaders SamSequenceDictionary.h ${ApiIncludeDir})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamConstants.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,96 @@ +// *************************************************************************** +// SamConstants.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides constants for SAM header +// *************************************************************************** + +#ifndef SAM_CONSTANTS_H +#define SAM_CONSTANTS_H + +#include <api/api_global.h> +#include <string> + +namespace BamTools { +namespace Constants { + +// basic char constants used in SAM format +const char SAM_COLON = ':'; +const char SAM_EQUAL = '='; +const char SAM_PERIOD = '.'; +const char SAM_STAR = '*'; +const char SAM_TAB = '\t'; +const std::string SAM_DIGITS = "0123456789"; + +// HD entries +const std::string SAM_HD_BEGIN_TOKEN = "@HD"; +const std::string SAM_HD_VERSION_TAG = "VN"; +const std::string SAM_HD_SORTORDER_TAG = "SO"; +const std::string SAM_HD_GROUPORDER_TAG = "GO"; + +// SQ entries +const std::string SAM_SQ_BEGIN_TOKEN = "@SQ"; +const std::string SAM_SQ_ASSEMBLYID_TAG = "AS"; +const std::string SAM_SQ_CHECKSUM_TAG = "M5"; +const std::string SAM_SQ_LENGTH_TAG = "LN"; +const std::string SAM_SQ_NAME_TAG = "SN"; +const std::string SAM_SQ_SPECIES_TAG = "SP"; +const std::string SAM_SQ_URI_TAG = "UR"; + +// RG entries +const std::string SAM_RG_BEGIN_TOKEN = "@RG"; +const std::string SAM_RG_DESCRIPTION_TAG = "DS"; +const std::string SAM_RG_FLOWORDER_TAG = "FO"; +const std::string SAM_RG_ID_TAG = "ID"; +const std::string SAM_RG_KEYSEQUENCE_TAG = "KS"; +const std::string SAM_RG_LIBRARY_TAG = "LB"; +const std::string SAM_RG_PLATFORMUNIT_TAG = "PU"; +const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI"; +const std::string SAM_RG_PRODUCTIONDATE_TAG = "DT"; +const std::string SAM_RG_PROGRAM_TAG = "PG"; +const std::string SAM_RG_SAMPLE_TAG = "SM"; +const std::string SAM_RG_SEQCENTER_TAG = "CN"; +const std::string SAM_RG_SEQTECHNOLOGY_TAG = "PL"; + +// PG entries +const std::string SAM_PG_BEGIN_TOKEN = "@PG"; +const std::string SAM_PG_COMMANDLINE_TAG = "CL"; +const std::string SAM_PG_ID_TAG = "ID"; +const std::string SAM_PG_NAME_TAG = "PN"; +const std::string SAM_PG_PREVIOUSPROGRAM_TAG = "PP"; +const std::string SAM_PG_VERSION_TAG = "VN"; + +// CO entries +const std::string SAM_CO_BEGIN_TOKEN = "@CO"; + +// HD:SO values +const std::string SAM_HD_SORTORDER_COORDINATE = "coordinate"; +const std::string SAM_HD_SORTORDER_QUERYNAME = "queryname"; +const std::string SAM_HD_SORTORDER_UNKNOWN = "unknown"; +const std::string SAM_HD_SORTORDER_UNSORTED = "unsorted"; + +// HD:GO values +const std::string SAM_HD_GROUPORDER_NONE = "none"; +const std::string SAM_HD_GROUPORDER_QUERY = "query"; +const std::string SAM_HD_GROUPORDER_REFERENCE = "reference"; + +// SQ:LN values +const unsigned int SAM_SQ_LENGTH_MIN = 1; +const unsigned int SAM_SQ_LENGTH_MAX = 536870911; // 2^29 - 1 + +// RG:PL values +const std::string SAM_RG_SEQTECHNOLOGY_CAPILLARY = "CAPILLARY"; +const std::string SAM_RG_SEQTECHNOLOGY_HELICOS = "HELICOS"; +const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA = "ILLUMINA"; +const std::string SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT"; +const std::string SAM_RG_SEQTECHNOLOGY_LS454 = "LS454"; +const std::string SAM_RG_SEQTECHNOLOGY_PACBIO = "PACBIO"; +const std::string SAM_RG_SEQTECHNOLOGY_SOLID = "SOLID"; + +} // namespace Constants +} // namespace BamTools + +#endif // SAM_CONSTANTS_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamHeader.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,185 @@ +// *************************************************************************** +// SamHeader.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM header data fields. +// *************************************************************************** + +#include <api/SamConstants.h> +#include <api/SamHeader.h> +#include <api/internal/SamFormatParser_p.h> +#include <api/internal/SamFormatPrinter_p.h> +#include <api/internal/SamHeaderValidator_p.h> +using namespace BamTools; +using namespace BamTools::Internal; +using namespace std; + +/*! \struct BamTools::SamHeader + \brief Represents the SAM-formatted text header that is part of the BAM file header. + + Provides direct read/write access to the SAM header data fields. + + \sa \samSpecURL +*/ +/*! \var SamHeader::Version + \brief corresponds to \@HD VN:\<Version\> + + Required for valid SAM header, if @HD record is present. +*/ +/*! \var SamHeader::SortOrder + \brief corresponds to \@HD SO:\<SortOrder\> +*/ +/*! \var SamHeader::GroupOrder + \brief corresponds to \@HD GO:\<GroupOrder\> +*/ +/*! \var SamHeader::Sequences + \brief corresponds to \@SQ entries + \sa SamSequence, SamSequenceDictionary +*/ +/*! \var SamHeader::ReadGroups + \brief corresponds to \@RG entries + \sa SamReadGroup, SamReadGroupDictionary +*/ +/*! \var SamHeader::ProgramName + \brief corresponds to \@PG ID:\<ProgramName\> +*/ +/*! \var SamHeader::ProgramVersion + \brief corresponds to \@PG VN:\<ProgramVersion\> +*/ +/*! \var SamHeader::ProgramCommandLine + \brief corresponds to \@PG CL:\<ProgramCommandLine\> +*/ +/*! \var SamHeader::Comments + \brief corresponds to \@CO entries +*/ + +/*! \fn SamHeader::SamHeader(const std::string& headerText = "") + \brief constructor +*/ +SamHeader::SamHeader(const std::string& headerText) + : Version("") + , SortOrder(Constants::SAM_HD_SORTORDER_UNKNOWN) + , GroupOrder("") +{ + SamFormatParser parser(*this); + parser.Parse(headerText); +} + +/*! \fn SamHeader::SamHeader(const SamHeader& other) + \brief copy constructor +*/ +SamHeader::SamHeader(const SamHeader& other) + : Version(other.Version) + , SortOrder(other.SortOrder) + , GroupOrder(other.GroupOrder) + , Sequences(other.Sequences) + , ReadGroups(other.ReadGroups) + , Programs(other.Programs) +{ } + +/*! \fn SamHeader::~SamHeader(void) + \brief destructor +*/ +SamHeader::~SamHeader(void) { } + +/*! \fn void SamHeader::Clear(void) + \brief Clears all header contents. +*/ +void SamHeader::Clear(void) { + Version.clear(); + SortOrder.clear(); + GroupOrder.clear(); + Sequences.Clear(); + ReadGroups.Clear(); + Programs.Clear(); + Comments.clear(); +} + +/*! \fn bool SamHeader::HasVersion(void) const + \brief Returns \c true if header contains \@HD ID:\<Version\> +*/ +bool SamHeader::HasVersion(void) const { + return (!Version.empty()); +} + +/*! \fn bool SamHeader::HasSortOrder(void) const + \brief Returns \c true if header contains \@HD SO:\<SortOrder\> +*/ +bool SamHeader::HasSortOrder(void) const { + return (!SortOrder.empty()); +} + +/*! \fn bool SamHeader::HasGroupOrder(void) const + \brief Returns \c true if header contains \@HD GO:\<GroupOrder\> +*/ +bool SamHeader::HasGroupOrder(void) const { + return (!GroupOrder.empty()); +} + +/*! \fn bool SamHeader::HasSequences(void) const + \brief Returns \c true if header contains any \@SQ entries +*/ +bool SamHeader::HasSequences(void) const { + return (!Sequences.IsEmpty()); +} + +/*! \fn bool SamHeader::HasReadGroups(void) const + \brief Returns \c true if header contains any \@RG entries +*/ +bool SamHeader::HasReadGroups(void) const { + return (!ReadGroups.IsEmpty()); +} + +/*! \fn bool SamHeader::HasPrograms(void) const + \brief Returns \c true if header contains any \@PG entries +*/ +bool SamHeader::HasPrograms(void) const { + return (!Programs.IsEmpty()); +} + +/*! \fn bool SamHeader::HasComments(void) const + \brief Returns \c true if header contains any \@CO entries +*/ +bool SamHeader::HasComments(void) const { + return (!Comments.empty()); +} + +/*! \fn bool SamHeader::IsValid(bool verbose = false) const + \brief Checks header contents for required data and proper formatting. + \param verbose If set to true, validation errors & warnings will be printed to stderr. + Otherwise, output is suppressed and only validation check occurs. + \return \c true if SAM header is well-formed +*/ +bool SamHeader::IsValid(bool verbose) const { + SamHeaderValidator validator(*this); + return validator.Validate(verbose); +} + +/*! \fn void SamHeader::SetHeaderText(const std::string& headerText) + \brief Replaces header contents with \a headerText. + \param headerText SAM formatted-text that will be parsed into data fields +*/ +void SamHeader::SetHeaderText(const std::string& headerText) { + + // clear prior data + Clear(); + + // parse header text into data + SamFormatParser parser(*this); + parser.Parse(headerText); +} + +/*! \fn std::string SamHeader::ToString(void) const + \brief Converts data fields to SAM-formatted text. + + Applies any local modifications made since creating this object or calling SetHeaderText(). + + \return SAM-formatted header text +*/ +string SamHeader::ToString(void) const { + SamFormatPrinter printer(*this); + return printer.ToString(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamHeader.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,69 @@ +// *************************************************************************** +// SamHeader.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM header data fields. +// *************************************************************************** + +#ifndef SAM_HEADER_H +#define SAM_HEADER_H + +#include <api/api_global.h> +#include <api/SamProgramChain.h> +#include <api/SamReadGroupDictionary.h> +#include <api/SamSequenceDictionary.h> +#include <string> +#include <vector> + +namespace BamTools { + +struct API_EXPORT SamHeader { + + // ctor & dtor + SamHeader(const std::string& headerText = ""); + SamHeader(const SamHeader& other); + ~SamHeader(void); + + // query/modify entire SamHeader + void Clear(void); // clears all header contents + bool IsValid(bool verbose = false) const; // returns true if SAM header is well-formed + void SetHeaderText(const std::string& headerText); // replaces data fields with contents of SAM-formatted text + std::string ToString(void) const; // returns the printable, SAM-formatted header text + + // convenience query methods + bool HasVersion(void) const; // returns true if header contains format version entry + bool HasSortOrder(void) const; // returns true if header contains sort order entry + bool HasGroupOrder(void) const; // returns true if header contains group order entry + bool HasSequences(void) const; // returns true if header contains any sequence entries + bool HasReadGroups(void) const; // returns true if header contains any read group entries + bool HasPrograms(void) const; // returns true if header contains any program record entries + bool HasComments(void) const; // returns true if header contains comments + + // -------------- + // data members + // -------------- + + // header metadata (@HD line) + std::string Version; // VN:<Version> *Required for valid SAM header, if @HD record is present* + std::string SortOrder; // SO:<SortOrder> + std::string GroupOrder; // GO:<GroupOrder> + + // header sequences (@SQ entries) + SamSequenceDictionary Sequences; + + // header read groups (@RG entries) + SamReadGroupDictionary ReadGroups; + + // header program data (@PG entries) + SamProgramChain Programs; + + // header comments (@CO entries) + std::vector<std::string> Comments; +}; + +} // namespace BamTools + +#endif // SAM_HEADER_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamProgram.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,140 @@ +// *************************************************************************** +// SamProgram.cpp (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM header program records. +// *************************************************************************** + +#include <api/SamProgram.h> +using namespace BamTools; +using namespace std; + +/*! \struct BamTools::SamProgram + \brief Represents a SAM program record. + + Provides direct read/write access to the SAM header program records. + + \sa \samSpecURL +*/ +/*! \var SamProgram::CommandLine + \brief corresponds to \@PG CL:\<CommandLine\> +*/ +/*! \var SamProgram::ID + \brief corresponds to \@PG ID:\<ID\> + + Required for valid SAM header. +*/ +/*! \var SamProgram::Name + \brief corresponds to \@PG PN:\<Name\> +*/ +/*! \var SamProgram::PreviousProgramID + \brief corresponds to \@PG PP:\<PreviousProgramID\> +*/ +/*! \var SamProgram::Version + \brief corresponds to \@PG VN:\<Version\> +*/ +/*! \var SamProgram::NextProgramID + \internal + Holds ID of the "next" program record in a SamProgramChain +*/ + +/*! \fn SamProgram::SamProgram(void) + \brief default constructor +*/ +SamProgram::SamProgram(void) + : CommandLine("") + , ID("") + , Name("") + , PreviousProgramID("") + , Version("") + , NextProgramID("") +{ } + +/*! \fn SamProgram::SamProgram(const std::string& id) + \brief constructs program record with \a id + + \param id desired program record ID +*/ +SamProgram::SamProgram(const std::string& id) + : CommandLine("") + , ID(id) + , Name("") + , PreviousProgramID("") + , Version("") + , NextProgramID("") +{ } + +/*! \fn SamProgram::SamProgram(const SamProgram& other) + \brief copy constructor +*/ +SamProgram::SamProgram(const SamProgram& other) + : CommandLine(other.CommandLine) + , ID(other.ID) + , Name(other.Name) + , PreviousProgramID(other.PreviousProgramID) + , Version(other.Version) + , NextProgramID(other.NextProgramID) +{ } + +/*! \fn SamProgram::~SamProgram(void) + \brief destructor +*/ +SamProgram::~SamProgram(void) { } + +/*! \fn void SamProgram::Clear(void) + \brief Clears all data fields. +*/ +void SamProgram::Clear(void) { + CommandLine.clear(); + ID.clear(); + Name.clear(); + PreviousProgramID.clear(); + Version.clear(); + NextProgramID.clear(); +} + +/*! \fn bool SamProgram::HasCommandLine(void) const + \brief Returns \c true if program record contains \@PG: CL:\<CommandLine\> +*/ +bool SamProgram::HasCommandLine(void) const { + return (!CommandLine.empty()); +} + +/*! \fn bool SamProgram::HasID(void) const + \brief Returns \c true if program record contains \@PG: ID:\<ID\> +*/ +bool SamProgram::HasID(void) const { + return (!ID.empty()); +} + +/*! \fn bool SamProgram::HasName(void) const + \brief Returns \c true if program record contains \@PG: PN:\<Name\> +*/ +bool SamProgram::HasName(void) const { + return (!Name.empty()); +} + +/*! \fn bool SamProgram::HasNextProgramID(void) const + \internal + \return true if program has a "next" record in a SamProgramChain +*/ +bool SamProgram::HasNextProgramID(void) const { + return (!NextProgramID.empty()); +} + +/*! \fn bool SamProgram::HasPreviousProgramID(void) const + \brief Returns \c true if program record contains \@PG: PP:\<PreviousProgramID\> +*/ +bool SamProgram::HasPreviousProgramID(void) const { + return (!PreviousProgramID.empty()); +} + +/*! \fn bool SamProgram::HasVersion(void) const + \brief Returns \c true if program record contains \@PG: VN:\<Version\> +*/ +bool SamProgram::HasVersion(void) const { + return (!Version.empty()); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamProgram.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,62 @@ +// *************************************************************************** +// SamProgram.h (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM header program records. +// *************************************************************************** + +#ifndef SAM_PROGRAM_H +#define SAM_PROGRAM_H + +#include "api/api_global.h" +#include <string> + +namespace BamTools { + +class SamProgramChain; + +struct API_EXPORT SamProgram { + + // ctor & dtor + SamProgram(void); + SamProgram(const std::string& id); + SamProgram(const SamProgram& other); + ~SamProgram(void); + + // query/modify entire program record + void Clear(void); // clears all data fields + + // convenience query methods + bool HasCommandLine(void) const; // returns true if program record has a command line entry + bool HasID(void) const; // returns true if program record has an ID + bool HasName(void) const; // returns true if program record has a name + bool HasPreviousProgramID(void) const; // returns true if program record has a 'previous program ID' + bool HasVersion(void) const; // returns true if program record has a version + + // data members + std::string CommandLine; // CL:<CommandLine> + std::string ID; // ID:<ID> *Required for valid SAM header* + std::string Name; // PN:<Name> + std::string PreviousProgramID; // PP:<PreviousProgramID> + std::string Version; // VN:<Version> + + // internal (non-standard) methods & fields + private: + bool HasNextProgramID(void) const; + std::string NextProgramID; + friend class BamTools::SamProgramChain; +}; + +/*! \fn bool operator==(const SamProgram& lhs, const SamProgram& rhs) + \brief tests equality by comparing program IDs +*/ +API_EXPORT inline bool operator==(const SamProgram& lhs, const SamProgram& rhs) { + return lhs.ID == rhs.ID; +} + +} // namespace BamTools + +#endif // SAM_PROGRAM_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamProgramChain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,352 @@ +// *************************************************************************** +// SamProgramChain.cpp (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides methods for operating on a SamProgram record "chain" +// *************************************************************************** + +#include <api/SamProgramChain.h> +using namespace BamTools; + +#include <algorithm> +#include <iostream> +#include <cstdlib> +using namespace std; + +/*! \class BamTools::SamProgramChain + \brief Sorted container "chain" of SamProgram records. + + Provides methods for operating on a collection of SamProgram records. + + N.B. - Underlying container is *NOT* ordered by linkage, but by order of + appearance in SamHeader and subsequent Add() calls. Using the current + iterators will not allow you to step through the header's program history. + Instead use First()/Last() to access oldest/newest records, respectively. +*/ + +/*! \fn SamProgramChain::SamProgramChain(void) + \brief constructor +*/ +SamProgramChain::SamProgramChain(void) { } + +/*! \fn SamProgramChain::SamProgramChain(const SamProgramChain& other) + \brief copy constructor +*/ +SamProgramChain::SamProgramChain(const SamProgramChain& other) + : m_data(other.m_data) +{ } + +/*! \fn SamProgramChain::~SamProgramChain(void) + \brief destructor +*/ +SamProgramChain::~SamProgramChain(void) { } + +/*! \fn void SamProgramChain::Add(SamProgram& program) + \brief Appends a program to program chain. + + Duplicate entries are silently discarded. + + N.B. - Underlying container is *NOT* ordered by linkage, but by order of + appearance in SamHeader and subsequent Add() calls. Using the current + iterators will not allow you to step through the header's program history. + Instead use First()/Last() to access oldest/newest records, respectively. + + \param program entry to be appended +*/ +void SamProgramChain::Add(SamProgram& program) { + + // ignore duplicated records + if ( Contains(program) ) + return; + + // if other programs already in chain, try to find the "next" record + // tries to match another record's PPID with @program's ID + if ( !IsEmpty() ) + program.NextProgramID = NextIdFor(program.ID); + + // store program record + m_data.push_back(program); +} + +/*! \fn void SamProgramChain::Add(const std::vector<SamProgram>& programs) + \brief Appends a batch of programs to the end of the chain. + + This is an overloaded function. + + \param programs batch of program records to append + \sa Add() +*/ +void SamProgramChain::Add(std::vector<SamProgram>& programs) { + vector<SamProgram>::iterator pgIter = programs.begin(); + vector<SamProgram>::iterator pgEnd = programs.end(); + for ( ; pgIter != pgEnd; ++pgIter ) + Add(*pgIter); +} + +/*! \fn SamProgramIterator SamProgramChain::Begin(void) + \return an STL iterator pointing to the first (oldest) program record + \sa ConstBegin(), End(), First() +*/ +SamProgramIterator SamProgramChain::Begin(void) { + return m_data.begin(); +} + +/*! \fn SamProgramConstIterator SamProgramChain::Begin(void) const + \return an STL const_iterator pointing to the first (oldest) program record + + This is an overloaded function. + + \sa ConstBegin(), End(), First() +*/ +SamProgramConstIterator SamProgramChain::Begin(void) const { + return m_data.begin(); +} + +/*! \fn void SamProgramChain::Clear(void) + \brief Clears all program records. +*/ +void SamProgramChain::Clear(void) { + m_data.clear(); +} + +/*! \fn SamProgramConstIterator SamProgramChain::ConstBegin(void) const + \return an STL const_iterator pointing to the first (oldest) program record + \sa Begin(), ConstEnd(), First() +*/ +SamProgramConstIterator SamProgramChain::ConstBegin(void) const { + return m_data.begin(); +} + +/*! \fn SamProgramConstIterator SamProgramChain::ConstEnd(void) const + \return an STL const_iterator pointing to the imaginary entry after the last (newest) program record + \sa ConstBegin(), End(), Last() +*/ +SamProgramConstIterator SamProgramChain::ConstEnd(void) const { + return m_data.end(); +} + +/*! \fn bool SamProgramChain::Contains(const SamProgram& program) const + \brief Returns true if chains has this program record (matching on ID). + + This is an overloaded function. + + \param program SamProgram to search for + \return \c true if chain contains program (matching on ID) +*/ +bool SamProgramChain::Contains(const SamProgram& program) const { + return Contains(program.ID); +} + +/*! \fn bool SamProgramChain::Contains(const std::string& programId) const + \brief Returns true if chains has a program record with this ID + \param programId search for program matching this ID + \return \c true if chain contains a program record with this ID +*/ +bool SamProgramChain::Contains(const std::string& programId) const { + return ( IndexOf(programId) != (int)m_data.size() ); +} + +/*! \fn SamProgramIterator SamProgramChain::End(void) + \return an STL iterator pointing to the imaginary entry after the last (newest) program record + \sa Begin(), ConstEnd(), Last() +*/ +SamProgramIterator SamProgramChain::End(void) { + return m_data.end(); +} + +/*! \fn SamProgramConstIterator SamProgramChain::End(void) const + \return an STL const_iterator pointing to the imaginary entry after the last (newest) program record + + This is an overloaded function. + + \sa Begin(), ConstEnd(), Last() +*/ +SamProgramConstIterator SamProgramChain::End(void) const { + return m_data.end(); +} + +/*! \fn SamProgram& SamProgramChain::First(void) + \brief Fetches first (oldest) record in the chain. + + N.B. - This function will fail if the chain is empty. If this is possible, + check the result of IsEmpty() before calling this function. + + \return a modifiable reference to the first (oldest) program entry + \sa Begin(), Last() +*/ +SamProgram& SamProgramChain::First(void) { + + // find first record in container that has no PreviousProgramID entry + SamProgramIterator iter = Begin(); + SamProgramIterator end = End(); + for ( ; iter != end; ++iter ) { + SamProgram& current = (*iter); + if ( !current.HasPreviousProgramID() ) + return current; + } + + // otherwise error + cerr << "SamProgramChain ERROR - could not find any record without a PP tag" << endl; + exit(1); +} + +/*! \fn const SamProgram& SamProgramChain::First(void) const + \brief Fetches first (oldest) record in the chain. + + This is an overloaded function. + + N.B. - This function will fail if the chain is empty. If this is possible, + check the result of IsEmpty() before calling this function. + + \return a read-only reference to the first (oldest) program entry + \sa Begin(), ConstBegin(), Last() +*/ +const SamProgram& SamProgramChain::First(void) const { + + // find first record in container that has no PreviousProgramID entry + SamProgramConstIterator iter = ConstBegin(); + SamProgramConstIterator end = ConstEnd(); + for ( ; iter != end; ++iter ) { + const SamProgram& current = (*iter); + if ( !current.HasPreviousProgramID() ) + return current; + } + + // otherwise error + cerr << "SamProgramChain ERROR - could not find any record without a PP tag" << endl; + exit(1); +} + +/*! \fn int SamProgramChain::IndexOf(const std::string& programId) const + \internal + \return index of program record if found. + Otherwise, returns vector::size() (invalid index). +*/ +int SamProgramChain::IndexOf(const std::string& programId) const { + SamProgramConstIterator begin = ConstBegin(); + SamProgramConstIterator iter = begin; + SamProgramConstIterator end = ConstEnd(); + for ( ; iter != end; ++iter ) { + const SamProgram& current = (*iter); + if ( current.ID == programId ) + break; + } + return distance( begin, iter ); +} + +/*! \fn bool SamProgramChain::IsEmpty(void) const + \brief Returns \c true if chain contains no records + \sa Size() +*/ +bool SamProgramChain::IsEmpty(void) const { + return m_data.empty(); +} + +/*! \fn SamProgram& SamProgramChain::Last(void) + \brief Fetches last (newest) record in the chain. + + N.B. - This function will fail if the chain is empty. If this is possible, + check the result of IsEmpty() before calling this function. + + \return a modifiable reference to the last (newest) program entry + \sa End(), First() +*/ +SamProgram& SamProgramChain::Last(void) { + // find first record in container that has no NextProgramID entry + SamProgramIterator iter = Begin(); + SamProgramIterator end = End(); + for ( ; iter != end; ++iter ) { + SamProgram& current = (*iter); + if ( !current.HasNextProgramID() ) + return current; + } + + // otherwise error + cerr << "SamProgramChain ERROR - could not determine last record" << endl; + exit(1); +} + +/*! \fn const SamProgram& SamProgramChain::Last(void) const + \brief Fetches last (newest) record in the chain. + + This is an overloaded function. + + N.B. - This function will fail if the chain is empty. If this is possible, + check the result of IsEmpty() before calling this function. + + \return a read-only reference to the last (newest) program entry + \sa End(), ConstEnd(), First() +*/ +const SamProgram& SamProgramChain::Last(void) const { + // find first record in container that has no NextProgramID entry + SamProgramConstIterator iter = ConstBegin(); + SamProgramConstIterator end = ConstEnd(); + for ( ; iter != end; ++iter ) { + const SamProgram& current = (*iter); + if ( !current.HasNextProgramID() ) + return current; + } + + // otherwise error + cerr << "SamProgramChain ERROR - could not determine last record" << endl; + exit(1); +} + +/*! \fn const std::string SamProgramChain::NextIdFor(const std::string& programId) const + \internal + \return ID of program record, whose PreviousProgramID matches \a programId. + Otherwise, returns empty string if none found. +*/ +const std::string SamProgramChain::NextIdFor(const std::string& programId) const { + + // find first record in container whose PreviousProgramID matches @programId + SamProgramConstIterator iter = ConstBegin(); + SamProgramConstIterator end = ConstEnd(); + for ( ; iter != end; ++iter ) { + const SamProgram& current = (*iter); + if ( !current.HasPreviousProgramID() && + current.PreviousProgramID == programId + ) + { + return current.ID; + } + } + + // none found + return string(); +} + +/*! \fn int SamProgramChain::Size(void) const + \brief Returns number of program records in the chain. + \sa IsEmpty() +*/ +int SamProgramChain::Size(void) const { + return m_data.size(); +} + +/*! \fn SamProgram& SamProgramChain::operator[](const std::string& programId) + \brief Retrieves the modifiable SamProgram record that matches \a programId. + + NOTE - If the chain contains no read group matching this ID, this function will + print an error and terminate. + + \param programId ID of program record to retrieve + \return a modifiable reference to the SamProgram associated with the ID +*/ +SamProgram& SamProgramChain::operator[](const std::string& programId) { + + // look up program record matching this ID + int index = IndexOf(programId); + + // if record not found + if ( index == (int)m_data.size() ) { + cerr << "SamProgramChain ERROR - unknown programId: " << programId << endl; + exit(1); + } + + // otherwise return program record at index + return m_data.at(index); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamProgramChain.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,86 @@ +// *************************************************************************** +// SamProgramChain.h (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides methods for operating on a SamProgram record "chain" +// *************************************************************************** + +#ifndef SAM_PROGRAMCHAIN_H +#define SAM_PROGRAMCHAIN_H + +#include <api/api_global.h> +#include <api/SamProgram.h> +#include <string> +#include <vector> + +namespace BamTools { + +// chain is *NOT* sorted in any order +// use First()/Last() to retrieve oldest/newest programs, respectively +typedef std::vector<SamProgram> SamProgramContainer; +typedef SamProgramContainer::iterator SamProgramIterator; +typedef SamProgramContainer::const_iterator SamProgramConstIterator; + +class API_EXPORT SamProgramChain { + + // ctor & dtor + public: + SamProgramChain(void); + SamProgramChain(const SamProgramChain& other); + ~SamProgramChain(void); + + // query/modify program data + public: + // appends a program record to the chain + void Add(SamProgram& program); + void Add(std::vector<SamProgram>& programs); + + // clears all read group entries + void Clear(void); + + // returns true if chain contains this program record (matches on ID) + bool Contains(const SamProgram& program) const; + bool Contains(const std::string& programId) const; + + // returns the first (oldest) program in the chain + SamProgram& First(void); + const SamProgram& First(void) const; + + // returns true if chain is empty + bool IsEmpty(void) const; + + // returns last (most recent) program in the chain + SamProgram& Last(void); + const SamProgram& Last(void) const; + + // returns number of program records in the chain + int Size(void) const; + + // retrieves a modifiable reference to the SamProgram object associated with this ID + SamProgram& operator[](const std::string& programId); + + // retrieve STL-compatible iterators + public: + SamProgramIterator Begin(void); // returns iterator to begin() + SamProgramConstIterator Begin(void) const; // returns const_iterator to begin() + SamProgramConstIterator ConstBegin(void) const; // returns const_iterator to begin() + SamProgramIterator End(void); // returns iterator to end() + SamProgramConstIterator End(void) const; // returns const_iterator to end() + SamProgramConstIterator ConstEnd(void) const; // returns const_iterator to end() + + // internal methods + private: + int IndexOf(const std::string& programId) const; + const std::string NextIdFor(const std::string& programId) const; + + // data members + private: + SamProgramContainer m_data; +}; + +} // namespace BamTools + +#endif // SAM_PROGRAMCHAIN_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamReadGroup.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,222 @@ +// *************************************************************************** +// SamReadGroup.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM read group data fields. +// *************************************************************************** + +#include <api/SamReadGroup.h> +using namespace BamTools; +using namespace std; + +/*! \struct BamTools::SamReadGroup + \brief Represents a SAM read group entry. + + Provides direct read/write access to the SAM read group data fields. + + \sa \samSpecURL +*/ +/*! \var SamReadGroup::Description + \brief corresponds to \@RG DS:\<Description\> +*/ +/*! \var SamReadGroup::FlowOrder + \brief corresponds to \@RG FO:\<FlowOrder\> +*/ +/*! \var SamReadGroup::ID + \brief corresponds to \@RG ID:\<ID\> + + Required for valid SAM header. +*/ +/*! \var SamReadGroup::KeySequence + \brief corresponds to \@RG KS:\<KeySequence\> +*/ +/*! \var SamReadGroup::Library + \brief corresponds to \@RG LB:\<Library\> +*/ +/*! \var SamReadGroup::PlatformUnit + \brief corresponds to \@RG PU:\<PlatformUnit\> +*/ +/*! \var SamReadGroup::PredictedInsertSize + \brief corresponds to \@RG PI:\<PredictedInsertSize\> +*/ +/*! \var SamReadGroup::ProductionDate + \brief corresponds to \@RG DT:\<ProductionDate\> +*/ +/*! \var SamReadGroup::Program + \brief corresponds to \@RG PG:\<Program\> +*/ +/*! \var SamReadGroup::Sample + \brief corresponds to \@RG SM:\<Sample\> +*/ +/*! \var SamReadGroup::SequencingCenter + \brief corresponds to \@RG CN:\<SequencingCenter\> +*/ +/*! \var SamReadGroup::SequencingTechnology + \brief corresponds to \@RG PL:\<SequencingTechnology\> +*/ + +/*! \fn SamReadGroup::SamReadGroup(void) + \brief default constructor +*/ +SamReadGroup::SamReadGroup(void) + : Description("") + , FlowOrder("") + , ID("") + , KeySequence("") + , Library("") + , PlatformUnit("") + , PredictedInsertSize("") + , ProductionDate("") + , Program("") + , Sample("") + , SequencingCenter("") + , SequencingTechnology("") +{ } + +/*! \fn SamReadGroup::SamReadGroup(const std::string& id) + \brief constructs read group with \a id + + \param id desired read group ID +*/ +SamReadGroup::SamReadGroup(const std::string& id) + : Description("") + , FlowOrder("") + , ID(id) + , KeySequence("") + , Library("") + , PlatformUnit("") + , PredictedInsertSize("") + , ProductionDate("") + , Program("") + , Sample("") + , SequencingCenter("") + , SequencingTechnology("") +{ } + +/*! \fn SamReadGroup::SamReadGroup(const SamReadGroup& other) + \brief copy constructor +*/ +SamReadGroup::SamReadGroup(const SamReadGroup& other) + : Description(other.Description) + , FlowOrder(other.FlowOrder) + , ID(other.ID) + , KeySequence(other.KeySequence) + , Library(other.Library) + , PlatformUnit(other.PlatformUnit) + , PredictedInsertSize(other.PredictedInsertSize) + , ProductionDate(other.ProductionDate) + , Program(other.Program) + , Sample(other.Sample) + , SequencingCenter(other.SequencingCenter) + , SequencingTechnology(other.SequencingTechnology) +{ } + +/*! \fn SamReadGroup::~SamReadGroup(void) + \brief destructor +*/ +SamReadGroup::~SamReadGroup(void) { } + +/*! \fn void SamReadGroup::Clear(void) + \brief Clears all data fields. +*/ +void SamReadGroup::Clear(void) { + Description.clear(); + FlowOrder.clear(); + ID.clear(); + KeySequence.clear(); + Library.clear(); + PlatformUnit.clear(); + PredictedInsertSize.clear(); + ProductionDate.clear(); + Program.clear(); + Sample.clear(); + SequencingCenter.clear(); + SequencingTechnology.clear(); +} + +/*! \fn bool SamReadGroup::HasDescription(void) const + \brief Returns \c true if read group contains \@RG DS:\<Description\> +*/ +bool SamReadGroup::HasDescription(void) const { + return (!Description.empty()); +} + +/*! \fn bool SamReadGroup::HasFlowOrder(void) const + \brief Returns \c true if read group contains \@RG FO:\<FlowOrder\> +*/ +bool SamReadGroup::HasFlowOrder(void) const { + return (!FlowOrder.empty()); +} + +/*! \fn bool SamReadGroup::HasID(void) const + \brief Returns \c true if read group contains \@RG: ID:\<ID\> +*/ +bool SamReadGroup::HasID(void) const { + return (!ID.empty()); +} + +/*! \fn bool SamReadGroup::HasKeySequence(void) const + \brief Returns \c true if read group contains \@RG KS:\<KeySequence\> +*/ +bool SamReadGroup::HasKeySequence(void) const { + return (!KeySequence.empty()); +} + +/*! \fn bool SamReadGroup::HasLibrary(void) const + \brief Returns \c true if read group contains \@RG LB:\<Library\> +*/ +bool SamReadGroup::HasLibrary(void) const { + return (!Library.empty()); +} + +/*! \fn bool SamReadGroup::HasPlatformUnit(void) const + \brief Returns \c true if read group contains \@RG PU:\<PlatformUnit\> +*/ +bool SamReadGroup::HasPlatformUnit(void) const { + return (!PlatformUnit.empty()); +} + +/*! \fn bool SamReadGroup::HasPredictedInsertSize(void) const + \brief Returns \c true if read group contains \@RG PI:\<PredictedInsertSize\> +*/ +bool SamReadGroup::HasPredictedInsertSize(void) const { + return (!PredictedInsertSize.empty()); +} + +/*! \fn bool SamReadGroup::HasProductionDate(void) const + \brief Returns \c true if read group contains \@RG DT:\<ProductionDate\> +*/ +bool SamReadGroup::HasProductionDate(void) const { + return (!ProductionDate.empty()); +} + +/*! \fn bool SamReadGroup::HasProgram(void) const + \brief Returns \c true if read group contains \@RG PG:\<Program\> +*/ +bool SamReadGroup::HasProgram(void) const { + return (!Program.empty()); +} + +/*! \fn bool SamReadGroup::HasSample(void) const + \brief Returns \c true if read group contains \@RG SM:\<Sample\> +*/ +bool SamReadGroup::HasSample(void) const { + return (!Sample.empty()); +} + +/*! \fn bool SamReadGroup::HasSequencingCenter(void) const + \brief Returns \c true if read group contains \@RG CN:\<SequencingCenter\> +*/ +bool SamReadGroup::HasSequencingCenter(void) const { + return (!SequencingCenter.empty()); +} + +/*! \fn bool SamReadGroup::HasSequencingTechnology(void) const + \brief Returns \c true if read group contains \@RG PL:\<SequencingTechnology\> +*/ +bool SamReadGroup::HasSequencingTechnology(void) const { + return (!SequencingTechnology.empty()); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamReadGroup.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,69 @@ +// *************************************************************************** +// SamReadGroup.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM read group data fields. +// *************************************************************************** + +#ifndef SAM_READGROUP_H +#define SAM_READGROUP_H + +#include "api/api_global.h" +#include <string> + +namespace BamTools { + +struct API_EXPORT SamReadGroup { + + // ctor & dtor + SamReadGroup(void); + SamReadGroup(const std::string& id); + SamReadGroup(const SamReadGroup& other); + ~SamReadGroup(void); + + // query/modify entire read group + void Clear(void); // clears all data fields + + // convenience query methods + bool HasDescription(void) const; // returns true if read group has a description + bool HasFlowOrder(void) const; // returns true if read group has a flow order entry + bool HasID(void) const; // returns true if read group has a group ID + bool HasKeySequence(void) const; // returns true if read group has a key sequence + bool HasLibrary(void) const; // returns true if read group has a library name + bool HasPlatformUnit(void) const; // returns true if read group has a platform unit ID + bool HasPredictedInsertSize(void) const; // returns true if read group has a predicted insert size + bool HasProductionDate(void) const; // returns true if read group has a production date + bool HasProgram(void) const; // returns true if read group has a program entry + bool HasSample(void) const; // returns true if read group has a sample name + bool HasSequencingCenter(void) const; // returns true if read group has a sequencing center ID + bool HasSequencingTechnology(void) const; // returns true if read group has a sequencing technology ID + + + // data fields + std::string Description; // DS:<Description> + std::string FlowOrder; // FO:<FlowOrder> + std::string ID; // ID:<ID> *Required for valid SAM header* + std::string KeySequence; // KS:<KeySequence> + std::string Library; // LB:<Library> + std::string PlatformUnit; // PU:<PlatformUnit> + std::string PredictedInsertSize; // PI:<PredictedInsertSize> + std::string ProductionDate; // DT:<ProductionDate> + std::string Program; // PG:<Program> + std::string Sample; // SM:<Sample> + std::string SequencingCenter; // CN:<SequencingCenter> + std::string SequencingTechnology; // PL:<SequencingTechnology> +}; + +/*! \fn bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) + \brief tests equality by comparing read group IDs +*/ +API_EXPORT inline bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) { + return lhs.ID == rhs.ID; +} + +} // namespace BamTools + +#endif // SAM_READGROUP_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamReadGroupDictionary.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,290 @@ +// *************************************************************************** +// SamReadGroupDictionary.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides methods for operating on a collection of SamReadGroup entries. +// *************************************************************************** + +#include <api/SamReadGroupDictionary.h> +using namespace BamTools; + +#include <algorithm> +#include <iostream> +using namespace std; + +/*! \class BamTools::SamReadGroupDictionary + \brief Container of SamReadGroup entries. + + Provides methods for operating on a collection of SamReadGroup entries. +*/ + +/*! \fn SamReadGroupDictionary::SamReadGroupDictionary(void) + \brief constructor +*/ +SamReadGroupDictionary::SamReadGroupDictionary(void) { } + +/*! \fn SamReadGroupDictionary::SamReadGroupDictionary(const SamReadGroupDictionary& other) + \brief copy constructor +*/ +SamReadGroupDictionary::SamReadGroupDictionary(const SamReadGroupDictionary& other) + : m_data(other.m_data) +{ } + +/*! \fn SamReadGroupDictionary::~SamReadGroupDictionary(void) + \brief destructor +*/ +SamReadGroupDictionary::~SamReadGroupDictionary(void) { } + +/*! \fn void SamReadGroupDictionary::Add(const SamReadGroup& readGroup) + \brief Adds a read group to the dictionary. + + Duplicate entries are silently discarded. + + \param readGroup entry to be added +*/ +void SamReadGroupDictionary::Add(const SamReadGroup& readGroup) { + + // TODO: report error on attempted duplicate? + + if ( IsEmpty() || !Contains(readGroup) ) + m_data.push_back(readGroup); +} + +/*! \fn void SamReadGroupDictionary::Add(const std::string& readGroupId) + \brief Adds a read group to the dictionary. + + This is an overloaded function. + + \param readGroupId ID of read group to be added + \sa Add() +*/ +void SamReadGroupDictionary::Add(const std::string& readGroupId) { + Add( SamReadGroup(readGroupId) ); +} + +/*! \fn void SamReadGroupDictionary::Add(const std::vector<SamReadGroup>& readGroups) + \brief Adds multiple read groups to the dictionary. + + This is an overloaded function. + + \param readGroups entries to be added + \sa Add() +*/ +void SamReadGroupDictionary::Add(const std::vector<SamReadGroup>& readGroups) { + vector<SamReadGroup>::const_iterator rgIter = readGroups.begin(); + vector<SamReadGroup>::const_iterator rgEnd = readGroups.end(); + for ( ; rgIter!= rgEnd; ++rgIter ) + Add(*rgIter); +} + +/*! \fn void SamReadGroupDictionary::Add(const std::vector<std::string>& readGroupIds) + \brief Adds multiple read groups to the dictionary. + + This is an overloaded function. + + \param readGroupIds IDs of read groups to be added + \sa Add() +*/ +void SamReadGroupDictionary::Add(const std::vector<std::string>& readGroupIds) { + vector<string>::const_iterator rgIter = readGroupIds.begin(); + vector<string>::const_iterator rgEnd = readGroupIds.end(); + for ( ; rgIter!= rgEnd; ++rgIter ) + Add(*rgIter); +} + +/*! \fn SamReadGroupIterator SamReadGroupDictionary::Begin(void) + \return an STL iterator pointing to the first read group + \sa ConstBegin(), End() +*/ +SamReadGroupIterator SamReadGroupDictionary::Begin(void) { + return m_data.begin(); +} + +/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::Begin(void) const + \return an STL const_iterator pointing to the first read group + + This is an overloaded function. + + \sa ConstBegin(), End() +*/ +SamReadGroupConstIterator SamReadGroupDictionary::Begin(void) const { + return m_data.begin(); +} + +/*! \fn void SamReadGroupDictionary::Clear(void) + \brief Clears all read group entries. +*/ +void SamReadGroupDictionary::Clear(void) { + m_data.clear(); +} + +/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::ConstBegin(void) const + \return an STL const_iterator pointing to the first read group + \sa Begin(), ConstEnd() +*/ +SamReadGroupConstIterator SamReadGroupDictionary::ConstBegin(void) const { + return m_data.begin(); +} + +/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::ConstEnd(void) const + \return an STL const_iterator pointing to the imaginary entry after the last read group + \sa ConstBegin(), End() +*/ +SamReadGroupConstIterator SamReadGroupDictionary::ConstEnd(void) const { + return m_data.end(); +} + +/*! \fn bool SamReadGroupDictionary::Contains(const std::string& readGroupId) const + \brief Returns true if dictionary contains read group. + \param readGroupId search for read group matching this ID + \return \c true if dictionary contains a read group with this ID +*/ +bool SamReadGroupDictionary::Contains(const std::string& readGroupId) const { + return ( IndexOf(readGroupId) != (int)m_data.size() ); +} + +/*! \fn bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const + \brief Returns true if dictionary contains read group (matching on ID). + + This is an overloaded function. + + \param readGroup search for this read group + \return \c true if dictionary contains read group (matching on ID). +*/ +bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const { + return Contains( readGroup.ID ); +} + +/*! \fn SamReadGroupIterator SamReadGroupDictionary::End(void) + \return an STL iterator pointing to the imaginary entry after the last read group + \sa Begin(), ConstEnd() +*/ +SamReadGroupIterator SamReadGroupDictionary::End(void) { + return m_data.end(); +} + +/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::End(void) const + \return an STL const_iterator pointing to the imaginary entry after the last read group + + This is an overloaded function. + + \sa Begin(), ConstEnd() +*/ +SamReadGroupConstIterator SamReadGroupDictionary::End(void) const { + return m_data.end(); +} + +/*! \fn int SamReadGroupDictionary::IndexOf(const std::string& readGroupId) const + \internal + \return index of read group if found. Otherwise, returns vector::size() (invalid index). +*/ +int SamReadGroupDictionary::IndexOf(const std::string& readGroupId) const { + SamReadGroupConstIterator begin = ConstBegin(); + SamReadGroupConstIterator iter = begin; + SamReadGroupConstIterator end = ConstEnd(); + for ( ; iter != end; ++iter ) { + const SamReadGroup& current = (*iter); + if ( current.ID == readGroupId ) + break; + } + return distance( begin, iter ); +} + +/*! \fn bool SamReadGroupDictionary::IsEmpty(void) const + \brief Returns \c true if dictionary contains no read groups + \sa Size() +*/ +bool SamReadGroupDictionary::IsEmpty(void) const { + return m_data.empty(); +} + +/*! \fn void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup) + \brief Removes read group from dictionary, if found (matching on ID). + + This is an overloaded function. + + \param readGroup read group to remove (matches on ID) +*/ +void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup) { + Remove( readGroup.ID ); +} + +/*! \fn void SamReadGroupDictionary::Remove(const std::string& readGroupId) + \brief Removes read group from dictionary, if found. + \param readGroupId ID of read group to remove + \sa Remove() +*/ +void SamReadGroupDictionary::Remove(const std::string& readGroupId) { + if ( Contains(readGroupId) ) + m_data.erase( m_data.begin() + IndexOf(readGroupId) ); +} + +/*! \fn void SamReadGroupDictionary::Remove(const std::vector<SamReadGroup>& readGroups) + \brief Removes multiple read groups from dictionary (matching on ID). + + This is an overloaded function. + + \param readGroups read groups to remove + \sa Remove() +*/ +void SamReadGroupDictionary::Remove(const std::vector<SamReadGroup>& readGroups) { + vector<SamReadGroup>::const_iterator rgIter = readGroups.begin(); + vector<SamReadGroup>::const_iterator rgEnd = readGroups.end(); + for ( ; rgIter!= rgEnd; ++rgIter ) + Remove(*rgIter); +} + +/*! \fn void SamReadGroupDictionary::Remove(const std::vector<std::string>& readGroupIds) + \brief Removes multiple read groups from dictionary. + + This is an overloaded function. + + \param readGroupIds IDs of the read groups to remove + \sa Remove() +*/ +void SamReadGroupDictionary::Remove(const std::vector<std::string>& readGroupIds) { + vector<string>::const_iterator rgIter = readGroupIds.begin(); + vector<string>::const_iterator rgEnd = readGroupIds.end(); + for ( ; rgIter!= rgEnd; ++rgIter ) + Remove(*rgIter); +} + +/*! \fn int SamReadGroupDictionary::Size(void) const + \brief Returns number of read groups in dictionary. + \sa IsEmpty() +*/ +int SamReadGroupDictionary::Size(void) const { + return m_data.size(); +} + +/*! \fn SamReadGroup& SamReadGroupDictionary::operator[](const std::string& readGroupId) + \brief Retrieves the modifiable SamReadGroup that matches \a readGroupId. + + NOTE - If the dictionary contains no read group matching this ID, this function inserts + a new one with this ID, and returns a reference to it. + + If you want to avoid this insertion behavior, check the result of Contains() before + using this operator. + + \param readGroupId ID of read group to retrieve + \return a modifiable reference to the SamReadGroup associated with the ID +*/ +SamReadGroup& SamReadGroupDictionary::operator[](const std::string& readGroupId) { + + // look up read group ID + int index = IndexOf(readGroupId); + + // if found, return read group at index + if ( index != (int)m_data.size() ) + return m_data[index]; + + // otherwise, append new read group and return reference + else { + SamReadGroup rg(readGroupId); + m_data.push_back(rg); + return m_data.back(); + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamReadGroupDictionary.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,87 @@ +// *************************************************************************** +// SamReadGroupDictionary.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides methods for operating on a collection of SamReadGroup entries. +// *************************************************************************** + +#ifndef SAM_READGROUP_DICTIONARY_H +#define SAM_READGROUP_DICTIONARY_H + +#include <api/api_global.h> +#include <api/SamReadGroup.h> +#include <string> +#include <vector> + +namespace BamTools { + +typedef std::vector<SamReadGroup> SamReadGroupContainer; +typedef SamReadGroupContainer::iterator SamReadGroupIterator; +typedef SamReadGroupContainer::const_iterator SamReadGroupConstIterator; + +class API_EXPORT SamReadGroupDictionary { + + // ctor & dtor + public: + SamReadGroupDictionary(void); + SamReadGroupDictionary(const SamReadGroupDictionary& other); + ~SamReadGroupDictionary(void); + + // query/modify read group data + public: + // adds a read group + void Add(const SamReadGroup& readGroup); + void Add(const std::string& readGroupId); + + // adds multiple read groups + void Add(const std::vector<SamReadGroup>& readGroups); + void Add(const std::vector<std::string>& readGroupIds); + + // clears all read group entries + void Clear(void); + + // returns true if dictionary contains this read group + bool Contains(const SamReadGroup& readGroup) const; + bool Contains(const std::string& readGroupId) const; + + // returns true if dictionary is empty + bool IsEmpty(void) const; + + // removes read group, if found + void Remove(const SamReadGroup& readGroup); + void Remove(const std::string& readGroupId); + + // removes multiple read groups + void Remove(const std::vector<SamReadGroup>& readGroups); + void Remove(const std::vector<std::string>& readGroupIds); + + // returns number of read groups in dictionary + int Size(void) const; + + // retrieves a modifiable reference to the SamReadGroup object associated with this ID + SamReadGroup& operator[](const std::string& readGroupId); + + // retrieve STL-compatible iterators + public: + SamReadGroupIterator Begin(void); // returns iterator to begin() + SamReadGroupConstIterator Begin(void) const; // returns const_iterator to begin() + SamReadGroupConstIterator ConstBegin(void) const; // returns const_iterator to begin() + SamReadGroupIterator End(void); // returns iterator to end() + SamReadGroupConstIterator End(void) const; // returns const_iterator to end() + SamReadGroupConstIterator ConstEnd(void) const; // returns const_iterator to end() + + // internal methods + private: + int IndexOf(const std::string& readGroupId) const; + + // data members + private: + SamReadGroupContainer m_data; +}; + +} // namespace BamTools + +#endif // SAM_READGROUP_DICTIONARY_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamSequence.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,162 @@ +// *************************************************************************** +// SamSequence.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM sequence data fields. +// *************************************************************************** + +#include <api/SamSequence.h> +#include <sstream> +using namespace BamTools; +using namespace std; + +/*! \struct BamTools::SamSequence + \brief Represents a SAM sequence entry. + + Provides direct read/write access to the SAM sequence data fields. + + \sa \samSpecURL +*/ +/*! \var SamSequence::AssemblyID + \brief corresponds to \@SQ AS:\<AssemblyID\> +*/ +/*! \var SamSequence::Checksum + \brief corresponds to \@SQ M5:\<Checksum\> +*/ +/*! \var SamSequence::Length + \brief corresponds to \@SQ LN:\<Length\> + + Required for valid SAM header. +*/ +/*! \var SamSequence::Name + \brief corresponds to \@SQ SN:\<Name\> + + Required for valid SAM header. +*/ +/*! \var SamSequence::Species + \brief corresponds to \@SQ SP:\<Species\> +*/ +/*! \var SamSequence::URI + \brief corresponds to \@SQ UR:\<URI\> +*/ + +/*! \fn SamSequence::SamSequence(void) + \brief default constructor +*/ +SamSequence::SamSequence(void) + : AssemblyID("") + , Checksum("") + , Length("") + , Name("") + , Species("") + , URI("") +{ } + +/*! \fn SamSequence::SamSequence(const std::string& name, const int& length) + \brief constructs sequence with \a name and \a length + + \param name desired sequence name + \param length desired sequence length (numeric value) +*/ +SamSequence::SamSequence(const std::string& name, + const int& length) + : AssemblyID("") + , Checksum("") + , Name(name) + , Species("") + , URI("") +{ + stringstream s(""); + s << length; + Length = s.str(); +} + +/*! \fn SamSequence::SamSequence(const std::string& name, const std::string& length) + \brief constructs sequence with \a name and \a length + + \param name desired sequence name + \param length desired sequence length (string value) +*/ +SamSequence::SamSequence(const std::string& name, + const std::string& length) + : AssemblyID("") + , Checksum("") + , Length(length) + , Name(name) + , Species("") + , URI("") +{ } + +/*! \fn SamSequence::SamSequence(const SamSequence& other) + \brief copy constructor +*/ +SamSequence::SamSequence(const SamSequence& other) + : AssemblyID(other.AssemblyID) + , Checksum(other.Checksum) + , Length(other.Length) + , Name(other.Name) + , Species(other.Species) + , URI(other.URI) +{ } + +/*! \fn SamSequence::~SamSequence(void) + \brief destructor +*/ +SamSequence::~SamSequence(void) { } + +/*! \fn void SamSequence::Clear(void) + \brief Clears all data fields. +*/ +void SamSequence::Clear(void) { + AssemblyID.clear(); + Checksum.clear(); + Length.clear(); + Name.clear(); + Species.clear(); + URI.clear(); +} + +/*! \fn bool SamSequence::HasAssemblyID(void) const + \brief Returns \c true if sequence contains \@SQ AS:\<AssemblyID\> +*/ +bool SamSequence::HasAssemblyID(void) const { + return (!AssemblyID.empty()); +} + +/*! \fn bool SamSequence::HasChecksum(void) const + \brief Returns \c true if sequence contains \@SQ M5:\<Checksum\> +*/ +bool SamSequence::HasChecksum(void) const { + return (!Checksum.empty()); +} + +/*! \fn bool SamSequence::HasLength(void) const + \brief Returns \c true if sequence contains \@SQ LN:\<Length\> +*/ +bool SamSequence::HasLength(void) const { + return (!Length.empty()); +} + +/*! \fn bool SamSequence::HasName(void) const + \brief Returns \c true if sequence contains \@SQ SN:\<Name\> +*/ +bool SamSequence::HasName(void) const { + return (!Name.empty()); +} + +/*! \fn bool SamSequence::HasSpecies(void) const + \brief Returns \c true if sequence contains \@SQ SP:\<Species\> +*/ +bool SamSequence::HasSpecies(void) const { + return (!Species.empty()); +} + +/*! \fn bool SamSequence::HasURI(void) const + \brief Returns \c true if sequence contains \@SQ UR:\<URI\> +*/ +bool SamSequence::HasURI(void) const { + return (!URI.empty()); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamSequence.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,61 @@ +// *************************************************************************** +// SamSequence.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides direct read/write access to the SAM sequence data fields. +// *************************************************************************** + +#ifndef SAM_SEQUENCE_H +#define SAM_SEQUENCE_H + +#include <api/api_global.h> +#include <string> + +namespace BamTools { + +struct API_EXPORT SamSequence { + + // ctor & dtor + SamSequence(void); + SamSequence(const std::string& name, const int& length); + SamSequence(const std::string& name, const std::string& length); + SamSequence(const SamSequence& other); + ~SamSequence(void); + + // query/modify entire sequence + void Clear(void); // clears all contents + + // convenience query methods + bool HasAssemblyID(void) const; // returns true if sequence has an assembly ID + bool HasChecksum(void) const; // returns true if sequence has an MD5 checksum + bool HasLength(void) const; // returns true if sequence has a length + bool HasName(void) const; // returns true if sequence has a name + bool HasSpecies(void) const; // returns true if sequence has a species ID + bool HasURI(void) const; // returns true if sequence has a URI + + // data members + std::string AssemblyID; // AS:<AssemblyID> + std::string Checksum; // M5:<Checksum> + std::string Length; // LN:<Length> *Required for valid SAM header* + std::string Name; // SN:<Name> *Required for valid SAM header* + std::string Species; // SP:<Species> + std::string URI; // UR:<URI> +}; + +/*! \fn bool operator==(const SamSequence& lhs, const SamSequence& rhs) + \brief tests equality by comparing sequence names, lengths, & checksums (if available) +*/ +API_EXPORT inline bool operator==(const SamSequence& lhs, const SamSequence& rhs) { + if ( lhs.Name != rhs.Name ) return false; + if ( lhs.Length != rhs.Length ) return false; + if ( lhs.HasChecksum() && rhs.HasChecksum() ) + return (lhs.Checksum == rhs.Checksum); + else return true; +} + +} // namespace BamTools + +#endif // SAM_SEQUENCE_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamSequenceDictionary.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,293 @@ +// *************************************************************************** +// SamSequenceDictionary.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides methods for operating on a collection of SamSequence entries. +// ************************************************************************* + +#include <api/SamSequenceDictionary.h> +using namespace BamTools; + +#include <iostream> +using namespace std; + +/*! \class BamTools::SamSequenceDictionary + \brief Container of SamSequence entries. + + Provides methods for operating on a collection of SamSequence entries. +*/ + +/*! \fn SamSequenceDictionary::SamSequenceDictionary(void) + \brief constructor +*/ +SamSequenceDictionary::SamSequenceDictionary(void) { } + +/*! \fn SamSequenceDictionary::SamSequenceDictionary(const SamSequenceDictionary& other) + \brief copy constructor +*/ +SamSequenceDictionary::SamSequenceDictionary(const SamSequenceDictionary& other) + : m_data(other.m_data) +{ } + +/*! \fn SamSequenceDictionary::~SamSequenceDictionary(void) + \brief destructor +*/ +SamSequenceDictionary::~SamSequenceDictionary(void) { } + +/*! \fn void SamSequenceDictionary::Add(const SamSequence& sequence) + \brief Adds a sequence to the dictionary. + + Duplicate entries are silently discarded. + + \param sequence entry to be added +*/ +void SamSequenceDictionary::Add(const SamSequence& sequence) { + + // TODO: report error on attempted duplicate? + + if ( IsEmpty() || !Contains(sequence) ) + m_data.push_back(sequence); +} + +/*! \fn void SamSequenceDictionary::Add(const std::string& name, const int& length) + \brief Adds a sequence to the dictionary. + + This is an overloaded function. + + \param name name of sequence entry to be added + \param length length of sequence entry to be added + \sa Add() +*/ +void SamSequenceDictionary::Add(const std::string& name, const int& length) { + Add( SamSequence(name, length) ); +} + +/*! \fn void SamSequenceDictionary::Add(const std::vector<SamSequence>& sequences) + \brief Adds multiple sequences to the dictionary. + + This is an overloaded function. + + \param sequences entries to be added + \sa Add() +*/ +void SamSequenceDictionary::Add(const std::vector<SamSequence>& sequences) { + vector<SamSequence>::const_iterator seqIter = sequences.begin(); + vector<SamSequence>::const_iterator seqEnd = sequences.end(); + for ( ; seqIter!= seqEnd; ++seqIter ) + Add(*seqIter); +} + +/*! \fn void SamSequenceDictionary::Add(const std::map<std::string, int>& sequenceMap) + \brief Adds multiple sequences to the dictionary. + + This is an overloaded function. + + \param sequenceMap map of sequence entries (name => length) to be added + \sa Add() +*/ +void SamSequenceDictionary::Add(const std::map<std::string, int>& sequenceMap) { + map<string, int>::const_iterator seqIter = sequenceMap.begin(); + map<string, int>::const_iterator seqEnd = sequenceMap.end(); + for ( ; seqIter != seqEnd; ++seqIter ) { + const string& name = (*seqIter).first; + const int& length = (*seqIter).second; + Add( SamSequence(name, length) ); + } +} + +/*! \fn SamSequenceIterator SamSequenceDictionary::Begin(void) + \return an STL iterator pointing to the first sequence + \sa ConstBegin(), End() +*/ +SamSequenceIterator SamSequenceDictionary::Begin(void) { + return m_data.begin(); +} + +/*! \fn SamSequenceConstIterator SamSequenceDictionary::Begin(void) const + \return an STL const_iterator pointing to the first sequence + + This is an overloaded function. + + \sa ConstBegin(), End() +*/ +SamSequenceConstIterator SamSequenceDictionary::Begin(void) const { + return m_data.begin(); +} + +/*! \fn void SamSequenceDictionary::Clear(void) + \brief Clears all sequence entries. +*/ +void SamSequenceDictionary::Clear(void) { + m_data.clear(); +} + +/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const + \return an STL const_iterator pointing to the first sequence + \sa Begin(), ConstEnd() +*/ +SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const { + return m_data.begin(); +} + +/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstEnd(void) const + \return an STL const_iterator pointing to the imaginary entry after the last sequence + \sa End(), ConstBegin() +*/ +SamSequenceConstIterator SamSequenceDictionary::ConstEnd(void) const { + return m_data.end(); +} + +/*! \fn bool SamSequenceDictionary::Contains(const std::string& sequenceName) const + \brief Returns true if dictionary contains sequence. + \param sequenceName search for sequence matching this name + \return \c true if dictionary contains a sequence with this name +*/ +bool SamSequenceDictionary::Contains(const std::string& sequenceName) const { + return ( IndexOf(sequenceName) != (int)m_data.size() ); +} + +/*! \fn bool SamSequenceDictionary::Contains(const SamSequence& sequence) const + \brief Returns true if dictionary contains sequence (matches on name). + + This is an overloaded function. + + \param sequence search for this sequence + \return \c true if dictionary contains sequence (matching on name) +*/ +bool SamSequenceDictionary::Contains(const SamSequence& sequence) const { + return ( IndexOf(sequence.Name) != (int)m_data.size() ); +} + +/*! \fn SamSequenceIterator SamSequenceDictionary::End(void) + \return an STL iterator pointing to the imaginary entry after the last sequence + \sa Begin(), ConstEnd() +*/ +SamSequenceIterator SamSequenceDictionary::End(void) { + return m_data.end(); +} + +/*! \fn SamSequenceConstIterator SamSequenceDictionary::End(void) const + \return an STL const_iterator pointing to the imaginary entry after the last sequence + + This is an overloaded function. + + \sa Begin(), ConstEnd() +*/ +SamSequenceConstIterator SamSequenceDictionary::End(void) const { + return m_data.end(); +} + +/*! \fn int SamSequenceDictionary::IndexOf(const std::string& name) const + \internal + \return index of sequence if found (matching on name). Otherwise, returns vector::size() (invalid index). +*/ +int SamSequenceDictionary::IndexOf(const std::string& name) const { + SamSequenceConstIterator begin = ConstBegin(); + SamSequenceConstIterator iter = begin; + SamSequenceConstIterator end = ConstEnd(); + for ( ; iter != end; ++iter ) { + const SamSequence& currentSeq = (*iter); + if ( currentSeq.Name == name ) + break; + } + return distance( begin, iter ); +} + +/*! \fn bool SamSequenceDictionary::IsEmpty(void) const + \brief Returns \c true if dictionary contains no sequences + \sa Size() +*/ +bool SamSequenceDictionary::IsEmpty(void) const { + return m_data.empty(); +} + +/*! \fn void SamSequenceDictionary::Remove(const SamSequence& sequence) + \brief Removes sequence from dictionary, if found (matches on name). + + This is an overloaded function. + + \param sequence SamSequence to remove (matching on name) +*/ +void SamSequenceDictionary::Remove(const SamSequence& sequence) { + Remove( sequence.Name ); +} + +/*! \fn void SamSequenceDictionary::Remove(const std::string& sequenceName) + \brief Removes sequence from dictionary, if found. + + \param sequenceName name of sequence to remove + \sa Remove() +*/ +void SamSequenceDictionary::Remove(const std::string& sequenceName) { + if ( Contains(sequenceName) ) + m_data.erase( m_data.begin() + IndexOf(sequenceName) ); +} + +/*! \fn void SamSequenceDictionary::Remove(const std::vector<SamSequence>& sequences) + \brief Removes multiple sequences from dictionary. + + This is an overloaded function. + + \param sequences sequences to remove + \sa Remove() +*/ +void SamSequenceDictionary::Remove(const std::vector<SamSequence>& sequences) { + vector<SamSequence>::const_iterator rgIter = sequences.begin(); + vector<SamSequence>::const_iterator rgEnd = sequences.end(); + for ( ; rgIter!= rgEnd; ++rgIter ) + Remove(*rgIter); +} + +/*! \fn void SamSequenceDictionary::Remove(const std::vector<std::string>& sequenceNames) + \brief Removes multiple sequences from dictionary. + + This is an overloaded function. + + \param sequenceNames names of the sequences to remove + \sa Remove() +*/ +void SamSequenceDictionary::Remove(const std::vector<std::string>& sequenceNames) { + vector<string>::const_iterator rgIter = sequenceNames.begin(); + vector<string>::const_iterator rgEnd = sequenceNames.end(); + for ( ; rgIter!= rgEnd; ++rgIter ) + Remove(*rgIter); +} + +/*! \fn int SamSequenceDictionary::Size(void) const + \brief Returns number of sequences in dictionary. + \sa IsEmpty() +*/ +int SamSequenceDictionary::Size(void) const { + return m_data.size(); +} + +/*! \fn SamSequence& SamSequenceDictionary::operator[](const std::string& sequenceName) + \brief Retrieves the modifiable SamSequence that matches \a sequenceName. + + NOTE - If the dictionary contains no sequence matching this name, this function inserts + a new one with this name (length:0), and returns a reference to it. + + If you want to avoid this insertion behavior, check the result of Contains() before + using this operator. + + \param sequenceName name of sequence to retrieve + \return a modifiable reference to the SamSequence associated with the name +*/ +SamSequence& SamSequenceDictionary::operator[](const std::string& sequenceName) { + + // look up sequence ID + int index = IndexOf(sequenceName); + + // if found, return sequence at index + if ( index != (int)m_data.size() ) + return m_data[index]; + + // otherwise, append new sequence and return reference + else { + m_data.push_back( SamSequence(sequenceName, 0) ); + return m_data.back(); + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/SamSequenceDictionary.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,89 @@ +// *************************************************************************** +// SamSequenceDictionary.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 +// --------------------------------------------------------------------------- +// Provides methods for operating on a collection of SamSequence entries. +// *************************************************************************** + +#ifndef SAM_SEQUENCE_DICTIONARY_H +#define SAM_SEQUENCE_DICTIONARY_H + +#include <api/api_global.h> +#include <api/SamSequence.h> +#include <string> +#include <map> +#include <vector> + +namespace BamTools { + +typedef std::vector<SamSequence> SamSequenceContainer; +typedef SamSequenceContainer::iterator SamSequenceIterator; +typedef SamSequenceContainer::const_iterator SamSequenceConstIterator; + +class API_EXPORT SamSequenceDictionary { + + // ctor & dtor + public: + SamSequenceDictionary(void); + SamSequenceDictionary(const SamSequenceDictionary& other); + ~SamSequenceDictionary(void); + + // query/modify sequence data + public: + // adds a sequence + void Add(const SamSequence& sequence); + void Add(const std::string& name, const int& length); + + // adds multiple sequences + void Add(const std::vector<SamSequence>& sequences); + void Add(const std::map<std::string, int>& sequenceMap); + + // clears all sequence entries + void Clear(void); + + // returns true if dictionary contains this sequence + bool Contains(const SamSequence& sequence) const; + bool Contains(const std::string& sequenceName) const; + + // returns true if dictionary is empty + bool IsEmpty(void) const; + + // removes sequence, if found + void Remove(const SamSequence& sequence); + void Remove(const std::string& sequenceName); + + // removes multiple sequences + void Remove(const std::vector<SamSequence>& sequences); + void Remove(const std::vector<std::string>& sequenceNames); + + // returns number of sequences in dictionary + int Size(void) const; + + // retrieves a modifiable reference to the SamSequence object associated with this name + SamSequence& operator[](const std::string& sequenceName); + + // retrieve STL-compatible iterators + public: + SamSequenceIterator Begin(void); // returns iterator to begin() + SamSequenceConstIterator Begin(void) const; // returns const_iterator to begin() + SamSequenceConstIterator ConstBegin(void) const; // returns const_iterator to begin() + SamSequenceIterator End(void); // returns iterator to end() + SamSequenceConstIterator End(void) const; // returns const_iterator to end() + SamSequenceConstIterator ConstEnd(void) const; // returns const_iterator to end() + + // internal methods + private: + int IndexOf(const std::string& name) const; + + // data members + private: + SamSequenceContainer m_data; +}; + +} // namespace BamTools + +#endif // SAM_SEQUENCE_DICTIONARY_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/api_global.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,22 @@ +// *************************************************************************** +// api_global.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 November 2010 (DB) +// --------------------------------------------------------------------------- +// Provides macros for exporting & importing BamTools API library symbols +// *************************************************************************** + +#ifndef API_GLOBAL_H +#define API_GLOBAL_H + +#include "shared/bamtools_global.h" + +#ifdef BAMTOOLS_API_LIBRARY +# define API_EXPORT BAMTOOLS_LIBRARY_EXPORT +#else +# define API_EXPORT BAMTOOLS_LIBRARY_IMPORT +#endif + +#endif // API_GLOBAL_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamHeader_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,133 @@ +// *************************************************************************** +// BamHeader_p.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 21 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for handling BAM headers. +// *************************************************************************** + +#include <api/BamAux.h> +#include <api/BamConstants.h> +#include <api/internal/BamHeader_p.h> +#include <api/internal/BgzfStream_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <cstdio> +#include <cstdlib> +#include <cstring> +#include <iostream> +using namespace std; + +// ctor +BamHeader::BamHeader(void) { } + +// dtor +BamHeader::~BamHeader(void) { } + +// reads magic number from BGZF stream, returns true if valid +bool BamHeader::CheckMagicNumber(BgzfStream* stream) { + + // try to read magic number + char buffer[Constants::BAM_HEADER_MAGIC_LENGTH]; + if ( stream->Read(buffer, Constants::BAM_HEADER_MAGIC_LENGTH) != (int)Constants::BAM_HEADER_MAGIC_LENGTH ) { + fprintf(stderr, "BamHeader ERROR: could not read magic number\n"); + return false; + } + + // validate magic number + if ( strncmp(buffer, Constants::BAM_HEADER_MAGIC, Constants::BAM_HEADER_MAGIC_LENGTH) != 0 ) { + fprintf(stderr, "BamHeader ERROR: invalid magic number\n"); + return false; + } + + // all checks out + return true; +} + +// clear SamHeader data +void BamHeader::Clear(void) { + m_header.Clear(); +} + +// return true if SamHeader data is valid +bool BamHeader::IsValid(void) const { + return m_header.IsValid(); +} + +// load BAM header ('magic number' and SAM header text) from BGZF stream +// returns true if all OK +bool BamHeader::Load(BgzfStream* stream) { + + // cannot load if invalid stream + if ( stream == 0 ) + return false; + + // cannot load if magic number is invalid + if ( !CheckMagicNumber(stream) ) + return false; + + // cannot load header if cannot read header length + uint32_t length(0); + if ( !ReadHeaderLength(stream, length) ) + return false; + + // cannot load header if cannot read header text + if ( !ReadHeaderText(stream, length) ) + return false; + + // otherwise, everything OK + return true; +} + +// reads SAM header text length from BGZF stream, stores it in @length +// returns read success/fail status +bool BamHeader::ReadHeaderLength(BgzfStream* stream, uint32_t& length) { + + // attempt to read BAM header text length + char buffer[sizeof(uint32_t)]; + if ( stream->Read(buffer, sizeof(uint32_t)) != sizeof(uint32_t) ) { + fprintf(stderr, "BamHeader ERROR: could not read header length\n"); + return false; + } + + // convert char buffer to length, return success + length = BamTools::UnpackUnsignedInt(buffer); + if ( BamTools::SystemIsBigEndian() ) + BamTools::SwapEndian_32(length); + return true; +} + +// reads SAM header text from BGZF stream, stores in SamHeader object +// returns read success/fail status +bool BamHeader::ReadHeaderText(BgzfStream* stream, const uint32_t& length) { + + // set up destination buffer + char* headerText = (char*)calloc(length + 1, 1); + + // attempt to read header text + const unsigned bytesRead = stream->Read(headerText, length); + const bool readOk = ( bytesRead == length ); + if ( readOk ) + m_header.SetHeaderText( (string)((const char*)headerText) ); + else + fprintf(stderr, "BamHeader ERROR: could not read header text\n"); + + // clean up calloc-ed temp variable (on success or fail) + free(headerText); + + // return read success + return readOk; +} + +// returns *copy* of SamHeader data object +SamHeader BamHeader::ToSamHeader(void) const { + return m_header; +} + +// returns SAM-formatted string of header data +string BamHeader::ToString(void) const { + return m_header.ToString(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamHeader_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,72 @@ +// *************************************************************************** +// BamHeader_p.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 26 January 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for handling BAM headers. +// *************************************************************************** + +#ifndef BAMHEADER_P_H +#define BAMHEADER_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <api/SamHeader.h> +#include <string> + +namespace BamTools { +namespace Internal { + +class BgzfStream; + +class BamHeader { + + // ctor & dtor + public: + BamHeader(void); + ~BamHeader(void); + + // BamHeader interface + public: + // clear SamHeader data + void Clear(void); + // return true if SamHeader data is valid + bool IsValid(void) const; + // load BAM header ('magic number' and SAM header text) from BGZF stream + // returns true if all OK + bool Load(BgzfStream* stream); + // returns (editable) copy of SamHeader data object + SamHeader ToSamHeader(void) const; + // returns SAM-formatted string of header data + std::string ToString(void) const; + + // internal methods + private: + // reads magic number from BGZF stream, returns true if valid + bool CheckMagicNumber(BgzfStream* stream); + // reads SAM header length from BGZF stream, stores it in @length + // returns read success/fail status + bool ReadHeaderLength(BgzfStream* stream, uint32_t& length); + // reads SAM header text from BGZF stream, stores in SamHeader object + // returns read success/fail status + bool ReadHeaderText(BgzfStream* stream, const uint32_t& length); + + // data members + private: + SamHeader m_header; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMHEADER_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamIndexFactory_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,113 @@ +// *************************************************************************** +// BamIndexFactory_p.cpp (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides interface for generating BamIndex implementations +// *************************************************************************** + +#include <api/BamAux.h> +#include <api/internal/BamIndexFactory_p.h> +#include <api/internal/BamStandardIndex_p.h> +#include <api/internal/BamToolsIndex_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <cstdio> +using namespace std; + +// generates index filename from BAM filename (depending on requested type) +// if type is unknown, returns empty string +const string BamIndexFactory::CreateIndexFilename(const string& bamFilename, + const BamIndex::IndexType& type) +{ + switch ( type ) { + case ( BamIndex::STANDARD ) : return ( bamFilename + BamStandardIndex::Extension() ); + case ( BamIndex::BAMTOOLS ) : return ( bamFilename + BamToolsIndex::Extension() ); + default : + cerr << "BamIndexFactory ERROR: unknown index type" << type << endl; + return string(); + } +} + +// creates a new BamIndex object, depending on extension of @indexFilename +BamIndex* BamIndexFactory::CreateIndexFromFilename(const string& indexFilename, BamReaderPrivate* reader) { + + // if file doesn't exist, return null index + if ( !BamTools::FileExists(indexFilename) ) + return 0; + + // get file extension from index filename, including dot (".EXT") + // if can't get file extension, return null index + const string extension = FileExtension(indexFilename); + if ( extension.empty() ) + return 0; + + // create index based on extension + if ( extension == BamStandardIndex::Extension() ) return new BamStandardIndex(reader); + else if ( extension == BamToolsIndex::Extension() ) return new BamToolsIndex(reader); + else + return 0; +} + +// creates a new BamIndex, object of requested @type +BamIndex* BamIndexFactory::CreateIndexOfType(const BamIndex::IndexType& type, + BamReaderPrivate* reader) +{ + switch ( type ) { + case ( BamIndex::STANDARD ) : return new BamStandardIndex(reader); + case ( BamIndex::BAMTOOLS ) : return new BamToolsIndex(reader); + default : + cerr << "BamIndexFactory ERROR: unknown index type " << type << endl; + return 0; + } +} + +// retrieves file extension (including '.') +const string BamIndexFactory::FileExtension(const string& filename) { + + // if filename cannot contain valid path + extension, return empty string + if ( filename.empty() || filename.length() <= 4 ) + return string(); + + // look for last dot in filename + size_t lastDotPosition = filename.find_last_of('.'); + + // if none found, return empty string + if ( lastDotPosition == string::npos ) + return string(); + + // return substring from last dot position + return filename.substr(lastDotPosition); +} + +// returns name of existing index file that corresponds to @bamFilename +// will defer to @preferredType if possible, if not will attempt to load any supported type +// returns empty string if not found +const string BamIndexFactory::FindIndexFilename(const string& bamFilename, + const BamIndex::IndexType& preferredType) +{ + // try to find index of preferred type first + // return index filename if found + string indexFilename = CreateIndexFilename(bamFilename, preferredType); + if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) ) + return indexFilename; + + // couldn't find preferred type, try the other supported types + // return index filename if found + if ( preferredType != BamIndex::STANDARD ) { + indexFilename = CreateIndexFilename(bamFilename, BamIndex::STANDARD); + if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) ) + return indexFilename; + } + if ( preferredType != BamIndex::BAMTOOLS ) { + indexFilename = CreateIndexFilename(bamFilename, BamIndex::BAMTOOLS); + if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) ) + return indexFilename; + } + + // otherwise couldn't find any index matching this filename + return string(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamIndexFactory_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,50 @@ +// *************************************************************************** +// BamIndexFactory_p.h (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides interface for generating BamIndex implementations +// *************************************************************************** + +#ifndef BAMINDEX_FACTORY_P_H +#define BAMINDEX_FACTORY_P_H + +#include <api/BamIndex.h> +#include <string> + +namespace BamTools { +namespace Internal { + +class BamIndexFactory { + + // static interface methods + public: + // creates a new BamIndex object, depending on extension of @indexFilename + static BamIndex* CreateIndexFromFilename(const std::string& indexFilename, + BamReaderPrivate* reader); + // creates a new BamIndex object, of requested @type + static BamIndex* CreateIndexOfType(const BamIndex::IndexType& type, + BamReaderPrivate* reader); + // returns name of existing index file that corresponds to @bamFilename + // will defer to @preferredType if possible + // if @preferredType not found, will attempt to load any supported index type + // returns empty string if no index file (of any type) is found + static const std::string FindIndexFilename(const std::string& bamFilename, + const BamIndex::IndexType& preferredType); + + // internal methods + public: + // generates index filename from BAM filename (depending on requested type) + // if type is unknown, returns empty string + static const std::string CreateIndexFilename(const std::string& bamFilename, + const BamIndex::IndexType& type); + // retrieves file extension (including '.') + static const std::string FileExtension(const std::string& filename); +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMINDEX_FACTORY_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamMultiMerger_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,295 @@ +// *************************************************************************** +// BamMultiMerger_p.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides merging functionality for BamMultiReader. At this point, supports +// sorting results by (refId, position) or by read name. +// *************************************************************************** + +#ifndef BAMMULTIMERGER_P_H +#define BAMMULTIMERGER_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <api/BamAlignment.h> +#include <api/BamReader.h> +#include <map> +#include <queue> +#include <string> +#include <utility> + +namespace BamTools { +namespace Internal { + +typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment; + +// generic MultiMerger interface +class IBamMultiMerger { + + public: + IBamMultiMerger(void) { } + virtual ~IBamMultiMerger(void) { } + + public: + virtual void Add(const ReaderAlignment& value) =0; + virtual void Clear(void) =0; + virtual const ReaderAlignment& First(void) const =0; + virtual bool IsEmpty(void) const =0; + virtual void Remove(BamReader* reader) =0; + virtual int Size(void) const =0; + virtual ReaderAlignment TakeFirst(void) =0; +}; + +// IBamMultiMerger implementation - sorted on BamAlignment: (RefId, Position) +class PositionMultiMerger : public IBamMultiMerger { + + public: + PositionMultiMerger(void) : IBamMultiMerger() { } + ~PositionMultiMerger(void) { } + + public: + void Add(const ReaderAlignment& value); + void Clear(void); + const ReaderAlignment& First(void) const; + bool IsEmpty(void) const; + void Remove(BamReader* reader); + int Size(void) const; + ReaderAlignment TakeFirst(void); + + private: + typedef std::pair<int, int> KeyType; + typedef ReaderAlignment ValueType; + typedef std::pair<KeyType, ValueType> ElementType; + + typedef std::multimap<KeyType, ValueType> ContainerType; + typedef ContainerType::iterator DataIterator; + typedef ContainerType::const_iterator DataConstIterator; + + ContainerType m_data; +}; + +// IBamMultiMerger implementation - sorted on BamAlignment: Name +class ReadNameMultiMerger : public IBamMultiMerger { + + public: + ReadNameMultiMerger(void) : IBamMultiMerger() { } + ~ReadNameMultiMerger(void) { } + + public: + void Add(const ReaderAlignment& value); + void Clear(void); + const ReaderAlignment& First(void) const; + bool IsEmpty(void) const; + void Remove(BamReader* reader); + int Size(void) const; + ReaderAlignment TakeFirst(void); + + private: + typedef std::string KeyType; + typedef ReaderAlignment ValueType; + typedef std::pair<KeyType, ValueType> ElementType; + + typedef std::multimap<KeyType, ValueType> ContainerType; + typedef ContainerType::iterator DataIterator; + typedef ContainerType::const_iterator DataConstIterator; + + ContainerType m_data; +}; + +// IBamMultiMerger implementation - unsorted BAM file(s) +class UnsortedMultiMerger : public IBamMultiMerger { + + public: + UnsortedMultiMerger(void) : IBamMultiMerger() { } + ~UnsortedMultiMerger(void) { } + + public: + void Add(const ReaderAlignment& value); + void Clear(void); + const ReaderAlignment& First(void) const; + bool IsEmpty(void) const; + void Remove(BamReader* reader); + int Size(void) const; + ReaderAlignment TakeFirst(void); + + private: + typedef ReaderAlignment ElementType; + typedef std::vector<ReaderAlignment> ContainerType; + typedef ContainerType::iterator DataIterator; + typedef ContainerType::const_iterator DataConstIterator; + + ContainerType m_data; +}; + +// ------------------------------------------ +// PositionMultiMerger implementation + +inline void PositionMultiMerger::Add(const ReaderAlignment& value) { + const KeyType key( value.second->RefID, value.second->Position ); + m_data.insert( ElementType(key, value) ); +} + +inline void PositionMultiMerger::Clear(void) { + m_data.clear(); +} + +inline const ReaderAlignment& PositionMultiMerger::First(void) const { + const ElementType& entry = (*m_data.begin()); + return entry.second; +} + +inline bool PositionMultiMerger::IsEmpty(void) const { + return m_data.empty(); +} + +inline void PositionMultiMerger::Remove(BamReader* reader) { + + if ( reader == 0 ) return; + const std::string filenameToRemove = reader->GetFilename(); + + // iterate over readers in cache + DataIterator dataIter = m_data.begin(); + DataIterator dataEnd = m_data.end(); + for ( ; dataIter != dataEnd; ++dataIter ) { + const ValueType& entry = (*dataIter).second; + const BamReader* entryReader = entry.first; + if ( entryReader == 0 ) continue; + + // remove iterator on match + if ( entryReader->GetFilename() == filenameToRemove ) { + m_data.erase(dataIter); + return; + } + } +} + +inline int PositionMultiMerger::Size(void) const { + return m_data.size(); +} + +inline ReaderAlignment PositionMultiMerger::TakeFirst(void) { + DataIterator first = m_data.begin(); + ReaderAlignment next = (*first).second; + m_data.erase(first); + return next; +} + +// ------------------------------------------ +// ReadNameMultiMerger implementation + +inline void ReadNameMultiMerger::Add(const ReaderAlignment& value) { + const KeyType key(value.second->Name); + m_data.insert( ElementType(key, value) ); +} + +inline void ReadNameMultiMerger::Clear(void) { + m_data.clear(); +} + +inline const ReaderAlignment& ReadNameMultiMerger::First(void) const { + const ElementType& entry = (*m_data.begin()); + return entry.second; +} + +inline bool ReadNameMultiMerger::IsEmpty(void) const { + return m_data.empty(); +} + +inline void ReadNameMultiMerger::Remove(BamReader* reader) { + + if ( reader == 0 ) return; + const std::string filenameToRemove = reader->GetFilename(); + + // iterate over readers in cache + DataIterator dataIter = m_data.begin(); + DataIterator dataEnd = m_data.end(); + for ( ; dataIter != dataEnd; ++dataIter ) { + const ValueType& entry = (*dataIter).second; + const BamReader* entryReader = entry.first; + if ( entryReader == 0 ) continue; + + // remove iterator on match + if ( entryReader->GetFilename() == filenameToRemove ) { + m_data.erase(dataIter); + return; + } + } + +} + +inline int ReadNameMultiMerger::Size(void) const { + return m_data.size(); +} + +inline ReaderAlignment ReadNameMultiMerger::TakeFirst(void) { + DataIterator first = m_data.begin(); + ReaderAlignment next = (*first).second; + m_data.erase(first); + return next; +} + +// ------------------------------------------ +// UnsortedMultiMerger implementation + +inline void UnsortedMultiMerger::Add(const ReaderAlignment& value) { + m_data.push_back(value); +} + +inline void UnsortedMultiMerger::Clear(void) { + for (size_t i = 0; i < m_data.size(); ++i ) + m_data.pop_back(); +} + +inline const ReaderAlignment& UnsortedMultiMerger::First(void) const { + return m_data.front(); +} + +inline bool UnsortedMultiMerger::IsEmpty(void) const { + return m_data.empty(); +} + +inline void UnsortedMultiMerger::Remove(BamReader* reader) { + + if ( reader == 0 ) return; + const std::string filenameToRemove = reader->GetFilename(); + + // iterate over readers in cache + DataIterator dataIter = m_data.begin(); + DataIterator dataEnd = m_data.end(); + for ( ; dataIter != dataEnd; ++dataIter ) { + const BamReader* entryReader = (*dataIter).first; + if ( entryReader == 0 ) continue; + + // remove iterator on match + if ( entryReader->GetFilename() == filenameToRemove ) { + m_data.erase(dataIter); + return; + } + } +} + +inline int UnsortedMultiMerger::Size(void) const { + return m_data.size(); +} + +inline ReaderAlignment UnsortedMultiMerger::TakeFirst(void) { + ReaderAlignment first = m_data.front(); + m_data.erase( m_data.begin() ); + return first; +} + +} // namespace Internal +} // namespace BamTools + +#endif // BAMMULTIMERGER_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamMultiReader_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,802 @@ +// *************************************************************************** +// BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011 (DB) +// --------------------------------------------------------------------------- +// Functionality for simultaneously reading multiple BAM files +// ************************************************************************* + +#include <api/BamAlignment.h> +#include <api/BamMultiReader.h> +#include <api/internal/BamMultiMerger_p.h> +#include <api/internal/BamMultiReader_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <algorithm> +#include <fstream> +#include <iostream> +#include <iterator> +#include <sstream> +using namespace std; + +// ctor +BamMultiReaderPrivate::BamMultiReaderPrivate(void) + : m_alignments(0) + , m_isCoreMode(false) + , m_sortOrder(BamMultiReader::SortedByPosition) +{ } + +// dtor +BamMultiReaderPrivate::~BamMultiReaderPrivate(void) { + + // close all open BAM readers + Close(); + + // clean up alignment cache + delete m_alignments; + m_alignments = 0; +} + +// close all BAM files +void BamMultiReaderPrivate::Close(void) { + CloseFiles( Filenames() ); +} + +// close requested BAM file +void BamMultiReaderPrivate::CloseFile(const string& filename) { + vector<string> filenames(1, filename); + CloseFiles(filenames); +} + +// close requested BAM files +void BamMultiReaderPrivate::CloseFiles(const vector<string>& filenames) { + + // iterate over filenames + vector<string>::const_iterator filesIter = filenames.begin(); + vector<string>::const_iterator filesEnd = filenames.end(); + for ( ; filesIter != filesEnd; ++filesIter ) { + const string& filename = (*filesIter); + if ( filename.empty() ) continue; + + // iterate over readers + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // if reader matches requested filename + if ( reader->GetFilename() == filename ) { + + // remove reader/alignment from alignment cache + m_alignments->Remove(reader); + + // close & delete reader + reader->Close(); + delete reader; + reader = 0; + + // delete reader's alignment entry + BamAlignment* alignment = (*readerIter).second; + delete alignment; + alignment = 0; + + // remove reader from container + m_readers.erase(readerIter); + + // on match, just go on to next filename + // (no need to keep looking and iterator is invalid now anyway) + break; + } + } + } + + // make sure alignment cache is cleared if all readers are now closed + if ( m_readers.empty() && m_alignments != 0 ) + m_alignments->Clear(); +} + +// creates index files for BAM files that don't have them +bool BamMultiReaderPrivate::CreateIndexes(const BamIndex::IndexType& type) { + + bool result = true; + + // iterate over readers + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // if reader doesn't have an index, create one + if ( !reader->HasIndex() ) + result &= reader->CreateIndex(type); + } + + return result; +} + +IBamMultiMerger* BamMultiReaderPrivate::CreateMergerForCurrentSortOrder(void) const { + switch ( m_sortOrder ) { + case ( BamMultiReader::SortedByPosition ) : return new PositionMultiMerger; + case ( BamMultiReader::SortedByReadName ) : return new ReadNameMultiMerger; + case ( BamMultiReader::Unsorted ) : return new UnsortedMultiMerger; + default : + cerr << "BamMultiReader ERROR: requested sort order is unknown" << endl; + return 0; + } +} + +const string BamMultiReaderPrivate::ExtractReadGroup(const string& headerLine) const { + + string readGroup(""); + stringstream headerLineSs(headerLine); + string part; + + // parse @RG header line, looking for the ID: tag + while( getline(headerLineSs, part, '\t') ) { + stringstream partSs(part); + string subtag; + getline(partSs, subtag, ':'); + if ( subtag == "ID" ) { + getline(partSs, readGroup, ':'); + break; + } + } + return readGroup; +} + +const vector<string> BamMultiReaderPrivate::Filenames(void) const { + + // init filename container + vector<string> filenames; + filenames.reserve( m_readers.size() ); + + // iterate over readers + vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + const BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // store filename if not empty + const string filename = reader->GetFilename(); + if ( !filename.empty() ) + filenames.push_back( reader->GetFilename() ); + } + + // return result + return filenames; +} + +SamHeader BamMultiReaderPrivate::GetHeader(void) const { + string text = GetHeaderText(); + return SamHeader(text); +} + +// makes a virtual, unified header for all the bam files in the multireader +string BamMultiReaderPrivate::GetHeaderText(void) const { + + // TODO: merge SamHeader objects instead of parsing string data (again) + + // if only one reader is open + if ( m_readers.size() == 1 ) { + + // just return reader's header text + const ReaderAlignment& ra = m_readers.front(); + const BamReader* reader = ra.first; + if ( reader ) return reader->GetHeaderText(); + + // invalid reader + return string(); + } + + string mergedHeader(""); + map<string, bool> readGroups; + + // foreach extraction entry (each BAM file) + vector<ReaderAlignment>::const_iterator readerBegin = m_readers.begin(); + vector<ReaderAlignment>::const_iterator readerIter = readerBegin; + vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + const BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // get header from reader + string headerText = reader->GetHeaderText(); + if ( headerText.empty() ) continue; + + // store header text in lines + map<string, bool> currentFileReadGroups; + const vector<string> lines = SplitHeaderText(headerText); + + // iterate over header lines + vector<string>::const_iterator linesIter = lines.begin(); + vector<string>::const_iterator linesEnd = lines.end(); + for ( ; linesIter != linesEnd; ++linesIter ) { + + // get next line from header, skip if empty + const string headerLine = (*linesIter); + if ( headerLine.empty() ) continue; + + // if first file, save HD & SQ entries + // TODO: what if first file has empty header, should just check for empty 'mergedHeader' instead ? + if ( readerIter == readerBegin ) { + if ( headerLine.find("@HD") == 0 || headerLine.find("@SQ") == 0) { + mergedHeader.append(headerLine.c_str()); + mergedHeader.append(1, '\n'); + } + } + + // (for all files) append RG entries if they are unique + if ( headerLine.find("@RG") == 0 ) { + + // extract read group name from line + const string readGroup = ExtractReadGroup(headerLine); + + // make sure not to duplicate @RG entries + if ( readGroups.find(readGroup) == readGroups.end() ) { + mergedHeader.append(headerLine.c_str() ); + mergedHeader.append(1, '\n'); + readGroups[readGroup] = true; + currentFileReadGroups[readGroup] = true; + } else { + // warn iff we are reading one file and discover duplicated @RG tags in the header + // otherwise, we emit no warning, as we might be merging multiple BAM files with identical @RG tags + if ( currentFileReadGroups.find(readGroup) != currentFileReadGroups.end() ) { + cerr << "BamMultiReader WARNING: duplicate @RG tag " << readGroup + << " entry in header of " << reader->GetFilename() << endl; + } + } + } + } + } + + // return merged header text + return mergedHeader; +} + +// get next alignment among all files +bool BamMultiReaderPrivate::GetNextAlignment(BamAlignment& al) { + m_isCoreMode = false; + return LoadNextAlignment(al); +} + +// get next alignment among all files without parsing character data from alignments +bool BamMultiReaderPrivate::GetNextAlignmentCore(BamAlignment& al) { + m_isCoreMode = true; + return LoadNextAlignment(al); +} + +// --------------------------------------------------------------------------------------- +// +// NB: The following GetReferenceX() functions assume that we have identical +// references for all BAM files. We enforce this by invoking the +// ValidateReaders() method to verify that our reference data is the same +// across all files on Open - so we will not encounter a situation in which +// there is a mismatch and we are still live. +// +// --------------------------------------------------------------------------------------- + +// returns the number of reference sequences +int BamMultiReaderPrivate::GetReferenceCount(void) const { + + // handle empty multireader + if ( m_readers.empty() ) + return 0; + + // return reference count from first reader + const ReaderAlignment& ra = m_readers.front(); + const BamReader* reader = ra.first; + if ( reader ) return reader->GetReferenceCount(); + + // invalid reader + return 0; +} + +// returns vector of reference objects +const RefVector BamMultiReaderPrivate::GetReferenceData(void) const { + + // handle empty multireader + if ( m_readers.empty() ) + return RefVector(); + + // return reference data from first BamReader + const ReaderAlignment& ra = m_readers.front(); + const BamReader* reader = ra.first; + if ( reader ) return reader->GetReferenceData(); + + // invalid reader + return RefVector(); +} + +// returns refID from reference name +int BamMultiReaderPrivate::GetReferenceID(const string& refName) const { + + // handle empty multireader + if ( m_readers.empty() ) + return -1; + + // return reference ID from first BamReader + const ReaderAlignment& ra = m_readers.front(); + const BamReader* reader = ra.first; + if ( reader ) return reader->GetReferenceID(refName); + + // invalid reader + return -1; +} +// --------------------------------------------------------------------------------------- + +// checks if any readers still have alignments +bool BamMultiReaderPrivate::HasAlignmentData(void) const { + if ( m_alignments == 0 ) + return false; + return !m_alignments->IsEmpty(); +} + +// returns true if all readers have index data available +// this is useful to indicate whether Jump() or SetRegion() are possible +bool BamMultiReaderPrivate::HasIndexes(void) const { + + // handle empty multireader + if ( m_readers.empty() ) + return false; + + bool result = true; + + // iterate over readers + vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + const BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // see if current reader has index data + result &= reader->HasIndex(); + } + + return result; +} + +// returns true if multireader has open readers +bool BamMultiReaderPrivate::HasOpenReaders(void) { + + // iterate over readers + vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + const BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // return true whenever an open reader is found + if ( reader->IsOpen() ) return true; + } + + // no readers open + return false; +} + +// performs random-access jump using (refID, position) as a left-bound +bool BamMultiReaderPrivate::Jump(int refID, int position) { + + // NB: While it may make sense to track readers in which we can + // successfully Jump, in practice a failure of Jump means "no + // alignments here." It makes sense to simply accept the failure, + // UpdateAlignments(), and continue. + + // iterate over readers + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // attempt jump() on each + if ( !reader->Jump(refID, position) ) { + cerr << "BamMultiReader ERROR: could not jump " << reader->GetFilename() + << " to " << refID << ":" << position << endl; + } + } + + // update alignment cache & return success + UpdateAlignmentCache(); + return true; +} + +bool BamMultiReaderPrivate::LoadNextAlignment(BamAlignment& al) { + + // bail out if no more data to process + if ( !HasAlignmentData() ) + return false; + + // "pop" next alignment and reader + ReaderAlignment nextReaderAlignment = m_alignments->TakeFirst(); + BamReader* reader = nextReaderAlignment.first; + BamAlignment* alignment = nextReaderAlignment.second; + + // store cached alignment into destination parameter (by copy) + al = *alignment; + + // peek to next alignment & store in cache + SaveNextAlignment(reader, alignment); + + // return success + return true; +} + +// locate (& load) index files for BAM readers that don't already have one loaded +bool BamMultiReaderPrivate::LocateIndexes(const BamIndex::IndexType& preferredType) { + + bool result = true; + + // iterate over readers + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // if reader has no index, try to locate one + if ( !reader->HasIndex() ) + result &= reader->LocateIndex(preferredType); + } + + return result; +} + +// opens BAM files +bool BamMultiReaderPrivate::Open(const vector<string>& filenames) { + + // create alignment cache if neccessary + if ( m_alignments == 0 ) { + m_alignments = CreateMergerForCurrentSortOrder(); + if ( m_alignments == 0 ) return false; + } + + // iterate over filenames + vector<string>::const_iterator filenameIter = filenames.begin(); + vector<string>::const_iterator filenameEnd = filenames.end(); + for ( ; filenameIter != filenameEnd; ++filenameIter ) { + const string& filename = (*filenameIter); + if ( filename.empty() ) continue; + + // attempt to open BamReader on filename + BamReader* reader = OpenReader(filename); + if ( reader == 0 ) continue; + + // store reader with new alignment + m_readers.push_back( make_pair(reader, new BamAlignment) ); + } + + // validate & rewind any opened readers, also refreshes alignment cache + if ( !m_readers.empty() ) { + ValidateReaders(); + Rewind(); + } + + // return success + return true; +} + +bool BamMultiReaderPrivate::OpenFile(const std::string& filename) { + vector<string> filenames(1, filename); + return Open(filenames); +} + +bool BamMultiReaderPrivate::OpenIndexes(const vector<string>& indexFilenames) { + + // TODO: This needs to be cleaner - should not assume same order. + // And either way, shouldn't start at first reader. Should start at + // first reader without an index? + + // make sure same number of index filenames as readers + if ( m_readers.size() != indexFilenames.size() || !indexFilenames.empty() ) + return false; + + // init result flag + bool result = true; + + // iterate over BamReaders + vector<string>::const_iterator indexFilenameIter = indexFilenames.begin(); + vector<string>::const_iterator indexFilenameEnd = indexFilenames.end(); + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + + // open index filename on reader + if ( reader ) { + const string& indexFilename = (*indexFilenameIter); + result &= reader->OpenIndex(indexFilename); + } + + // increment filename iterator, skip if no more index files to open + if ( ++indexFilenameIter == indexFilenameEnd ) + break; + } + + // TODO: validation ?? + + // return success/fail + return result; +} + +BamReader* BamMultiReaderPrivate::OpenReader(const std::string& filename) { + + // create new BamReader + BamReader* reader = new BamReader; + + // if reader opens OK + if ( reader->Open(filename) ) { + + // attempt to read first alignment (sanity check) + // if ok, then return BamReader pointer + BamAlignment al; + if ( reader->GetNextAlignmentCore(al) ) + return reader; + + // could not read alignment + else { + cerr << "BamMultiReader WARNING: Could not read first alignment from " + << filename << ", ignoring file" << endl; + } + } + + // reader could not open + else { + cerr << "BamMultiReader WARNING: Could not open " + << filename << ", ignoring file" << endl; + } + + // if we get here, there was a problem with this BAM file (opening or reading) + // clean up memory allocation & return null pointer + delete reader; + return 0; +} + +// print associated filenames to stdout +void BamMultiReaderPrivate::PrintFilenames(void) const { + const vector<string>& filenames = Filenames(); + vector<string>::const_iterator filenameIter = filenames.begin(); + vector<string>::const_iterator filenameEnd = filenames.end(); + for ( ; filenameIter != filenameEnd; ++filenameIter ) + cout << (*filenameIter) << endl; +} + +// returns BAM file pointers to beginning of alignment data & resets alignment cache +bool BamMultiReaderPrivate::Rewind(void) { + + // clear out alignment cache + m_alignments->Clear(); + + // attempt to rewind files + if ( !RewindReaders() ) { + cerr << "BamMultiReader ERROR: could not rewind file(s) successfully"; + return false; + } + + // reset cache & return success + UpdateAlignmentCache(); + return true; +} + +// returns BAM file pointers to beginning of alignment data +bool BamMultiReaderPrivate::RewindReaders(void) { + + bool result = true; + + // iterate over readers + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // attempt rewind on BamReader + result &= reader->Rewind(); + } + + return result; +} + +void BamMultiReaderPrivate::SaveNextAlignment(BamReader* reader, BamAlignment* alignment) { + + // must be in core mode && NOT sorting by read name to call GNACore() + if ( m_isCoreMode && m_sortOrder != BamMultiReader::SortedByReadName ) { + if ( reader->GetNextAlignmentCore(*alignment) ) + m_alignments->Add( make_pair(reader, alignment) ); + } + + // not in core mode and/or sorting by readname, must call GNA() + else { + if ( reader->GetNextAlignment(*alignment) ) + m_alignments->Add( make_pair(reader, alignment) ); + } +} + +// sets the index caching mode on the readers +void BamMultiReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode mode) { + + // iterate over readers + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // set reader's index cache mode + reader->SetIndexCacheMode(mode); + } +} + +bool BamMultiReaderPrivate::SetRegion(const BamRegion& region) { + + // NB: While it may make sense to track readers in which we can + // successfully SetRegion, In practice a failure of SetRegion means "no + // alignments here." It makes sense to simply accept the failure, + // UpdateAlignments(), and continue. + + // iterate over alignments + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + + // attempt to set BamReader's region of interest + if ( !reader->SetRegion(region) ) { + cerr << "BamMultiReader WARNING: could not jump " << reader->GetFilename() << " to " + << region.LeftRefID << ":" << region.LeftPosition << ".." + << region.RightRefID << ":" << region.RightPosition << endl; + } + } + + // update alignment cache & return success + UpdateAlignmentCache(); + return true; +} + +void BamMultiReaderPrivate::SetSortOrder(const BamMultiReader::SortOrder& order) { + + // skip if no change needed + if ( m_sortOrder == order ) return; + + // set new sort order + m_sortOrder = order; + + // create new alignment cache based on sort order + IBamMultiMerger* newAlignmentCache = CreateMergerForCurrentSortOrder(); + if ( newAlignmentCache == 0 ) return; // print error? + + // copy old cache contents to new cache + while ( m_alignments->Size() > 0 ) { + ReaderAlignment value = m_alignments->TakeFirst(); // retrieves & 'pops' + newAlignmentCache->Add(value); + } + + // remove old cache structure & point to new cache + delete m_alignments; + m_alignments = newAlignmentCache; +} + +// splits the entire header into a list of strings +const vector<string> BamMultiReaderPrivate::SplitHeaderText(const string& headerText) const { + + stringstream header(headerText); + string item; + + vector<string> lines; + while ( getline(header, item) ) + lines.push_back(item); + return lines; +} + +// updates our alignment cache +void BamMultiReaderPrivate::UpdateAlignmentCache(void) { + + // skip if invalid alignment cache + if ( m_alignments == 0 ) return; + + // clear the cache + m_alignments->Clear(); + + // seed cache with fully-populated alignments + // further updates will fill with full/core-only as requested + m_isCoreMode = false; + + // iterate over readers + vector<ReaderAlignment>::iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + BamReader* reader = (*readerIter).first; + BamAlignment* alignment = (*readerIter).second; + if ( reader == 0 || alignment == 0 ) continue; + + // save next alignment from each reader in cache + SaveNextAlignment(reader, alignment); + } +} + +// ValidateReaders checks that all the readers point to BAM files representing +// alignments against the same set of reference sequences, and that the +// sequences are identically ordered. If these checks fail the operation of +// the multireader is undefined, so we force program exit. +void BamMultiReaderPrivate::ValidateReaders(void) const { + + // retrieve first reader data + const BamReader* firstReader = m_readers.front().first; + if ( firstReader == 0 ) return; + const RefVector firstReaderRefData = firstReader->GetReferenceData(); + const int firstReaderRefCount = firstReader->GetReferenceCount(); + const int firstReaderRefSize = firstReaderRefData.size(); + + // iterate over all readers + vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin(); + vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end(); + for ( ; readerIter != readerEnd; ++readerIter ) { + + // get current reader data + BamReader* reader = (*readerIter).first; + if ( reader == 0 ) continue; + const RefVector currentReaderRefData = reader->GetReferenceData(); + const int currentReaderRefCount = reader->GetReferenceCount(); + const int currentReaderRefSize = currentReaderRefData.size(); + + // init container iterators + RefVector::const_iterator firstRefIter = firstReaderRefData.begin(); + RefVector::const_iterator firstRefEnd = firstReaderRefData.end(); + RefVector::const_iterator currentRefIter = currentReaderRefData.begin(); + + // compare reference counts from BamReader ( & container size, in case of BR error) + if ( (currentReaderRefCount != firstReaderRefCount) || + (firstReaderRefSize != currentReaderRefSize) ) + { + cerr << "BamMultiReader ERROR: mismatched number of references in " << reader->GetFilename() + << " expected " << firstReaderRefCount + << " reference sequences but only found " << currentReaderRefCount << endl; + exit(1); + } + + // this will be ok; we just checked above that we have identically-sized sets of references + // here we simply check if they are all, in fact, equal in content + while ( firstRefIter != firstRefEnd ) { + const RefData& firstRef = (*firstRefIter); + const RefData& currentRef = (*currentRefIter); + + // compare reference name & length + if ( (firstRef.RefName != currentRef.RefName) || + (firstRef.RefLength != currentRef.RefLength) ) + { + cerr << "BamMultiReader ERROR: mismatched references found in " << reader->GetFilename() + << " expected: " << endl; + + // print first reader's reference data + RefVector::const_iterator refIter = firstReaderRefData.begin(); + RefVector::const_iterator refEnd = firstReaderRefData.end(); + for ( ; refIter != refEnd; ++refIter ) { + const RefData& entry = (*refIter); + cerr << entry.RefName << " " << entry.RefLength << endl; + } + + cerr << "but found: " << endl; + + // print current reader's reference data + refIter = currentReaderRefData.begin(); + refEnd = currentReaderRefData.end(); + for ( ; refIter != refEnd; ++refIter ) { + const RefData& entry = (*refIter); + cerr << entry.RefName << " " << entry.RefLength << endl; + } + + exit(1); + } + + // update iterators + ++firstRefIter; + ++currentRefIter; + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamMultiReader_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,102 @@ +// *************************************************************************** +// BamMultiReader_p.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 13 March 2011 (DB) +// --------------------------------------------------------------------------- +// Functionality for simultaneously reading multiple BAM files +// ************************************************************************* + +#ifndef BAMMULTIREADER_P_H +#define BAMMULTIREADER_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <api/SamHeader.h> +#include <api/BamMultiReader.h> +#include <string> +#include <vector> + +namespace BamTools { +namespace Internal { + +class IBamMultiMerger; + +class BamMultiReaderPrivate { + + // constructor / destructor + public: + BamMultiReaderPrivate(void); + ~BamMultiReaderPrivate(void); + + // public interface + public: + + // file operations + void Close(void); + void CloseFile(const std::string& filename); + void CloseFiles(const std::vector<std::string>& filenames); + const std::vector<std::string> Filenames(void) const; + bool Jump(int refID, int position = 0); + bool Open(const std::vector<std::string>& filenames); + bool OpenFile(const std::string& filename); + void PrintFilenames(void) const; + bool Rewind(void); + bool SetRegion(const BamRegion& region); + + // access alignment data + bool GetNextAlignment(BamAlignment& al); + bool GetNextAlignmentCore(BamAlignment& al); + bool HasOpenReaders(void); + void SetSortOrder(const BamMultiReader::SortOrder& order); + + // access auxiliary data + SamHeader GetHeader(void) const; + std::string GetHeaderText(void) const; + int GetReferenceCount(void) const; + const BamTools::RefVector GetReferenceData(void) const; + int GetReferenceID(const std::string& refName) const; + + // BAM index operations + bool CreateIndexes(const BamIndex::IndexType& type = BamIndex::STANDARD); + bool HasIndexes(void) const; + bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD); + bool OpenIndexes(const std::vector<std::string>& indexFilenames); + void SetIndexCacheMode(const BamIndex::IndexCacheMode mode); + + // 'internal' methods + public: + IBamMultiMerger* CreateMergerForCurrentSortOrder(void) const; + const std::string ExtractReadGroup(const std::string& headerLine) const; + bool HasAlignmentData(void) const; + bool LoadNextAlignment(BamAlignment& al); + BamTools::BamReader* OpenReader(const std::string& filename); + bool RewindReaders(void); + void SaveNextAlignment(BamTools::BamReader* reader, BamTools::BamAlignment* alignment); + const std::vector<std::string> SplitHeaderText(const std::string& headerText) const; + void UpdateAlignmentCache(void); + void ValidateReaders(void) const; + + // data members + public: + typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment; + std::vector<ReaderAlignment> m_readers; + + IBamMultiMerger* m_alignments; + bool m_isCoreMode; + BamMultiReader::SortOrder m_sortOrder; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMMULTIREADER_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamRandomAccessController_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,273 @@ +// *************************************************************************** +// BamRandomAccessController_p.cpp (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011(DB) +// --------------------------------------------------------------------------- +// Manages random access operations in a BAM file +// ************************************************************************** + +#include <api/BamIndex.h> +#include <api/internal/BamRandomAccessController_p.h> +#include <api/internal/BamReader_p.h> +#include <api/internal/BamIndexFactory_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <iostream> +using namespace std; + +BamRandomAccessController::BamRandomAccessController(void) + : m_index(0) + , m_indexCacheMode(BamIndex::LimitedIndexCaching) + , m_hasAlignmentsInRegion(true) +{ } + +BamRandomAccessController::~BamRandomAccessController(void) { + Close(); +} + +void BamRandomAccessController::AdjustRegion(const int& referenceCount) { + + // skip if no index available + if ( m_index == 0 ) + return; + + // see if any references in region have alignments + m_hasAlignmentsInRegion = false; + int currentId = m_region.LeftRefID; + const int rightBoundRefId = ( m_region.isRightBoundSpecified() ? m_region.RightRefID : referenceCount - 1 ); + while ( currentId <= rightBoundRefId ) { + m_hasAlignmentsInRegion = m_index->HasAlignments(currentId); + if ( m_hasAlignmentsInRegion ) break; + ++currentId; + } + + // if no data found on any reference in region + if ( !m_hasAlignmentsInRegion ) + return; + + // if left bound of desired region had no data, use first reference that had data + // otherwise, leave requested region as-is + if ( currentId != m_region.LeftRefID ) { + m_region.LeftRefID = currentId; + m_region.LeftPosition = 0; + } +} + +// returns alignments' "RegionState": { Before|Overlaps|After } current region +BamRandomAccessController::RegionState +BamRandomAccessController::AlignmentState(const BamAlignment& alignment) const { + + // if region has no left bound at all + if ( !m_region.isLeftBoundSpecified() ) + return OverlapsRegion; + + // handle unmapped reads - return AFTER region to halt processing + if ( alignment.RefID == -1 ) + return AfterRegion; + + // if alignment is on any reference before left bound reference + if ( alignment.RefID < m_region.LeftRefID ) + return BeforeRegion; + + // if alignment is on left bound reference + else if ( alignment.RefID == m_region.LeftRefID ) { + + // if alignment starts at or after left bound position + if ( alignment.Position >= m_region.LeftPosition) { + + if ( m_region.isRightBoundSpecified() && // right bound is specified AND + m_region.LeftRefID == m_region.RightRefID && // left & right bounds on same reference AND + alignment.Position > m_region.RightPosition ) // alignment starts after right bound position + return AfterRegion; + + // otherwise, alignment overlaps region + else return OverlapsRegion; + } + + // alignment starts before left bound position + else { + + // if alignment overlaps left bound position + if ( alignment.GetEndPosition() >= m_region.LeftPosition ) + return OverlapsRegion; + else + return BeforeRegion; + } + } + + // otherwise alignment is on a reference after left bound reference + else { + + // if region has a right bound + if ( m_region.isRightBoundSpecified() ) { + + // alignment is on any reference between boundaries + if ( alignment.RefID < m_region.RightRefID ) + return OverlapsRegion; + + // alignment is on any reference after right boundary + else if ( alignment.RefID > m_region.RightRefID ) + return AfterRegion; + + // alignment is on right bound reference + else { + + // if alignment starts on or before right bound position + if ( alignment.Position <= m_region.RightPosition ) + return OverlapsRegion; + else + return AfterRegion; + } + } + + // otherwise, alignment starts after left bound and there is no right bound + else return OverlapsRegion; + } +} + +void BamRandomAccessController::Close(void) { + ClearIndex(); + ClearRegion(); +} + +void BamRandomAccessController::ClearIndex(void) { + delete m_index; + m_index = 0; +} + +void BamRandomAccessController::ClearRegion(void) { + m_region.clear(); + m_hasAlignmentsInRegion = true; +} + +bool BamRandomAccessController::CreateIndex(BamReaderPrivate* reader, + const BamIndex::IndexType& type) { + + // skip if reader is invalid + if ( reader == 0 ) + return false; + + // create new index of requested type + BamIndex* newIndex = BamIndexFactory::CreateIndexOfType(type, reader); + if ( newIndex == 0 ) { + cerr << "BamRandomAccessController ERROR: could not create index of type " << type << endl; + return false; + } + + // attempt to build index from current BamReader file + if ( !newIndex->Create() ) { + cerr << "BamRandomAccessController ERROR: could not create index for BAM file: " + << reader->Filename() << endl; + return false; + } + + // save new index + SetIndex(newIndex); + + // set new index's cache mode & return success + newIndex->SetCacheMode(m_indexCacheMode); + return true; +} + +bool BamRandomAccessController::HasIndex(void) const { + return ( m_index != 0 ); +} + +bool BamRandomAccessController::HasRegion(void) const { + return ( !m_region.isNull() ); +} + +bool BamRandomAccessController::IndexHasAlignmentsForReference(const int& refId) { + return m_index->HasAlignments(refId); +} + +bool BamRandomAccessController::LocateIndex(BamReaderPrivate* reader, + const BamIndex::IndexType& preferredType) +{ + // look up index filename, deferring to preferredType if possible + const string& indexFilename = BamIndexFactory::FindIndexFilename(reader->Filename(), preferredType); + + // if no index file found (of any type) + if ( indexFilename.empty() ) { + cerr << "BamRandomAccessController WARNING: " + << "could not find index file for BAM: " + << reader->Filename() << endl; + return false; + } + + // otherwise open & use index file that was found + return OpenIndex(indexFilename, reader); +} + +bool BamRandomAccessController::OpenIndex(const string& indexFilename, BamReaderPrivate* reader) { + + // attempt create new index of type based on filename + BamIndex* index = BamIndexFactory::CreateIndexFromFilename(indexFilename, reader); + if ( index == 0 ) { + cerr << "BamRandomAccessController ERROR: could not create index for file: " << indexFilename << endl; + return false; + } + + // set cache mode + index->SetCacheMode(m_indexCacheMode); + + // attempt to load data from index file + if ( !index->Load(indexFilename) ) { + cerr << "BamRandomAccessController ERROR: could not load index data from file: " << indexFilename << endl; + return false; + } + + // save new index & return success + SetIndex(index); + return true; +} + +bool BamRandomAccessController::RegionHasAlignments(void) const { + return m_hasAlignmentsInRegion; +} + +void BamRandomAccessController::SetIndex(BamIndex* index) { + if ( m_index ) + ClearIndex(); + m_index = index; +} + +void BamRandomAccessController::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) { + m_indexCacheMode = mode; + if ( m_index ) + m_index->SetCacheMode(mode); +} + +bool BamRandomAccessController::SetRegion(BamReaderPrivate* reader, + const BamRegion& region, + const int& referenceCount) +{ + // store region + m_region = region; + + // cannot jump when no index is available + if ( !HasIndex() ) + return false; + + // adjust region as necessary to reflect where data actually begins + AdjustRegion(referenceCount); + + // if no data present, return true + // * Not an error, but future attempts to access alignments in this region will not return data + // Returning true is useful in a BamMultiReader setting where some BAM files may + // lack alignments in regions where other BAMs do have data. + if ( !m_hasAlignmentsInRegion ) + return true; + + // return success/failure of jump to specified region, + // + // * Index::Jump() is allowed to modify the m_hasAlignmentsInRegion flag + // This covers 'corner case' where a region is requested that lies beyond the last + // alignment on a reference. If this occurs, any subsequent calls to GetNextAlignment[Core] + // will not return data. BamMultiReader will still be able to successfully pull alignments + // from a region from multiple files even if one or more have no data. + return m_index->Jump(m_region, &m_hasAlignmentsInRegion); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamRandomAccessController_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,94 @@ +// *************************************************************************** +// BamRandomAccessController_p.h (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 24 February 2011(DB) +// --------------------------------------------------------------------------- +// Manages random access operations in a BAM file +// *************************************************************************** + +#ifndef BAMRACONTROLLER_P_H +#define BAMRACONTROLLER_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <api/BamAux.h> +#include <api/BamIndex.h> + +namespace BamTools { + +class BamAlignment; + +namespace Internal { + +class BamReaderPrivate; + +class BamRandomAccessController { + + // enums + public: enum RegionState { BeforeRegion = 0 + , OverlapsRegion + , AfterRegion + }; + + // ctor & dtor + public: + BamRandomAccessController(void); + ~BamRandomAccessController(void); + + // general interface + public: + void Close(void); + + // index operations + public: + // + void ClearIndex(void); + bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type); + bool HasIndex(void) const; + bool IndexHasAlignmentsForReference(const int& refId); + bool LocateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& preferredType); + bool OpenIndex(const std::string& indexFilename, BamReaderPrivate* reader); + void SetIndex(BamIndex* index); + void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode); + + // region operations + public: + void ClearRegion(void); + bool HasRegion(void) const; + RegionState AlignmentState(const BamAlignment& alignment) const; + bool RegionHasAlignments(void) const; + bool SetRegion(BamReaderPrivate* reader, + const BamRegion& region, + const int& referenceCount); + + // 'internal' methods + public: + // adjusts requested region if necessary (depending on where data actually begins) + void AdjustRegion(const int& referenceCount); + + // data members + private: + + // index data + BamIndex* m_index; // owns index, not a copy - responsible for deleting + BamIndex::IndexCacheMode m_indexCacheMode; + + // region data + BamRegion m_region; + bool m_hasAlignmentsInRegion; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMRACONTROLLER_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamReader_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,381 @@ +// *************************************************************************** +// BamReader_p.cpp (c) 2009 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 10 May 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for reading BAM files +// *************************************************************************** + +#include <api/BamConstants.h> +#include <api/BamReader.h> +#include <api/internal/BamHeader_p.h> +#include <api/internal/BamRandomAccessController_p.h> +#include <api/internal/BamReader_p.h> +#include <api/internal/BamStandardIndex_p.h> +#include <api/internal/BamToolsIndex_p.h> +#include <api/internal/BgzfStream_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <algorithm> +#include <iostream> +#include <iterator> +#include <vector> +using namespace std; + +// constructor +BamReaderPrivate::BamReaderPrivate(BamReader* parent) + : m_alignmentsBeginOffset(0) + , m_parent(parent) +{ + m_isBigEndian = BamTools::SystemIsBigEndian(); +} + +// destructor +BamReaderPrivate::~BamReaderPrivate(void) { + Close(); +} + +// closes the BAM file +void BamReaderPrivate::Close(void) { + + // clear header & reference data + m_references.clear(); + m_header.Clear(); + + // close internal + m_randomAccessController.Close(); + m_stream.Close(); + + // clear filename + m_filename.clear(); +} + +// creates an index file of requested type on current BAM file +bool BamReaderPrivate::CreateIndex(const BamIndex::IndexType& type) { + if ( !IsOpen() ) return false; + return m_randomAccessController.CreateIndex(this, type); +} + +// return path & filename of current BAM file +const string BamReaderPrivate::Filename(void) const { + return m_filename; +} + +// return header data as std::string +string BamReaderPrivate::GetHeaderText(void) const { + return m_header.ToString(); +} + +// return header data as SamHeader object +SamHeader BamReaderPrivate::GetSamHeader(void) const { + return m_header.ToSamHeader(); +} + +// get next alignment (with character data fully parsed) +bool BamReaderPrivate::GetNextAlignment(BamAlignment& alignment) { + + // if valid alignment found + if ( GetNextAlignmentCore(alignment) ) { + + // store alignment's "source" filename + alignment.Filename = m_filename; + + // return success/failure of parsing char data + return alignment.BuildCharData(); + } + + // no valid alignment found + return false; +} + +// retrieves next available alignment core data (returns success/fail) +// ** DOES NOT populate any character data fields (read name, bases, qualities, tag data, filename) +// these can be accessed, if necessary, from the supportData +// useful for operations requiring ONLY positional or other alignment-related information +bool BamReaderPrivate::GetNextAlignmentCore(BamAlignment& alignment) { + + // skip if region is set but has no alignments + if ( m_randomAccessController.HasRegion() && + !m_randomAccessController.RegionHasAlignments() ) + { + return false; + } + + // if can't read next alignment + if ( !LoadNextAlignment(alignment) ) + return false; + + // check alignment's region-overlap state + BamRandomAccessController::RegionState state = m_randomAccessController.AlignmentState(alignment); + + // if alignment starts after region, no need to keep reading + if ( state == BamRandomAccessController::AfterRegion ) + return false; + + // read until overlap is found + while ( state != BamRandomAccessController::OverlapsRegion ) { + + // if can't read next alignment + if ( !LoadNextAlignment(alignment) ) + return false; + + // check alignment's region-overlap state + state = m_randomAccessController.AlignmentState(alignment); + + // if alignment starts after region, no need to keep reading + if ( state == BamRandomAccessController::AfterRegion ) + return false; + } + + // if we get here, we found the next 'valid' alignment + // (e.g. overlaps current region if one was set, simply the next alignment if not) + alignment.SupportData.HasCoreOnly = true; + return true; +} + +int BamReaderPrivate::GetReferenceCount(void) const { + return m_references.size(); +} + +const RefVector& BamReaderPrivate::GetReferenceData(void) const { + return m_references; +} + +// returns RefID for given RefName (returns References.size() if not found) +int BamReaderPrivate::GetReferenceID(const string& refName) const { + + // retrieve names from reference data + vector<string> refNames; + RefVector::const_iterator refIter = m_references.begin(); + RefVector::const_iterator refEnd = m_references.end(); + for ( ; refIter != refEnd; ++refIter) + refNames.push_back( (*refIter).RefName ); + + // return 'index-of' refName (or -1 if not found) + int index = distance(refNames.begin(), find(refNames.begin(), refNames.end(), refName)); + if ( index == (int)m_references.size() ) return -1; + else return index; +} + +bool BamReaderPrivate::HasIndex(void) const { + return m_randomAccessController.HasIndex(); +} + +bool BamReaderPrivate::IsOpen(void) const { + return m_stream.IsOpen; +} + +// load BAM header data +bool BamReaderPrivate::LoadHeaderData(void) { + return m_header.Load(&m_stream); +} + +// populates BamAlignment with alignment data under file pointer, returns success/fail +bool BamReaderPrivate::LoadNextAlignment(BamAlignment& alignment) { + + // read in the 'block length' value, make sure it's not zero + char buffer[sizeof(uint32_t)]; + m_stream.Read(buffer, sizeof(uint32_t)); + alignment.SupportData.BlockLength = BamTools::UnpackUnsignedInt(buffer); + if ( m_isBigEndian ) BamTools::SwapEndian_32(alignment.SupportData.BlockLength); + if ( alignment.SupportData.BlockLength == 0 ) return false; + + // read in core alignment data, make sure the right size of data was read + char x[Constants::BAM_CORE_SIZE]; + if ( m_stream.Read(x, Constants::BAM_CORE_SIZE) != Constants::BAM_CORE_SIZE ) + return false; + + // swap core endian-ness if necessary + if ( m_isBigEndian ) { + for ( int i = 0; i < Constants::BAM_CORE_SIZE; i+=sizeof(uint32_t) ) + BamTools::SwapEndian_32p(&x[i]); + } + + // set BamAlignment 'core' and 'support' data + alignment.RefID = BamTools::UnpackSignedInt(&x[0]); + alignment.Position = BamTools::UnpackSignedInt(&x[4]); + + unsigned int tempValue = BamTools::UnpackUnsignedInt(&x[8]); + alignment.Bin = tempValue >> 16; + alignment.MapQuality = tempValue >> 8 & 0xff; + alignment.SupportData.QueryNameLength = tempValue & 0xff; + + tempValue = BamTools::UnpackUnsignedInt(&x[12]); + alignment.AlignmentFlag = tempValue >> 16; + alignment.SupportData.NumCigarOperations = tempValue & 0xffff; + + alignment.SupportData.QuerySequenceLength = BamTools::UnpackUnsignedInt(&x[16]); + alignment.MateRefID = BamTools::UnpackSignedInt(&x[20]); + alignment.MatePosition = BamTools::UnpackSignedInt(&x[24]); + alignment.InsertSize = BamTools::UnpackSignedInt(&x[28]); + + // set BamAlignment length + alignment.Length = alignment.SupportData.QuerySequenceLength; + + // read in character data - make sure proper data size was read + bool readCharDataOK = false; + const unsigned int dataLength = alignment.SupportData.BlockLength - Constants::BAM_CORE_SIZE; + char* allCharData = (char*)calloc(sizeof(char), dataLength); + + if ( m_stream.Read(allCharData, dataLength) == (signed int)dataLength ) { + + // store 'allCharData' in supportData structure + alignment.SupportData.AllCharData.assign((const char*)allCharData, dataLength); + + // set success flag + readCharDataOK = true; + + // save CIGAR ops + // need to calculate this here so that BamAlignment::GetEndPosition() performs correctly, + // even when GetNextAlignmentCore() is called + const unsigned int cigarDataOffset = alignment.SupportData.QueryNameLength; + uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset); + CigarOp op; + alignment.CigarData.clear(); + alignment.CigarData.reserve(alignment.SupportData.NumCigarOperations); + for ( unsigned int i = 0; i < alignment.SupportData.NumCigarOperations; ++i ) { + + // swap endian-ness if necessary + if ( m_isBigEndian ) BamTools::SwapEndian_32(cigarData[i]); + + // build CigarOp structure + op.Length = (cigarData[i] >> Constants::BAM_CIGAR_SHIFT); + op.Type = Constants::BAM_CIGAR_LOOKUP[ (cigarData[i] & Constants::BAM_CIGAR_MASK) ]; + + // save CigarOp + alignment.CigarData.push_back(op); + } + } + + // clean up & return parsing success/failure + free(allCharData); + return readCharDataOK; +} + +// loads reference data from BAM file +bool BamReaderPrivate::LoadReferenceData(void) { + + // get number of reference sequences + char buffer[sizeof(uint32_t)]; + m_stream.Read(buffer, sizeof(uint32_t)); + uint32_t numberRefSeqs = BamTools::UnpackUnsignedInt(buffer); + if ( m_isBigEndian ) BamTools::SwapEndian_32(numberRefSeqs); + m_references.reserve((int)numberRefSeqs); + + // iterate over all references in header + for ( unsigned int i = 0; i != numberRefSeqs; ++i ) { + + // get length of reference name + m_stream.Read(buffer, sizeof(uint32_t)); + uint32_t refNameLength = BamTools::UnpackUnsignedInt(buffer); + if ( m_isBigEndian ) BamTools::SwapEndian_32(refNameLength); + char* refName = (char*)calloc(refNameLength, 1); + + // get reference name and reference sequence length + m_stream.Read(refName, refNameLength); + m_stream.Read(buffer, sizeof(int32_t)); + int32_t refLength = BamTools::UnpackSignedInt(buffer); + if ( m_isBigEndian ) BamTools::SwapEndian_32(refLength); + + // store data for reference + RefData aReference; + aReference.RefName = (string)((const char*)refName); + aReference.RefLength = refLength; + m_references.push_back(aReference); + + // clean up calloc-ed temp variable + free(refName); + } + + // return success + return true; +} + +bool BamReaderPrivate::LocateIndex(const BamIndex::IndexType& preferredType) { + return m_randomAccessController.LocateIndex(this, preferredType); +} + +// opens BAM file (and index) +bool BamReaderPrivate::Open(const string& filename) { + + // close current BAM file if open + if ( m_stream.IsOpen ) + Close(); + + // attempt to open BgzfStream for reading + if ( !m_stream.Open(filename, "rb") ) { + cerr << "BamReader ERROR: Could not open BGZF stream for " << filename << endl; + return false; + } + + // attempt to load header data + if ( !LoadHeaderData() ) { + cerr << "BamReader ERROR: Could not load header data for " << filename << endl; + Close(); + return false; + } + + // attempt to load reference data + if ( !LoadReferenceData() ) { + cerr << "BamReader ERROR: Could not load reference data for " << filename << endl; + Close(); + return false; + } + + // if all OK, store filename & offset of first alignment + m_filename = filename; + m_alignmentsBeginOffset = m_stream.Tell(); + + // return success + return true; +} + +bool BamReaderPrivate::OpenIndex(const std::string& indexFilename) { + return m_randomAccessController.OpenIndex(indexFilename, this); +} + +// returns BAM file pointer to beginning of alignment data +bool BamReaderPrivate::Rewind(void) { + + // attempt rewind to first alignment + if ( !m_stream.Seek(m_alignmentsBeginOffset) ) + return false; + + // verify that we can read first alignment + BamAlignment al; + if ( !LoadNextAlignment(al) ) + return false; + + // reset region + m_randomAccessController.ClearRegion(); + + // rewind back to beginning of first alignment + // return success/fail of seek + return m_stream.Seek(m_alignmentsBeginOffset); +} + +bool BamReaderPrivate::Seek(const int64_t& position) { + return m_stream.Seek(position); +} + +void BamReaderPrivate::SetIndex(BamIndex* index) { + m_randomAccessController.SetIndex(index); +} + +// change the index caching behavior +void BamReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) { + m_randomAccessController.SetIndexCacheMode(mode); +} + +// sets current region & attempts to jump to it +// returns success/failure +bool BamReaderPrivate::SetRegion(const BamRegion& region) { + return m_randomAccessController.SetRegion(this, region, m_references.size()); +} + +int64_t BamReaderPrivate::Tell(void) const { + return m_stream.Tell(); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamReader_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,113 @@ +// *************************************************************************** +// BamReader_p.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for reading BAM files +// *************************************************************************** + +#ifndef BAMREADER_P_H +#define BAMREADER_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <api/BamAlignment.h> +#include <api/BamIndex.h> +#include <api/BamReader.h> +#include <api/SamHeader.h> +#include <api/internal/BamHeader_p.h> +#include <api/internal/BamRandomAccessController_p.h> +#include <api/internal/BgzfStream_p.h> +#include <string> + +namespace BamTools { +namespace Internal { + +class BamReaderPrivate { + + // ctor & dtor + public: + BamReaderPrivate(BamReader* parent); + ~BamReaderPrivate(void); + + // BamReader interface + public: + + // file operations + void Close(void); + const std::string Filename(void) const; + bool IsOpen(void) const; + bool Open(const std::string& filename); + bool Rewind(void); + bool SetRegion(const BamRegion& region); + + // access alignment data + bool GetNextAlignment(BamAlignment& alignment); + bool GetNextAlignmentCore(BamAlignment& alignment); + + // access auxiliary data + std::string GetHeaderText(void) const; + SamHeader GetSamHeader(void) const; + int GetReferenceCount(void) const; + const RefVector& GetReferenceData(void) const; + int GetReferenceID(const std::string& refName) const; + + // index operations + bool CreateIndex(const BamIndex::IndexType& type); + bool HasIndex(void) const; + bool LocateIndex(const BamIndex::IndexType& preferredType); + bool OpenIndex(const std::string& indexFilename); + void SetIndex(BamIndex* index); + void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode); + + // internal methods, but available as a BamReaderPrivate 'interface' + // + // these methods should only be used by BamTools::Internal classes + // (currently only used by the BamIndex subclasses) + public: + // retrieves header text from BAM file + bool LoadHeaderData(void); + // retrieves BAM alignment under file pointer + // (does no overlap checking or character data parsing) + bool LoadNextAlignment(BamAlignment& alignment); + // builds reference data structure from BAM file + bool LoadReferenceData(void); + // seek reader to file position + bool Seek(const int64_t& position); + // return reader's file position + int64_t Tell(void) const; + + // data members + public: + + // general BAM file data + int64_t m_alignmentsBeginOffset; + std::string m_filename; + RefVector m_references; + + // system data + bool m_isBigEndian; + + // parent BamReader + BamReader* m_parent; + + // BamReaderPrivate components + BamHeader m_header; + BamRandomAccessController m_randomAccessController; + BgzfStream m_stream; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMREADER_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamStandardIndex_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,974 @@ +// *************************************************************************** +// BamStandardIndex.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 16 June 2011 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the standardized BAM index format (".bai") +// *************************************************************************** + +#include <api/BamAlignment.h> +#include <api/internal/BamReader_p.h> +#include <api/internal/BamStandardIndex_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <cstdio> +#include <cstdlib> +#include <cstring> +#include <algorithm> +#include <iostream> +using namespace std; + +// static BamStandardIndex constants +const int BamStandardIndex::MAX_BIN = 37450; // =(8^6-1)/7+1 +const int BamStandardIndex::BAM_LIDX_SHIFT = 14; +const string BamStandardIndex::BAI_EXTENSION = ".bai"; +const char* const BamStandardIndex::BAI_MAGIC = "BAI\1"; +const int BamStandardIndex::SIZEOF_ALIGNMENTCHUNK = sizeof(uint64_t)*2; +const int BamStandardIndex::SIZEOF_BINCORE = sizeof(uint32_t) + sizeof(int32_t); +const int BamStandardIndex::SIZEOF_LINEAROFFSET = sizeof(uint64_t); + +// ctor +BamStandardIndex::BamStandardIndex(Internal::BamReaderPrivate* reader) + : BamIndex(reader) + , m_indexStream(0) + , m_cacheMode(BamIndex::LimitedIndexCaching) + , m_buffer(0) + , m_bufferLength(0) +{ + m_isBigEndian = BamTools::SystemIsBigEndian(); +} + +// dtor +BamStandardIndex::~BamStandardIndex(void) { + CloseFile(); +} + +bool BamStandardIndex::AdjustRegion(const BamRegion& region, uint32_t& begin, uint32_t& end) { + + // retrieve references from reader + const RefVector& references = m_reader->GetReferenceData(); + + // make sure left-bound position is valid + if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) + return false; + + // set region 'begin' + begin = (unsigned int)region.LeftPosition; + + // if right bound specified AND left&right bounds are on same reference + // OK to use right bound position as region 'end' + if ( region.isRightBoundSpecified() && ( region.LeftRefID == region.RightRefID ) ) + end = (unsigned int)region.RightPosition; + + // otherwise, set region 'end' to last reference base + else end = (unsigned int)references.at(region.LeftRefID).RefLength - 1; + + // return success + return true; +} + +void BamStandardIndex::CalculateCandidateBins(const uint32_t& begin, + const uint32_t& end, + set<uint16_t>& candidateBins) +{ + // initialize list, bin '0' is always a valid bin + candidateBins.insert(0); + + // get rest of bins that contain this region + unsigned int k; + for (k = 1 + (begin>>26); k <= 1 + (end>>26); ++k) { candidateBins.insert(k); } + for (k = 9 + (begin>>23); k <= 9 + (end>>23); ++k) { candidateBins.insert(k); } + for (k = 73 + (begin>>20); k <= 73 + (end>>20); ++k) { candidateBins.insert(k); } + for (k = 585 + (begin>>17); k <= 585 + (end>>17); ++k) { candidateBins.insert(k); } + for (k = 4681 + (begin>>14); k <= 4681 + (end>>14); ++k) { candidateBins.insert(k); } +} + +bool BamStandardIndex::CalculateCandidateOffsets(const BaiReferenceSummary& refSummary, + const uint64_t& minOffset, + set<uint16_t>& candidateBins, + vector<int64_t>& offsets) +{ + // attempt seek to first bin + if ( !Seek(refSummary.FirstBinFilePosition, SEEK_SET) ) + return false; + + // iterate over reference bins + uint32_t binId; + int32_t numAlignmentChunks; + set<uint16_t>::iterator candidateBinIter; + for ( int i = 0; i < refSummary.NumBins; ++i ) { + + // read bin contents (if successful, alignment chunks are now in m_buffer) + if ( !ReadBinIntoBuffer(binId, numAlignmentChunks) ) + return false; + + // see if bin is a 'candidate bin' + candidateBinIter = candidateBins.find(binId); + + // if not, move on to next bin + if ( candidateBinIter == candidateBins.end() ) + continue; + + // otherwise, check bin's contents against for overlap + else { + + unsigned int offset = 0; + uint64_t chunkStart; + uint64_t chunkStop; + + // iterate over alignment chunks + for (int j = 0; j < numAlignmentChunks; ++j ) { + + // read chunk start & stop from buffer + memcpy((char*)&chunkStart, m_buffer+offset, sizeof(uint64_t)); + offset += sizeof(uint64_t); + memcpy((char*)&chunkStop, m_buffer, sizeof(uint64_t)); + offset += sizeof(uint64_t); + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_64(chunkStart); + SwapEndian_64(chunkStop); + } + + // store alignment chunk's start offset + // if its stop offset is larger than our 'minOffset' + if ( chunkStop >= minOffset ) + offsets.push_back(chunkStart); + } + + // 'pop' bin ID from candidate bins set + candidateBins.erase(candidateBinIter); + + // quit if no more candidates + if ( candidateBins.empty() ) + break; + } + } + + // return success + return true; +} + +uint64_t BamStandardIndex::CalculateMinOffset(const BaiReferenceSummary& refSummary, + const uint32_t& begin) +{ + // if no linear offsets exist, return 0 + if ( refSummary.NumLinearOffsets == 0 ) + return 0; + + // if 'begin' starts beyond last linear offset, use the last linear offset as minimum + // else use the offset corresponding to the requested start position + const int shiftedBegin = begin>>BamStandardIndex::BAM_LIDX_SHIFT; + if ( shiftedBegin >= refSummary.NumLinearOffsets ) + return LookupLinearOffset( refSummary, refSummary.NumLinearOffsets-1 ); + else + return LookupLinearOffset( refSummary, shiftedBegin ); +} + +void BamStandardIndex::CheckBufferSize(char*& buffer, + unsigned int& bufferLength, + const unsigned int& requestedBytes) +{ + try { + if ( requestedBytes > bufferLength ) { + bufferLength = requestedBytes + 10; + delete[] buffer; + buffer = new char[bufferLength]; + } + } catch ( std::bad_alloc ) { + cerr << "BamStandardIndex ERROR: out of memory when allocating " + << requestedBytes << " byes" << endl; + exit(1); + } +} + +void BamStandardIndex::CheckBufferSize(unsigned char*& buffer, + unsigned int& bufferLength, + const unsigned int& requestedBytes) +{ + try { + if ( requestedBytes > bufferLength ) { + bufferLength = requestedBytes + 10; + delete[] buffer; + buffer = new unsigned char[bufferLength]; + } + } catch ( std::bad_alloc ) { + cerr << "BamStandardIndex ERROR: out of memory when allocating " + << requestedBytes << " byes" << endl; + exit(1); + } +} + +bool BamStandardIndex::CheckMagicNumber(void) { + + // check 'magic number' to see if file is BAI index + char magic[4]; + size_t elementsRead = fread(magic, sizeof(char), 4, m_indexStream); + if ( elementsRead != 4 ) { + cerr << "BamStandardIndex ERROR: could not read format 'magic number'" << endl; + return false; + } + + // compare to expected value + if ( strncmp(magic, BamStandardIndex::BAI_MAGIC, 4) != 0 ) { + cerr << "BamStandardIndex ERROR: invalid format" << endl; + return false; + } + + // otherwise OK + return true; +} + +void BamStandardIndex::ClearReferenceEntry(BaiReferenceEntry& refEntry) { + refEntry.ID = -1; + refEntry.Bins.clear(); + refEntry.LinearOffsets.clear(); +} + +void BamStandardIndex::CloseFile(void) { + + // close file stream + if ( IsFileOpen() ) + fclose(m_indexStream); + + // clear index file summary data + m_indexFileSummary.clear(); + + // clean up I/O buffer + delete[] m_buffer; + m_buffer = 0; + m_bufferLength = 0; +} + +// builds index from associated BAM file & writes out to index file +bool BamStandardIndex::Create(void) { + + // return false if BamReader is invalid or not open + if ( m_reader == 0 || !m_reader->IsOpen() ) { + cerr << "BamStandardIndex ERROR: BamReader is not open" + << ", aborting index creation" << endl; + return false; + } + + // rewind BamReader + if ( !m_reader->Rewind() ) { + cerr << "BamStandardIndex ERROR: could not rewind BamReader to create index" + << ", aborting index creation" << endl; + return false; + } + + // open new index file (read & write) + string indexFilename = m_reader->Filename() + Extension(); + if ( !OpenFile(indexFilename, "w+b") ) { + cerr << "BamStandardIndex ERROR: could not open ouput index file: " << indexFilename + << ", aborting index creation" << endl; + return false; + } + + // initialize BaiFileSummary with number of references + const int& numReferences = m_reader->GetReferenceCount(); + ReserveForSummary(numReferences); + + // initialize output file + bool createdOk = true; + createdOk &= WriteHeader(); + + // set up bin, ID, offset, & coordinate markers + const uint32_t defaultValue = 0xffffffffu; + uint32_t currentBin = defaultValue; + uint32_t lastBin = defaultValue; + int32_t currentRefID = defaultValue; + int32_t lastRefID = defaultValue; + uint64_t currentOffset = (uint64_t)m_reader->Tell(); + uint64_t lastOffset = currentOffset; + int32_t lastPosition = defaultValue; + + // iterate through alignments in BAM file + BamAlignment al; + BaiReferenceEntry refEntry; + while ( m_reader->LoadNextAlignment(al) ) { + + // changed to new reference + if ( lastRefID != al.RefID ) { + + // if not first reference, save previous reference data + if ( lastRefID != (int32_t)defaultValue ) { + + SaveAlignmentChunkToBin(refEntry.Bins, currentBin, currentOffset, lastOffset); + createdOk &= WriteReferenceEntry(refEntry); + ClearReferenceEntry(refEntry); + + // write any empty references between (but *NOT* including) lastRefID & al.RefID + for ( int i = lastRefID+1; i < al.RefID; ++i ) { + BaiReferenceEntry emptyEntry(i); + createdOk &= WriteReferenceEntry(emptyEntry); + } + + // update bin markers + currentOffset = lastOffset; + currentBin = al.Bin; + lastBin = al.Bin; + currentRefID = al.RefID; + } + + // first pass + // write any empty references up to (but *NOT* including) al.RefID + else { + for ( int i = 0; i < al.RefID; ++i ) { + BaiReferenceEntry emptyEntry(i); + createdOk &= WriteReferenceEntry(emptyEntry); + } + } + + // update reference markers + refEntry.ID = al.RefID; + lastRefID = al.RefID; + lastBin = defaultValue; + } + + // if lastPosition greater than current alignment position - file not sorted properly + else if ( lastPosition > al.Position ) { + cerr << "BamStandardIndex ERROR: BAM file is not properly sorted by coordinate" + << ", aborting index creation" + << endl + << "At alignment: " << al.Name + << " : previous position " << lastPosition + << " > this alignment position " << al.Position + << " on reference id: " << al.RefID << endl; + return false; + } + + // if alignment's ref ID is valid & its bin is not a 'leaf' + if ( (al.RefID >= 0) && (al.Bin < 4681) ) + SaveLinearOffsetEntry(refEntry.LinearOffsets, al.Position, al.GetEndPosition(), lastOffset); + + // changed to new BAI bin + if ( al.Bin != lastBin ) { + + // if not first bin on reference, save previous bin data + if ( currentBin != defaultValue ) + SaveAlignmentChunkToBin(refEntry.Bins, currentBin, currentOffset, lastOffset); + + // update markers + currentOffset = lastOffset; + currentBin = al.Bin; + lastBin = al.Bin; + currentRefID = al.RefID; + + // if invalid RefID, break out + if ( currentRefID < 0 ) + break; + } + + // make sure that current file pointer is beyond lastOffset + if ( m_reader->Tell() <= (int64_t)lastOffset ) { + cerr << "BamStandardIndex ERROR: calculating offsets failed" + << ", aborting index creation" << endl; + return false; + } + + // update lastOffset & lastPosition + lastOffset = m_reader->Tell(); + lastPosition = al.Position; + } + + // after finishing alignments, if any data was read, check: + if ( currentRefID >= 0 ) { + + // store last alignment chunk to its bin, then write last reference entry with data + SaveAlignmentChunkToBin(refEntry.Bins, currentBin, currentOffset, lastOffset); + createdOk &= WriteReferenceEntry(refEntry); + + // then write any empty references remaining at end of file + for ( int i = currentRefID+1; i < numReferences; ++i ) { + BaiReferenceEntry emptyEntry(i); + createdOk &= WriteReferenceEntry(emptyEntry); + } + } + + // rewind reader now that we're done building + createdOk &= m_reader->Rewind(); + + // return result + return createdOk; +} + +// returns format's file extension +const string BamStandardIndex::Extension(void) { + return BamStandardIndex::BAI_EXTENSION; +} + +bool BamStandardIndex::GetOffsets(const BamRegion& region, vector<int64_t>& offsets) { + + // cannot calculate offsets if unknown/invalid reference ID requested + if ( region.LeftRefID < 0 || region.LeftRefID >= (int)m_indexFileSummary.size() ) + return false; + + // retrieve index summary for left bound reference + const BaiReferenceSummary& refSummary = m_indexFileSummary.at(region.LeftRefID); + + // set up region boundaries based on actual BamReader data + uint32_t begin; + uint32_t end; + if ( !AdjustRegion(region, begin, end) ) { + cerr << "BamStandardIndex ERROR: cannot calculate offsets on invalid region" << endl; + return false; + } + + // retrieve all candidate bin IDs for region + set<uint16_t> candidateBins; + CalculateCandidateBins(begin, end, candidateBins); + + // use reference's linear offsets to calculate the minimum offset + // that must be considered to find overlap + const uint64_t& minOffset = CalculateMinOffset(refSummary, begin); + + // attempt to use reference summary, minOffset, & candidateBins to calculate offsets + // no data should not be error + if ( !CalculateCandidateOffsets(refSummary, minOffset, candidateBins, offsets) ) { + cerr << "BamStandardIndex ERROR: could not calculate candidate offsets for requested region" << endl; + return false; + } + + // ensure that offsets are sorted before returning + sort( offsets.begin(), offsets.end() ); + + // return succes + return true; +} + +// returns whether reference has alignments or no +bool BamStandardIndex::HasAlignments(const int& referenceID) const { + if ( referenceID < 0 || referenceID >= (int)m_indexFileSummary.size() ) + return false; + const BaiReferenceSummary& refSummary = m_indexFileSummary.at(referenceID); + return ( refSummary.NumBins > 0 ); +} + +bool BamStandardIndex::IsFileOpen(void) const { + return ( m_indexStream != 0 ); +} + +// attempts to use index data to jump to @region, returns success/fail +// a "successful" jump indicates no error, but not whether this region has data +// * thus, the method sets a flag to indicate whether there are alignments +// available after the jump position +bool BamStandardIndex::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) { + + // clear out flag + *hasAlignmentsInRegion = false; + + // skip if reader is not valid or is not open + if ( m_reader == 0 || !m_reader->IsOpen() ) + return false; + + // calculate offsets for this region + vector<int64_t> offsets; + if ( !GetOffsets(region, offsets) ) { + cerr << "BamStandardIndex ERROR: could not jump" + << ", unable to retrieve offsets for region" << endl; + return false; + } + + // iterate through candidate offsets + BamAlignment al; + vector<int64_t>::const_iterator offsetIter = offsets.begin(); + vector<int64_t>::const_iterator offsetEnd = offsets.end(); + for ( ; offsetIter != offsetEnd; ++offsetIter) { + + // attempt seek + if ( !m_reader->Seek(*offsetIter) ) { + cerr << "BamStandardIndex ERROR: could not jump" + << ", there was a problem seeking in BAM file" << endl; + return false; + } + + // load first available alignment, setting flag to true if data exists + *hasAlignmentsInRegion = m_reader->LoadNextAlignment(al); + + // if this alignment corresponds to desired position + // return success of seeking back to the offset before the 'current offset' (to cover overlaps) + if ( ((al.RefID == region.LeftRefID) && + ((al.Position + al.Length) > region.LeftPosition)) || + (al.RefID > region.LeftRefID) ) + { + if ( offsetIter != offsets.begin() ) + --offsetIter; + return m_reader->Seek(*offsetIter); + } + } + + // return success (no offset data is not an error, + // but hasAlignments flag will be marked accordingly) + return true; +} + +// loads existing data from file into memory +bool BamStandardIndex::Load(const std::string& filename) { + + // attempt open index file (read-only) + if ( !OpenFile(filename, "rb") ) { + cerr << "BamStandardIndex ERROR: could not open input index file: " << filename + << ", aborting index load" << endl; + return false; + } + + // if invalid format 'magic number', close & return failure + if ( !CheckMagicNumber() ) { + cerr << "BamStandardIndex ERROR: unexpected format for index file: " << filename + << ", aborting index load" << endl; + CloseFile(); + return false; + } + + // attempt to load index file summary, return success/failure + if ( !SummarizeIndexFile() ) { + cerr << "BamStandardIndex ERROR: could not generate a summary of index file " << filename + << ", aborting index load" << endl; + CloseFile(); + return false; + } + + // if we get here, index summary is loaded OK + return true; +} + +uint64_t BamStandardIndex::LookupLinearOffset(const BaiReferenceSummary& refSummary, const int& index) { + + // attempt seek to proper index file position + const int64_t linearOffsetFilePosition = (int64_t)refSummary.FirstLinearOffsetFilePosition + + index*BamStandardIndex::SIZEOF_LINEAROFFSET; + if ( !Seek(linearOffsetFilePosition, SEEK_SET) ) + return 0; + + // read linear offset from BAI file + uint64_t linearOffset(0); + if ( !ReadLinearOffset(linearOffset) ) + return 0; + return linearOffset; +} + +void BamStandardIndex::MergeAlignmentChunks(BaiAlignmentChunkVector& chunks) { + + // skip if chunks are empty, nothing to merge + if ( chunks.empty() ) + return; + + // set up merged alignment chunk container + BaiAlignmentChunkVector mergedChunks; + mergedChunks.push_back( chunks[0] ); + + // iterate over chunks + int i = 0; + BaiAlignmentChunkVector::iterator chunkIter = chunks.begin(); + BaiAlignmentChunkVector::iterator chunkEnd = chunks.end(); + for ( ++chunkIter; chunkIter != chunkEnd; ++chunkIter) { + + // get 'currentMergeChunk' based on numeric index + BaiAlignmentChunk& currentMergeChunk = mergedChunks[i]; + + // get sourceChunk based on source vector iterator + BaiAlignmentChunk& sourceChunk = (*chunkIter); + + // if currentMergeChunk ends where sourceChunk starts, then merge the two + if ( currentMergeChunk.Stop>>16 == sourceChunk.Start>>16 ) + currentMergeChunk.Stop = sourceChunk.Stop; + + // otherwise + else { + // append sourceChunk after currentMergeChunk + mergedChunks.push_back(sourceChunk); + + // update i, so the next iteration will consider the + // recently-appended sourceChunk as new mergeChunk candidate + ++i; + } + } + + // saved newly-merged chunks into (parameter) chunks + chunks = mergedChunks; +} + +bool BamStandardIndex::OpenFile(const std::string& filename, const char* mode) { + + // make sure any previous index file is closed + CloseFile(); + + // attempt to open file + m_indexStream = fopen(filename.c_str(), mode); + return IsFileOpen(); +} + +bool BamStandardIndex::ReadBinID(uint32_t& binId) { + size_t elementsRead = 0; + elementsRead += fread(&binId, sizeof(binId), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(binId); + return ( elementsRead == 1 ); +} + +bool BamStandardIndex::ReadBinIntoBuffer(uint32_t& binId, int32_t& numAlignmentChunks) { + + bool readOk = true; + + // read bin header + readOk &= ReadBinID(binId); + readOk &= ReadNumAlignmentChunks(numAlignmentChunks); + + // read bin contents + const unsigned int bytesRequested = numAlignmentChunks*BamStandardIndex::SIZEOF_ALIGNMENTCHUNK; + readOk &= ReadIntoBuffer(bytesRequested); + + // return success/failure + return readOk; +} + +bool BamStandardIndex::ReadIntoBuffer(const unsigned int& bytesRequested) { + + // ensure that our buffer is big enough for request + BamStandardIndex::CheckBufferSize(m_buffer, m_bufferLength, bytesRequested); + + // read from BAI file stream + size_t bytesRead = fread( m_buffer, sizeof(char), bytesRequested, m_indexStream ); + return ( bytesRead == (size_t)bytesRequested ); +} + +bool BamStandardIndex::ReadLinearOffset(uint64_t& linearOffset) { + size_t elementsRead = 0; + elementsRead += fread(&linearOffset, sizeof(linearOffset), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_64(linearOffset); + return ( elementsRead == 1 ); +} + +bool BamStandardIndex::ReadNumAlignmentChunks(int& numAlignmentChunks) { + size_t elementsRead = 0; + elementsRead += fread(&numAlignmentChunks, sizeof(numAlignmentChunks), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numAlignmentChunks); + return ( elementsRead == 1 ); +} + +bool BamStandardIndex::ReadNumBins(int& numBins) { + size_t elementsRead = 0; + elementsRead += fread(&numBins, sizeof(numBins), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numBins); + return ( elementsRead == 1 ); +} + +bool BamStandardIndex::ReadNumLinearOffsets(int& numLinearOffsets) { + size_t elementsRead = 0; + elementsRead += fread(&numLinearOffsets, sizeof(numLinearOffsets), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numLinearOffsets); + return ( elementsRead == 1 ); +} + +bool BamStandardIndex::ReadNumReferences(int& numReferences) { + size_t elementsRead = 0; + elementsRead += fread(&numReferences, sizeof(numReferences), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numReferences); + return ( elementsRead == 1 ); +} + +void BamStandardIndex::ReserveForSummary(const int& numReferences) { + m_indexFileSummary.clear(); + m_indexFileSummary.assign( numReferences, BaiReferenceSummary() ); +} + +void BamStandardIndex::SaveAlignmentChunkToBin(BaiBinMap& binMap, + const uint32_t& currentBin, + const uint64_t& currentOffset, + const uint64_t& lastOffset) +{ + // create new alignment chunk + BaiAlignmentChunk newChunk(currentOffset, lastOffset); + + + + // if no entry exists yet for this bin, create one and store alignment chunk + BaiBinMap::iterator binIter = binMap.find(currentBin); + if ( binIter == binMap.end() ) { + BaiAlignmentChunkVector newChunks; + newChunks.push_back(newChunk); + binMap.insert( pair<uint32_t, BaiAlignmentChunkVector>(currentBin, newChunks)); + } + + // otherwise, just append alignment chunk + else { + BaiAlignmentChunkVector& binChunks = (*binIter).second; + binChunks.push_back( newChunk ); + } +} + +void BamStandardIndex::SaveBinsSummary(const int& refId, const int& numBins) { + BaiReferenceSummary& refSummary = m_indexFileSummary.at(refId); + refSummary.NumBins = numBins; + refSummary.FirstBinFilePosition = Tell(); +} + +void BamStandardIndex::SaveLinearOffsetEntry(BaiLinearOffsetVector& offsets, + const int& alignmentStartPosition, + const int& alignmentStopPosition, + const uint64_t& lastOffset) +{ + // get converted offsets + const int beginOffset = alignmentStartPosition >> BamStandardIndex::BAM_LIDX_SHIFT; + const int endOffset = (alignmentStopPosition - 1) >> BamStandardIndex::BAM_LIDX_SHIFT; + + // resize vector if necessary + int oldSize = offsets.size(); + int newSize = endOffset + 1; + if ( oldSize < newSize ) + offsets.resize(newSize, 0); + + // store offset + for( int i = beginOffset + 1; i <= endOffset; ++i ) { + if ( offsets[i] == 0 ) + offsets[i] = lastOffset; + } +} + +void BamStandardIndex::SaveLinearOffsetsSummary(const int& refId, const int& numLinearOffsets) { + BaiReferenceSummary& refSummary = m_indexFileSummary.at(refId); + refSummary.NumLinearOffsets = numLinearOffsets; + refSummary.FirstLinearOffsetFilePosition = Tell(); +} + +// seek to position in index file stream +bool BamStandardIndex::Seek(const int64_t& position, const int& origin) { + return ( fseek64(m_indexStream, position, origin) == 0 ); +} + +// change the index caching behavior +void BamStandardIndex::SetCacheMode(const BamIndex::IndexCacheMode& mode) { + m_cacheMode = mode; + // do nothing else here ? cache mode will be ignored from now on, most likely +} + +bool BamStandardIndex::SkipBins(const int& numBins) { + uint32_t binId; + int32_t numAlignmentChunks; + bool skippedOk = true; + for (int i = 0; i < numBins; ++i) + skippedOk &= ReadBinIntoBuffer(binId, numAlignmentChunks); // results & buffer ignored + return skippedOk; +} + +bool BamStandardIndex::SkipLinearOffsets(const int& numLinearOffsets) { + const unsigned int bytesRequested = numLinearOffsets*BamStandardIndex::SIZEOF_LINEAROFFSET; + return ReadIntoBuffer(bytesRequested); +} + +void BamStandardIndex::SortLinearOffsets(BaiLinearOffsetVector& linearOffsets) { + sort( linearOffsets.begin(), linearOffsets.end() ); +} + +bool BamStandardIndex::SummarizeBins(BaiReferenceSummary& refSummary) { + + // load number of bins + int numBins; + if ( !ReadNumBins(numBins) ) + return false; + + // store bins summary for this reference + refSummary.NumBins = numBins; + refSummary.FirstBinFilePosition = Tell(); + + // attempt skip reference bins, return success/failure + if ( !SkipBins(numBins) ) + return false; + + // if we get here, bin summarized OK + return true; +} + +bool BamStandardIndex::SummarizeIndexFile(void) { + + // load number of reference sequences + int numReferences; + if ( !ReadNumReferences(numReferences) ) + return false; + + // initialize file summary data + ReserveForSummary(numReferences); + + // iterate over reference entries + bool loadedOk = true; + BaiFileSummary::iterator summaryIter = m_indexFileSummary.begin(); + BaiFileSummary::iterator summaryEnd = m_indexFileSummary.end(); + for ( int i = 0; summaryIter != summaryEnd; ++summaryIter, ++i ) + loadedOk &= SummarizeReference(*summaryIter); + + // return result + return loadedOk; +} + +bool BamStandardIndex::SummarizeLinearOffsets(BaiReferenceSummary& refSummary) { + + // load number of linear offsets + int numLinearOffsets; + if ( !ReadNumLinearOffsets(numLinearOffsets) ) + return false; + + // store bin summary data for this reference + refSummary.NumLinearOffsets = numLinearOffsets; + refSummary.FirstLinearOffsetFilePosition = Tell(); + + // skip linear offsets in index file + if ( !SkipLinearOffsets(numLinearOffsets) ) + return false; + + // if get here, linear offsets summarized OK + return true; +} + +bool BamStandardIndex::SummarizeReference(BaiReferenceSummary& refSummary) { + + bool loadedOk = true; + loadedOk &= SummarizeBins(refSummary); + loadedOk &= SummarizeLinearOffsets(refSummary); + return loadedOk; +} + +// return position of file pointer in index file stream +int64_t BamStandardIndex::Tell(void) const { + return ftell64(m_indexStream); +} + +bool BamStandardIndex::WriteAlignmentChunk(const BaiAlignmentChunk& chunk) { + + size_t elementsWritten = 0; + + // localize alignment chunk offsets + uint64_t start = chunk.Start; + uint64_t stop = chunk.Stop; + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_64(start); + SwapEndian_64(stop); + } + + // write to index file + elementsWritten += fwrite(&start, sizeof(start), 1, m_indexStream); + elementsWritten += fwrite(&stop, sizeof(stop), 1, m_indexStream); + + // return success/failure of write + return ( elementsWritten == 2 ); +} + +bool BamStandardIndex::WriteAlignmentChunks(BaiAlignmentChunkVector& chunks) { + + // make sure chunks are merged (simplified) before writing & saving summary + MergeAlignmentChunks(chunks); + + size_t elementsWritten = 0; + + // write chunks + int32_t chunkCount = chunks.size(); + if ( m_isBigEndian ) SwapEndian_32(chunkCount); + elementsWritten += fwrite(&chunkCount, sizeof(chunkCount), 1, m_indexStream); + + // iterate over chunks + bool chunksOk = true; + BaiAlignmentChunkVector::const_iterator chunkIter = chunks.begin(); + BaiAlignmentChunkVector::const_iterator chunkEnd = chunks.end(); + for ( ; chunkIter != chunkEnd; ++chunkIter ) + chunksOk &= WriteAlignmentChunk( (*chunkIter) ); + + // return success/failure of write + return ( (elementsWritten == 1) && chunksOk ); +} + +bool BamStandardIndex::WriteBin(const uint32_t& binId, BaiAlignmentChunkVector& chunks) { + + size_t elementsWritten = 0; + + // write BAM bin ID + uint32_t binKey = binId; + if ( m_isBigEndian ) SwapEndian_32(binKey); + elementsWritten += fwrite(&binKey, sizeof(binKey), 1, m_indexStream); + + // write bin's alignment chunks + bool chunksOk = WriteAlignmentChunks(chunks); + + // return success/failure of write + return ( (elementsWritten == 1) && chunksOk ); +} + +bool BamStandardIndex::WriteBins(const int& refId, BaiBinMap& bins) { + + size_t elementsWritten = 0; + + // write number of bins + int32_t binCount = bins.size(); + if ( m_isBigEndian ) SwapEndian_32(binCount); + elementsWritten += fwrite(&binCount, sizeof(binCount), 1, m_indexStream); + + // save summary for reference's bins + SaveBinsSummary(refId, bins.size()); + + // iterate over bins + bool binsOk = true; + BaiBinMap::iterator binIter = bins.begin(); + BaiBinMap::iterator binEnd = bins.end(); + for ( ; binIter != binEnd; ++binIter ) + binsOk &= WriteBin( (*binIter).first, (*binIter).second ); + + // return success/failure of write + return ( (elementsWritten == 1) && binsOk ); +} + +bool BamStandardIndex::WriteHeader(void) { + + size_t elementsWritten = 0; + + // write magic number + elementsWritten += fwrite(BamStandardIndex::BAI_MAGIC, sizeof(char), 4, m_indexStream); + + // write number of reference sequences + int32_t numReferences = m_indexFileSummary.size(); + if ( m_isBigEndian ) SwapEndian_32(numReferences); + elementsWritten += fwrite(&numReferences, sizeof(numReferences), 1, m_indexStream); + + // return success/failure of write + return (elementsWritten == 5); +} + +bool BamStandardIndex::WriteLinearOffsets(const int& refId, BaiLinearOffsetVector& linearOffsets) { + + // make sure linear offsets are sorted before writing & saving summary + SortLinearOffsets(linearOffsets); + + size_t elementsWritten = 0; + + // write number of linear offsets + int32_t offsetCount = linearOffsets.size(); + if ( m_isBigEndian ) SwapEndian_32(offsetCount); + elementsWritten += fwrite(&offsetCount, sizeof(offsetCount), 1, m_indexStream); + + // save summary for reference's linear offsets + SaveLinearOffsetsSummary(refId, linearOffsets.size()); + + // iterate over linear offsets + BaiLinearOffsetVector::const_iterator offsetIter = linearOffsets.begin(); + BaiLinearOffsetVector::const_iterator offsetEnd = linearOffsets.end(); + for ( ; offsetIter != offsetEnd; ++offsetIter ) { + + // write linear offset + uint64_t linearOffset = (*offsetIter); + if ( m_isBigEndian ) SwapEndian_64(linearOffset); + elementsWritten += fwrite(&linearOffset, sizeof(linearOffset), 1, m_indexStream); + } + + // return success/failure of write + return ( elementsWritten == (size_t)(linearOffsets.size() + 1) ); +} + +bool BamStandardIndex::WriteReferenceEntry(BaiReferenceEntry& refEntry) { + bool refOk = true; + refOk &= WriteBins(refEntry.ID, refEntry.Bins); + refOk &= WriteLinearOffsets(refEntry.ID, refEntry.LinearOffsets); + return refOk; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamStandardIndex_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,237 @@ +// *************************************************************************** +// BamStandardIndex.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the standardized BAM index format (".bai") +// *************************************************************************** + +#ifndef BAM_STANDARD_INDEX_FORMAT_H +#define BAM_STANDARD_INDEX_FORMAT_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to +// version without notice, or even be removed. +// +// We mean it. + +#include <api/BamAux.h> +#include <api/BamIndex.h> +#include <map> +#include <set> +#include <string> +#include <vector> + +namespace BamTools { +namespace Internal { + +// ----------------------------------------------------------------------------- +// BamStandardIndex data structures + +// defines start and end of a contiguous run of alignments +struct BaiAlignmentChunk { + + // data members + uint64_t Start; + uint64_t Stop; + + // constructor + BaiAlignmentChunk(const uint64_t& start = 0, + const uint64_t& stop = 0) + : Start(start) + , Stop(stop) + { } +}; + +// comparison operator (for sorting) +inline +bool operator<(const BaiAlignmentChunk& lhs, const BaiAlignmentChunk& rhs) { + return lhs.Start < rhs.Start; +} + +// convenience typedef for a list of all alignment 'chunks' in a BAI bin +typedef std::vector<BaiAlignmentChunk> BaiAlignmentChunkVector; + +// convenience typedef for a map of all BAI bins in a reference (ID => chunks) +typedef std::map<uint32_t, BaiAlignmentChunkVector> BaiBinMap; + +// convenience typedef for a list of all 'linear offsets' in a reference +typedef std::vector<uint64_t> BaiLinearOffsetVector; + +// contains all fields necessary for building, loading, & writing +// full BAI index data for a single reference +struct BaiReferenceEntry { + + // data members + int32_t ID; + BaiBinMap Bins; + BaiLinearOffsetVector LinearOffsets; + + // ctor + BaiReferenceEntry(const int32_t& id = -1) + : ID(id) + { } +}; + +// provides (persistent) summary of BaiReferenceEntry's index data +struct BaiReferenceSummary { + + // data members + int NumBins; + int NumLinearOffsets; + uint64_t FirstBinFilePosition; + uint64_t FirstLinearOffsetFilePosition; + + // ctor + BaiReferenceSummary(void) + : NumBins(0) + , NumLinearOffsets(0) + , FirstBinFilePosition(0) + , FirstLinearOffsetFilePosition(0) + { } +}; + +// convenience typedef for describing a full BAI index file summary +typedef std::vector<BaiReferenceSummary> BaiFileSummary; + +// end BamStandardIndex data structures +// ----------------------------------------------------------------------------- + +class BamStandardIndex : public BamIndex { + + // ctor & dtor + public: + BamStandardIndex(Internal::BamReaderPrivate* reader); + ~BamStandardIndex(void); + + // BamIndex implementation + public: + // builds index from associated BAM file & writes out to index file + bool Create(void); + // returns whether reference has alignments or no + bool HasAlignments(const int& referenceID) const; + // attempts to use index data to jump to @region, returns success/fail + // a "successful" jump indicates no error, but not whether this region has data + // * thus, the method sets a flag to indicate whether there are alignments + // available after the jump position + bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); + // loads existing data from file into memory + bool Load(const std::string& filename); + // change the index caching behavior + void SetCacheMode(const BamIndex::IndexCacheMode& mode); + public: + // returns format's file extension + static const std::string Extension(void); + + // internal file ops + private: + bool CheckMagicNumber(void); + void CloseFile(void); + bool IsFileOpen(void) const; + bool OpenFile(const std::string& filename, const char* mode); + bool Seek(const int64_t& position, const int& origin); + int64_t Tell(void) const; + + // internal BAI index building methods + private: + void ClearReferenceEntry(BaiReferenceEntry& refEntry); + void SaveAlignmentChunkToBin(BaiBinMap& binMap, + const uint32_t& currentBin, + const uint64_t& currentOffset, + const uint64_t& lastOffset); + void SaveLinearOffsetEntry(BaiLinearOffsetVector& offsets, + const int& alignmentStartPosition, + const int& alignmentStopPosition, + const uint64_t& lastOffset); + + // internal random-access methods + private: + bool AdjustRegion(const BamRegion& region, uint32_t& begin, uint32_t& end); + void CalculateCandidateBins(const uint32_t& begin, + const uint32_t& end, + std::set<uint16_t>& candidateBins); + bool CalculateCandidateOffsets(const BaiReferenceSummary& refSummary, + const uint64_t& minOffset, + std::set<uint16_t>& candidateBins, + std::vector<int64_t>& offsets); + uint64_t CalculateMinOffset(const BaiReferenceSummary& refSummary, const uint32_t& begin); + bool GetOffsets(const BamRegion& region, std::vector<int64_t>& offsets); + uint64_t LookupLinearOffset(const BaiReferenceSummary& refSummary, const int& index); + + // internal BAI summary (create/load) methods + private: + void ReserveForSummary(const int& numReferences); + void SaveBinsSummary(const int& refId, const int& numBins); + void SaveLinearOffsetsSummary(const int& refId, const int& numLinearOffsets); + bool SkipBins(const int& numBins); + bool SkipLinearOffsets(const int& numLinearOffsets); + bool SummarizeBins(BaiReferenceSummary& refSummary); + bool SummarizeIndexFile(void); + bool SummarizeLinearOffsets(BaiReferenceSummary& refSummary); + bool SummarizeReference(BaiReferenceSummary& refSummary); + + // internal BAI full index input methods + private: + bool ReadBinID(uint32_t& binId); + bool ReadBinIntoBuffer(uint32_t& binId, int32_t& numAlignmentChunks); + bool ReadIntoBuffer(const unsigned int& bytesRequested); + bool ReadLinearOffset(uint64_t& linearOffset); + bool ReadNumAlignmentChunks(int& numAlignmentChunks); + bool ReadNumBins(int& numBins); + bool ReadNumLinearOffsets(int& numLinearOffsets); + bool ReadNumReferences(int& numReferences); + + // internal BAI full index output methods + private: + void MergeAlignmentChunks(BaiAlignmentChunkVector& chunks); + void SortLinearOffsets(BaiLinearOffsetVector& linearOffsets); + bool WriteAlignmentChunk(const BaiAlignmentChunk& chunk); + bool WriteAlignmentChunks(BaiAlignmentChunkVector& chunks); + bool WriteBin(const uint32_t& binId, BaiAlignmentChunkVector& chunks); + bool WriteBins(const int& refId, BaiBinMap& bins); + bool WriteHeader(void); + bool WriteLinearOffsets(const int& refId, BaiLinearOffsetVector& linearOffsets); + bool WriteReferenceEntry(BaiReferenceEntry& refEntry); + + // data members + private: + FILE* m_indexStream; + bool m_isBigEndian; + BamIndex::IndexCacheMode m_cacheMode; + BaiFileSummary m_indexFileSummary; + + // our input buffer + char* m_buffer; + unsigned int m_bufferLength; + + // static methods + private: + // checks if the buffer is large enough to accomodate the requested size + static void CheckBufferSize(char*& buffer, + unsigned int& bufferLength, + const unsigned int& requestedBytes); + // checks if the buffer is large enough to accomodate the requested size + static void CheckBufferSize(unsigned char*& buffer, + unsigned int& bufferLength, + const unsigned int& requestedBytes); + // static constants + private: + static const int MAX_BIN; + static const int BAM_LIDX_SHIFT; + static const std::string BAI_EXTENSION; + static const char* const BAI_MAGIC; + static const int SIZEOF_ALIGNMENTCHUNK; + static const int SIZEOF_BINCORE; + static const int SIZEOF_LINEAROFFSET; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAM_STANDARD_INDEX_FORMAT_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamToolsIndex_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,642 @@ +// *************************************************************************** +// BamToolsIndex.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 27 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the BamTools index format (".bti") +// *************************************************************************** + +#include <api/BamAlignment.h> +#include <api/internal/BamReader_p.h> +#include <api/internal/BamToolsIndex_p.h> +#include <api/internal/BgzfStream_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <cstdio> +#include <cstdlib> +#include <cstring> +#include <algorithm> +#include <iostream> +#include <iterator> +#include <map> +using namespace std; + +// static BamToolsIndex constants +const int BamToolsIndex::DEFAULT_BLOCK_LENGTH = 1000; +const string BamToolsIndex::BTI_EXTENSION = ".bti"; +const char* const BamToolsIndex::BTI_MAGIC = "BTI\1"; +const int BamToolsIndex::SIZEOF_BLOCK = sizeof(int32_t)*2 + sizeof(int64_t); + +// ctor +BamToolsIndex::BamToolsIndex(Internal::BamReaderPrivate* reader) + : BamIndex(reader) + , m_indexStream(0) + , m_cacheMode(BamIndex::LimitedIndexCaching) + , m_blockSize(BamToolsIndex::DEFAULT_BLOCK_LENGTH) + , m_inputVersion(0) + , m_outputVersion(BTI_1_2) // latest version - used for writing new index files +{ + m_isBigEndian = BamTools::SystemIsBigEndian(); +} + +// dtor +BamToolsIndex::~BamToolsIndex(void) { + CloseFile(); +} + +bool BamToolsIndex::CheckMagicNumber(void) { + + // check 'magic number' to see if file is BTI index + char magic[4]; + size_t elementsRead = fread(magic, sizeof(char), 4, m_indexStream); + if ( elementsRead != 4 ) { + cerr << "BamToolsIndex ERROR: could not read format 'magic' number" << endl; + return false; + } + + if ( strncmp(magic, BamToolsIndex::BTI_MAGIC, 4) != 0 ) { + cerr << "BamToolsIndex ERROR: invalid format" << endl; + return false; + } + + // otherwise ok + return true; +} + +// check index file version, return true if OK +bool BamToolsIndex::CheckVersion(void) { + + // read version from file + size_t elementsRead = fread(&m_inputVersion, sizeof(m_inputVersion), 1, m_indexStream); + if ( elementsRead != 1 ) return false; + if ( m_isBigEndian ) SwapEndian_32(m_inputVersion); + + // if version is negative, or zero + if ( m_inputVersion <= 0 ) { + cerr << "BamToolsIndex ERROR: could not load index file: invalid version." + << endl; + return false; + } + + // if version is newer than can be supported by this version of bamtools + else if ( m_inputVersion > m_outputVersion ) { + cerr << "BamToolsIndex ERROR: could not load index file. This version of BamTools does not recognize new index file version" + << endl + << "Please update BamTools to a more recent version to support this index file." + << endl; + return false; + } + + // ------------------------------------------------------------------ + // check for deprecated, unsupported versions + // (typically whose format did not accomodate a particular bug fix) + + else if ( (Version)m_inputVersion == BamToolsIndex::BTI_1_0 ) { + cerr << "BamToolsIndex ERROR: could not load index file. This version of the index contains a bug related to accessing data near reference ends." + << endl << endl + << "Please run 'bamtools index -bti -in yourData.bam' to generate an up-to-date, fixed BTI file." + << endl << endl; + return false; + } + + else if ( (Version)m_inputVersion == BamToolsIndex::BTI_1_1 ) { + cerr << "BamToolsIndex ERROR: could not load index file. This version of the index contains a bug related to handling empty references." + << endl << endl + << "Please run 'bamtools index -bti -in yourData.bam' to generate an up-to-date, fixed BTI file." + << endl << endl; + return false; + } + + // otherwise ok + else return true; +} + +void BamToolsIndex::ClearReferenceEntry(BtiReferenceEntry& refEntry) { + refEntry.ID = -1; + refEntry.Blocks.clear(); +} + +void BamToolsIndex::CloseFile(void) { + if ( IsFileOpen() ) + fclose(m_indexStream); + m_indexFileSummary.clear(); +} + +// builds index from associated BAM file & writes out to index file +bool BamToolsIndex::Create(void) { + + // return false if BamReader is invalid or not open + if ( m_reader == 0 || !m_reader->IsOpen() ) { + cerr << "BamToolsIndex ERROR: BamReader is not open" + << ", aborting index creation" << endl; + return false; + } + + // rewind BamReader + if ( !m_reader->Rewind() ) { + cerr << "BamToolsIndex ERROR: could not rewind BamReader to create index" + << ", aborting index creation" << endl; + return false; + } + + // open new index file (read & write) + string indexFilename = m_reader->Filename() + Extension(); + if ( !OpenFile(indexFilename, "w+b") ) { + cerr << "BamToolsIndex ERROR: could not open ouput index file " << indexFilename + << ", aborting index creation" << endl; + return false; + } + + // initialize BtiFileSummary with number of references + const int& numReferences = m_reader->GetReferenceCount(); + InitializeFileSummary(numReferences); + + // initialize output file + bool createdOk = true; + createdOk &= WriteHeader(); + + // index building markers + int32_t currentBlockCount = 0; + int64_t currentAlignmentOffset = m_reader->Tell(); + int32_t blockRefId = -1; + int32_t blockMaxEndPosition = -1; + int64_t blockStartOffset = currentAlignmentOffset; + int32_t blockStartPosition = -1; + + // plow through alignments, storing index entries + BamAlignment al; + BtiReferenceEntry refEntry; + while ( m_reader->LoadNextAlignment(al) ) { + + // if moved to new reference + if ( al.RefID != blockRefId ) { + + // if first pass, check: + if ( currentBlockCount == 0 ) { + + // write any empty references up to (but not including) al.RefID + for ( int i = 0; i < al.RefID; ++i ) { + BtiReferenceEntry emptyEntry(i); + createdOk &= WriteReferenceEntry(emptyEntry); + } + } + + // not first pass: + else { + + // store previous BTI block data in reference entry + BtiBlock block(blockMaxEndPosition, blockStartOffset, blockStartPosition); + refEntry.Blocks.push_back(block); + + // write reference entry, then clear + createdOk &= WriteReferenceEntry(refEntry); + ClearReferenceEntry(refEntry); + + // write any empty references between (but not including) the last blockRefID and current al.RefID + for ( int i = blockRefId+1; i < al.RefID; ++i ) { + BtiReferenceEntry emptyEntry(i); + createdOk &= WriteReferenceEntry(emptyEntry); + } + + // reset block count + currentBlockCount = 0; + } + + // set ID for new reference entry + refEntry.ID = al.RefID; + } + + // if beginning of block, update counters + if ( currentBlockCount == 0 ) { + blockRefId = al.RefID; + blockStartOffset = currentAlignmentOffset; + blockStartPosition = al.Position; + blockMaxEndPosition = al.GetEndPosition(); + } + + // increment block counter + ++currentBlockCount; + + // check end position + int32_t alignmentEndPosition = al.GetEndPosition(); + if ( alignmentEndPosition > blockMaxEndPosition ) + blockMaxEndPosition = alignmentEndPosition; + + // if block is full, get offset for next block, reset currentBlockCount + if ( currentBlockCount == m_blockSize ) { + + // store previous block data in reference entry + BtiBlock block(blockMaxEndPosition, blockStartOffset, blockStartPosition); + refEntry.Blocks.push_back(block); + + // update markers + blockStartOffset = m_reader->Tell(); + currentBlockCount = 0; + } + + // not the best name, but for the next iteration, this value will be the offset of the *current* alignment + // necessary because we won't know if this next alignment is on a new reference until we actually read it + currentAlignmentOffset = m_reader->Tell(); + } + + // after finishing alignments, if any data was read, check: + if ( blockRefId >= 0 ) { + + // store last BTI block data in reference entry + BtiBlock block(blockMaxEndPosition, blockStartOffset, blockStartPosition); + refEntry.Blocks.push_back(block); + + // write last reference entry, then clear + createdOk &= WriteReferenceEntry(refEntry); + ClearReferenceEntry(refEntry); + + // then write any empty references remaining at end of file + for ( int i = blockRefId+1; i < numReferences; ++i ) { + BtiReferenceEntry emptyEntry(i); + createdOk &= WriteReferenceEntry(emptyEntry); + } + } + + // rewind reader & return result + createdOk &= m_reader->Rewind(); + + // return result + return createdOk; +} + +// returns format's file extension +const std::string BamToolsIndex::Extension(void) { + return BamToolsIndex::BTI_EXTENSION; +} + +bool BamToolsIndex::GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion) { + + // return false ref ID is not a valid index in file summary data + if ( region.LeftRefID < 0 || region.LeftRefID >= (int)m_indexFileSummary.size() ) + return false; + + // retrieve reference index data for left bound reference + BtiReferenceEntry refEntry(region.LeftRefID); + if ( !ReadReferenceEntry(refEntry) ) { + cerr << "BamToolsIndex ERROR: could not retrieve index data from BTI file" << endl; + return false; + } + + // binary search for an overlapping block (may not be first one though) + bool found = false; + typedef BtiBlockVector::const_iterator BtiBlockConstIterator; + BtiBlockConstIterator blockFirst = refEntry.Blocks.begin(); + BtiBlockConstIterator blockIter = blockFirst; + BtiBlockConstIterator blockLast = refEntry.Blocks.end(); + iterator_traits<BtiBlockConstIterator>::difference_type count = distance(blockFirst, blockLast); + iterator_traits<BtiBlockConstIterator>::difference_type step; + while ( count > 0 ) { + blockIter = blockFirst; + step = count/2; + advance(blockIter, step); + + const BtiBlock& block = (*blockIter); + if ( block.StartPosition <= region.RightPosition ) { + if ( block.MaxEndPosition >= region.LeftPosition ) { + offset = block.StartOffset; + break; + } + blockFirst = ++blockIter; + count -= step+1; + } + else count = step; + } + + // if we didn't search "off the end" of the blocks + if ( blockIter != blockLast ) { + + // "walk back" until we've gone too far + while ( blockIter != blockFirst ) { + const BtiBlock& currentBlock = (*blockIter); + + --blockIter; + const BtiBlock& previousBlock = (*blockIter); + if ( previousBlock.MaxEndPosition < region.LeftPosition ) { + offset = currentBlock.StartOffset; + found = true; + break; + } + } + + // if we walked all the way to first block, just return that and let the reader's + // region overlap parsing do the rest + if ( blockIter == blockFirst ) { + const BtiBlock& block = (*blockIter); + offset = block.StartOffset; + found = true; + } + } + + + // sets to false if blocks container is empty, or if no matching block could be found + *hasAlignmentsInRegion = found; + + // return success + return true; +} + +// returns whether reference has alignments or no +bool BamToolsIndex::HasAlignments(const int& referenceID) const { + if ( referenceID < 0 || referenceID >= (int)m_indexFileSummary.size() ) + return false; + const BtiReferenceSummary& refSummary = m_indexFileSummary.at(referenceID); + return ( refSummary.NumBlocks > 0 ); +} + +void BamToolsIndex::InitializeFileSummary(const int& numReferences) { + m_indexFileSummary.clear(); + for ( int i = 0; i < numReferences; ++i ) + m_indexFileSummary.push_back( BtiReferenceSummary() ); +} + +bool BamToolsIndex::IsFileOpen(void) const { + return ( m_indexStream != 0 ); +} + +// attempts to use index data to jump to @region, returns success/fail +// a "successful" jump indicates no error, but not whether this region has data +// * thus, the method sets a flag to indicate whether there are alignments +// available after the jump position +bool BamToolsIndex::Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) { + + // clear flag + *hasAlignmentsInRegion = false; + + // skip if invalid reader or not open + if ( m_reader == 0 || !m_reader->IsOpen() ) + return false; + + // make sure left-bound position is valid + const RefVector& references = m_reader->GetReferenceData(); + if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) + return false; + + // calculate nearest offset to jump to + int64_t offset; + if ( !GetOffset(region, offset, hasAlignmentsInRegion) ) { + cerr << "BamToolsIndex ERROR: could not jump" + << ", unable to calculate offset for specified region" << endl; + return false; + } + + // return success/failure of seek + return m_reader->Seek(offset); +} + +// loads existing data from file into memory +bool BamToolsIndex::Load(const std::string& filename) { + + // attempt open index file (read-only) + if ( !OpenFile(filename, "rb") ) { + cerr << "BamToolsIndex ERROR: could not open input index file " << filename + << ", aborting index load" << endl; + return false; + } + + // attempt to load & validate BTI header data + if ( !LoadHeader() ) { + cerr << "BamToolsIndex ERROR: could load header from index file " << filename + << ", aborting index load" << endl; + CloseFile(); + return false; + } + + // attempt to load index file summary + if ( !LoadFileSummary() ) { + cerr << "BamToolsIndex ERROR: could not generate a summary of index file " << filename + << ", aborting index load" << endl; + CloseFile(); + return false; + } + + // if we get here, index summary is loaded OK + return true; +} + +bool BamToolsIndex::LoadFileSummary(void) { + + // load number of reference sequences + int numReferences; + if ( !LoadNumReferences(numReferences) ) + return false; + + // initialize file summary data + InitializeFileSummary(numReferences); + + // iterate over reference entries + bool loadedOk = true; + BtiFileSummary::iterator summaryIter = m_indexFileSummary.begin(); + BtiFileSummary::iterator summaryEnd = m_indexFileSummary.end(); + for ( ; summaryIter != summaryEnd; ++summaryIter ) + loadedOk &= LoadReferenceSummary(*summaryIter); + + // return result + return loadedOk; +} + +bool BamToolsIndex::LoadHeader(void) { + + // if invalid format 'magic number' + if ( !CheckMagicNumber() ) + return false; + + // if invalid BTI version + if ( !CheckVersion() ) + return false; + + // use file's BTI block size to set member variable + size_t elementsRead = fread(&m_blockSize, sizeof(m_blockSize), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(m_blockSize); + return ( elementsRead == 1 ); +} + +bool BamToolsIndex::LoadNumBlocks(int& numBlocks) { + size_t elementsRead = 0; + elementsRead += fread(&numBlocks, sizeof(numBlocks), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numBlocks); + return ( elementsRead == 1 ); +} + +bool BamToolsIndex::LoadNumReferences(int& numReferences) { + size_t elementsRead = 0; + elementsRead += fread(&numReferences, sizeof(numReferences), 1, m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numReferences); + return ( elementsRead == 1 ); +} + +bool BamToolsIndex::LoadReferenceSummary(BtiReferenceSummary& refSummary) { + + // load number of blocks + int numBlocks; + if ( !LoadNumBlocks(numBlocks) ) + return false; + + // store block summary data for this reference + refSummary.NumBlocks = numBlocks; + refSummary.FirstBlockFilePosition = Tell(); + + // skip blocks in index file (and return status) + return SkipBlocks(numBlocks); +} + +bool BamToolsIndex::OpenFile(const std::string& filename, const char* mode) { + + // make sure any previous index file is closed + CloseFile(); + + // attempt to open file + m_indexStream = fopen(filename.c_str(), mode); + return IsFileOpen(); +} + +bool BamToolsIndex::ReadBlock(BtiBlock& block) { + + // read in block data members + size_t elementsRead = 0; + elementsRead += fread(&block.MaxEndPosition, sizeof(block.MaxEndPosition), 1, m_indexStream); + elementsRead += fread(&block.StartOffset, sizeof(block.StartOffset), 1, m_indexStream); + elementsRead += fread(&block.StartPosition, sizeof(block.StartPosition), 1, m_indexStream); + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_32(block.MaxEndPosition); + SwapEndian_64(block.StartOffset); + SwapEndian_32(block.StartPosition); + } + + // return success/failure + return ( elementsRead == 3 ); +} + +bool BamToolsIndex::ReadBlocks(const BtiReferenceSummary& refSummary, BtiBlockVector& blocks) { + + // prep blocks container + blocks.clear(); + blocks.reserve(refSummary.NumBlocks); + + // skip to first block entry + if ( !Seek( refSummary.FirstBlockFilePosition, SEEK_SET ) ) { + cerr << "BamToolsIndex ERROR: could not seek to position " + << refSummary.FirstBlockFilePosition << endl; + return false; + } + + // read & store block entries + bool readOk = true; + BtiBlock block; + for ( int i = 0; i < refSummary.NumBlocks; ++i ) { + readOk &= ReadBlock(block); + blocks.push_back(block); + } + return readOk; +} + +bool BamToolsIndex::ReadReferenceEntry(BtiReferenceEntry& refEntry) { + + // return false if refId not valid index in file summary structure + if ( refEntry.ID < 0 || refEntry.ID >= (int)m_indexFileSummary.size() ) + return false; + + // use index summary to assist reading the reference's BTI blocks + const BtiReferenceSummary& refSummary = m_indexFileSummary.at(refEntry.ID); + return ReadBlocks(refSummary, refEntry.Blocks); +} + +bool BamToolsIndex::Seek(const int64_t& position, const int& origin) { + return ( fseek64(m_indexStream, position, origin) == 0 ); +} + +// change the index caching behavior +void BamToolsIndex::SetCacheMode(const BamIndex::IndexCacheMode& mode) { + m_cacheMode = mode; + // do nothing else here ? cache mode will be ignored from now on, most likely +} + +bool BamToolsIndex::SkipBlocks(const int& numBlocks) { + return Seek( numBlocks*BamToolsIndex::SIZEOF_BLOCK, SEEK_CUR ); +} + +int64_t BamToolsIndex::Tell(void) const { + return ftell64(m_indexStream); +} + +bool BamToolsIndex::WriteBlock(const BtiBlock& block) { + + // copy entry data + int32_t maxEndPosition = block.MaxEndPosition; + int64_t startOffset = block.StartOffset; + int32_t startPosition = block.StartPosition; + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_32(maxEndPosition); + SwapEndian_64(startOffset); + SwapEndian_32(startPosition); + } + + // write the reference index entry + size_t elementsWritten = 0; + elementsWritten += fwrite(&maxEndPosition, sizeof(maxEndPosition), 1, m_indexStream); + elementsWritten += fwrite(&startOffset, sizeof(startOffset), 1, m_indexStream); + elementsWritten += fwrite(&startPosition, sizeof(startPosition), 1, m_indexStream); + return ( elementsWritten == 3 ); +} + +bool BamToolsIndex::WriteBlocks(const BtiBlockVector& blocks) { + bool writtenOk = true; + BtiBlockVector::const_iterator blockIter = blocks.begin(); + BtiBlockVector::const_iterator blockEnd = blocks.end(); + for ( ; blockIter != blockEnd; ++blockIter ) + writtenOk &= WriteBlock(*blockIter); + return writtenOk; +} + +bool BamToolsIndex::WriteHeader(void) { + + size_t elementsWritten = 0; + + // write BTI index format 'magic number' + elementsWritten += fwrite(BamToolsIndex::BTI_MAGIC, 1, 4, m_indexStream); + + // write BTI index format version + int32_t currentVersion = (int32_t)m_outputVersion; + if ( m_isBigEndian ) SwapEndian_32(currentVersion); + elementsWritten += fwrite(¤tVersion, sizeof(currentVersion), 1, m_indexStream); + + // write block size + int32_t blockSize = m_blockSize; + if ( m_isBigEndian ) SwapEndian_32(blockSize); + elementsWritten += fwrite(&blockSize, sizeof(blockSize), 1, m_indexStream); + + // write number of references + int32_t numReferences = m_indexFileSummary.size(); + if ( m_isBigEndian ) SwapEndian_32(numReferences); + elementsWritten += fwrite(&numReferences, sizeof(numReferences), 1, m_indexStream); + + // return success/failure of write + return ( elementsWritten == 7 ); +} + +bool BamToolsIndex::WriteReferenceEntry(const BtiReferenceEntry& refEntry) { + + size_t elementsWritten = 0; + + // write number of blocks this reference + uint32_t numBlocks = refEntry.Blocks.size(); + if ( m_isBigEndian ) SwapEndian_32(numBlocks); + elementsWritten += fwrite(&numBlocks, sizeof(numBlocks), 1, m_indexStream); + + // write actual block entries + const bool blocksOk = WriteBlocks(refEntry.Blocks); + + // return success/fail + return ( elementsWritten == 1) && blocksOk; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamToolsIndex_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,188 @@ +// *************************************************************************** +// BamToolsIndex.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the BamTools index format (".bti") +// *************************************************************************** + +#ifndef BAMTOOLS_INDEX_FORMAT_H +#define BAMTOOLS_INDEX_FORMAT_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to +// version without notice, or even be removed. +// +// We mean it. + +#include <api/BamAux.h> +#include <api/BamIndex.h> +#include <map> +#include <string> +#include <vector> + +namespace BamTools { +namespace Internal { + +// contains data for each 'block' in a BTI index +struct BtiBlock { + + // data members + int32_t MaxEndPosition; + int64_t StartOffset; + int32_t StartPosition; + + // ctor + BtiBlock(const int32_t& maxEndPosition = 0, + const int64_t& startOffset = 0, + const int32_t& startPosition = 0) + : MaxEndPosition(maxEndPosition) + , StartOffset(startOffset) + , StartPosition(startPosition) + { } +}; + +// convenience typedef for describing a a list of BTI blocks on a reference +typedef std::vector<BtiBlock> BtiBlockVector; + +// contains all fields necessary for building, loading, & writing +// full BTI index data for a single reference +struct BtiReferenceEntry { + + // data members + int32_t ID; + BtiBlockVector Blocks; + + // ctor + BtiReferenceEntry(const int& id = -1) + : ID(id) + { } +}; + +// provides (persistent) summary of BtiReferenceEntry's index data +struct BtiReferenceSummary { + + // data members + int NumBlocks; + uint64_t FirstBlockFilePosition; + + // ctor + BtiReferenceSummary(void) + : NumBlocks(0) + , FirstBlockFilePosition(0) + { } +}; + +// convenience typedef for describing a full BTI index file summary +typedef std::vector<BtiReferenceSummary> BtiFileSummary; + +class BamToolsIndex : public BamIndex { + + // keep a list of any supported versions here + // (might be useful later to handle any 'legacy' versions if the format changes) + // listed for example like: BTI_1_0 = 1, BTI_1_1 = 2, BTI_1_2 = 3, BTI_2_0 = 4, and so on + // + // so a change introduced in (hypothetical) BTI_1_2 would be handled from then on by: + // + // if ( indexVersion >= BTI_1_2 ) + // do something new + // else + // do the old thing + enum Version { BTI_1_0 = 1 + , BTI_1_1 + , BTI_1_2 + }; + + // ctor & dtor + public: + BamToolsIndex(Internal::BamReaderPrivate* reader); + ~BamToolsIndex(void); + + // BamIndex implementation + public: + // builds index from associated BAM file & writes out to index file + bool Create(void); + // returns whether reference has alignments or no + bool HasAlignments(const int& referenceID) const; + // attempts to use index data to jump to @region, returns success/fail + // a "successful" jump indicates no error, but not whether this region has data + // * thus, the method sets a flag to indicate whether there are alignments + // available after the jump position + bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); + // loads existing data from file into memory + bool Load(const std::string& filename); + // change the index caching behavior + void SetCacheMode(const BamIndex::IndexCacheMode& mode); + public: + // returns format's file extension + static const std::string Extension(void); + + // internal file ops + private: + bool CheckMagicNumber(void); + bool CheckVersion(void); + void CloseFile(void); + bool IsFileOpen(void) const; + bool OpenFile(const std::string& filename, const char* mode); + bool Seek(const int64_t& position, const int& origin); + int64_t Tell(void) const; + + // internal BTI index building methods + private: + void ClearReferenceEntry(BtiReferenceEntry& refEntry); + + // internal random-access methods + private: + bool GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion); + + // internal BTI summary data methods + private: + void InitializeFileSummary(const int& numReferences); + bool LoadFileSummary(void); + bool LoadHeader(void); + bool LoadNumBlocks(int& numBlocks); + bool LoadNumReferences(int& numReferences); + bool LoadReferenceSummary(BtiReferenceSummary& refSummary); + bool SkipBlocks(const int& numBlocks); + + // internal BTI full index input methods + private: + bool ReadBlock(BtiBlock& block); + bool ReadBlocks(const BtiReferenceSummary& refSummary, BtiBlockVector& blocks); + bool ReadReferenceEntry(BtiReferenceEntry& refEntry); + + // internal BTI full index output methods + private: + bool WriteBlock(const BtiBlock& block); + bool WriteBlocks(const BtiBlockVector& blocks); + bool WriteHeader(void); + bool WriteReferenceEntry(const BtiReferenceEntry& refEntry); + + // data members + private: + FILE* m_indexStream; + bool m_isBigEndian; + BamIndex::IndexCacheMode m_cacheMode; + BtiFileSummary m_indexFileSummary; + int m_blockSize; + int32_t m_inputVersion; // Version is serialized as int + Version m_outputVersion; + + // static constants + private: + static const int DEFAULT_BLOCK_LENGTH; + static const std::string BTI_EXTENSION; + static const char* const BTI_MAGIC; + static const int SIZEOF_BLOCK; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMTOOLS_INDEX_FORMAT_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamWriter_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,425 @@ +// *************************************************************************** +// BamWriter_p.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 16 June 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for producing BAM files +// *************************************************************************** + +#include <api/BamAlignment.h> +#include <api/BamConstants.h> +#include <api/internal/BamWriter_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <cstdio> +#include <cstdlib> +#include <cstring> +using namespace std; + +// ctor +BamWriterPrivate::BamWriterPrivate(void) + : m_isBigEndian( BamTools::SystemIsBigEndian() ) +{ } + +// dtor +BamWriterPrivate::~BamWriterPrivate(void) { + m_stream.Close(); +} + +// calculates minimum bin for a BAM alignment interval +unsigned int BamWriterPrivate::CalculateMinimumBin(const int begin, int end) const { + --end; + if ( (begin >> 14) == (end >> 14) ) return 4681 + (begin >> 14); + if ( (begin >> 17) == (end >> 17) ) return 585 + (begin >> 17); + if ( (begin >> 20) == (end >> 20) ) return 73 + (begin >> 20); + if ( (begin >> 23) == (end >> 23) ) return 9 + (begin >> 23); + if ( (begin >> 26) == (end >> 26) ) return 1 + (begin >> 26); + return 0; +} + +// closes the alignment archive +void BamWriterPrivate::Close(void) { + m_stream.Close(); +} + +// creates a cigar string from the supplied alignment +void BamWriterPrivate::CreatePackedCigar(const vector<CigarOp>& cigarOperations, string& packedCigar) { + + // initialize + const unsigned int numCigarOperations = cigarOperations.size(); + packedCigar.resize(numCigarOperations * Constants::BAM_SIZEOF_INT); + + // pack the cigar data into the string + unsigned int* pPackedCigar = (unsigned int*)packedCigar.data(); + + // iterate over cigar operations + vector<CigarOp>::const_iterator coIter = cigarOperations.begin(); + vector<CigarOp>::const_iterator coEnd = cigarOperations.end(); + for ( ; coIter != coEnd; ++coIter ) { + + // store op in packedCigar + unsigned int cigarOp; + switch ( coIter->Type ) { + case (Constants::BAM_CIGAR_MATCH_CHAR) : cigarOp = Constants::BAM_CIGAR_MATCH; break; + case (Constants::BAM_CIGAR_INS_CHAR) : cigarOp = Constants::BAM_CIGAR_INS; break; + case (Constants::BAM_CIGAR_DEL_CHAR) : cigarOp = Constants::BAM_CIGAR_DEL; break; + case (Constants::BAM_CIGAR_REFSKIP_CHAR) : cigarOp = Constants::BAM_CIGAR_REFSKIP; break; + case (Constants::BAM_CIGAR_SOFTCLIP_CHAR) : cigarOp = Constants::BAM_CIGAR_SOFTCLIP; break; + case (Constants::BAM_CIGAR_HARDCLIP_CHAR) : cigarOp = Constants::BAM_CIGAR_HARDCLIP; break; + case (Constants::BAM_CIGAR_PAD_CHAR) : cigarOp = Constants::BAM_CIGAR_PAD; break; + case (Constants::BAM_CIGAR_SEQMATCH_CHAR) : cigarOp = Constants::BAM_CIGAR_SEQMATCH; break; + case (Constants::BAM_CIGAR_MISMATCH_CHAR) : cigarOp = Constants::BAM_CIGAR_MISMATCH; break; + default: + fprintf(stderr, "BamWriter ERROR: unknown cigar operation found: %c\n", coIter->Type); + exit(1); + } + + *pPackedCigar = coIter->Length << Constants::BAM_CIGAR_SHIFT | cigarOp; + pPackedCigar++; + } +} + +// encodes the supplied query sequence into 4-bit notation +void BamWriterPrivate::EncodeQuerySequence(const string& query, string& encodedQuery) { + + // prepare the encoded query string + const unsigned int queryLen = query.size(); + const unsigned int encodedQueryLen = (unsigned int)((queryLen / 2.0) + 0.5); + encodedQuery.resize(encodedQueryLen); + char* pEncodedQuery = (char*)encodedQuery.data(); + const char* pQuery = (const char*)query.data(); + + unsigned char nucleotideCode; + bool useHighWord = true; + + while ( *pQuery ) { + switch ( *pQuery ) { + case (Constants::BAM_DNA_EQUAL) : nucleotideCode = Constants::BAM_BASECODE_EQUAL; break; + case (Constants::BAM_DNA_A) : nucleotideCode = Constants::BAM_BASECODE_A; break; + case (Constants::BAM_DNA_C) : nucleotideCode = Constants::BAM_BASECODE_C; break; + case (Constants::BAM_DNA_G) : nucleotideCode = Constants::BAM_BASECODE_G; break; + case (Constants::BAM_DNA_T) : nucleotideCode = Constants::BAM_BASECODE_T; break; + case (Constants::BAM_DNA_N) : nucleotideCode = Constants::BAM_BASECODE_N; break; + default: + fprintf(stderr, "BamWriter ERROR: only the following bases are supported in the BAM format: {=, A, C, G, T, N}. Found [%c]\n", *pQuery); + exit(1); + } + + // pack the nucleotide code + if ( useHighWord ) { + *pEncodedQuery = nucleotideCode << 4; + useHighWord = false; + } else { + *pEncodedQuery |= nucleotideCode; + ++pEncodedQuery; + useHighWord = true; + } + + // increment the query position + ++pQuery; + } +} + +// returns whether BAM file is open for writing or not +bool BamWriterPrivate::IsOpen(void) const { + return m_stream.IsOpen; +} + +// opens the alignment archive +bool BamWriterPrivate::Open(const string& filename, + const string& samHeaderText, + const RefVector& referenceSequences) +{ + // open the BGZF file for writing, return failure if error + if ( !m_stream.Open(filename, "wb") ) + return false; + + // write BAM file 'metadata' components + WriteMagicNumber(); + WriteSamHeaderText(samHeaderText); + WriteReferences(referenceSequences); + return true; +} + +// saves the alignment to the alignment archive +void BamWriterPrivate::SaveAlignment(const BamAlignment& al) { + + // if BamAlignment contains only the core data and a raw char data buffer + // (as a result of BamReader::GetNextAlignmentCore()) + if ( al.SupportData.HasCoreOnly ) { + + // write the block size + unsigned int blockSize = al.SupportData.BlockLength; + if ( m_isBigEndian ) BamTools::SwapEndian_32(blockSize); + m_stream.Write((char*)&blockSize, Constants::BAM_SIZEOF_INT); + + // re-calculate bin (in case BamAlignment's position has been previously modified) + const uint32_t alignmentBin = CalculateMinimumBin(al.Position, al.GetEndPosition()); + + // assign the BAM core data + uint32_t buffer[Constants::BAM_CORE_BUFFER_SIZE]; + buffer[0] = al.RefID; + buffer[1] = al.Position; + buffer[2] = (alignmentBin << 16) | (al.MapQuality << 8) | al.SupportData.QueryNameLength; + buffer[3] = (al.AlignmentFlag << 16) | al.SupportData.NumCigarOperations; + buffer[4] = al.SupportData.QuerySequenceLength; + buffer[5] = al.MateRefID; + buffer[6] = al.MatePosition; + buffer[7] = al.InsertSize; + + // swap BAM core endian-ness, if necessary + if ( m_isBigEndian ) { + for ( int i = 0; i < 8; ++i ) + BamTools::SwapEndian_32(buffer[i]); + } + + // write the BAM core + m_stream.Write((char*)&buffer, Constants::BAM_CORE_SIZE); + + // write the raw char data + m_stream.Write((char*)al.SupportData.AllCharData.data(), + al.SupportData.BlockLength-Constants::BAM_CORE_SIZE); + } + + // otherwise, BamAlignment should contain character in the standard fields: Name, QueryBases, etc + // ( resulting from BamReader::GetNextAlignment() *OR* being generated directly by client code ) + else { + + // calculate char lengths + const unsigned int nameLength = al.Name.size() + 1; + const unsigned int numCigarOperations = al.CigarData.size(); + const unsigned int queryLength = al.QueryBases.size(); + const unsigned int tagDataLength = al.TagData.size(); + + // no way to tell if BamAlignment.Bin is already defined (no default, invalid value) + // force calculation of Bin before storing + const int endPosition = al.GetEndPosition(); + const unsigned int alignmentBin = CalculateMinimumBin(al.Position, endPosition); + + // create our packed cigar string + string packedCigar; + CreatePackedCigar(al.CigarData, packedCigar); + const unsigned int packedCigarLength = packedCigar.size(); + + // encode the query + string encodedQuery; + EncodeQuerySequence(al.QueryBases, encodedQuery); + const unsigned int encodedQueryLength = encodedQuery.size(); + + // write the block size + const unsigned int dataBlockSize = nameLength + + packedCigarLength + + encodedQueryLength + + queryLength + + tagDataLength; + unsigned int blockSize = Constants::BAM_CORE_SIZE + dataBlockSize; + if ( m_isBigEndian ) BamTools::SwapEndian_32(blockSize); + m_stream.Write((char*)&blockSize, Constants::BAM_SIZEOF_INT); + + // assign the BAM core data + uint32_t buffer[Constants::BAM_CORE_BUFFER_SIZE]; + buffer[0] = al.RefID; + buffer[1] = al.Position; + buffer[2] = (alignmentBin << 16) | (al.MapQuality << 8) | nameLength; + buffer[3] = (al.AlignmentFlag << 16) | numCigarOperations; + buffer[4] = queryLength; + buffer[5] = al.MateRefID; + buffer[6] = al.MatePosition; + buffer[7] = al.InsertSize; + + // swap BAM core endian-ness, if necessary + if ( m_isBigEndian ) { + for ( int i = 0; i < 8; ++i ) + BamTools::SwapEndian_32(buffer[i]); + } + + // write the BAM core + m_stream.Write((char*)&buffer, Constants::BAM_CORE_SIZE); + + // write the query name + m_stream.Write(al.Name.c_str(), nameLength); + + // write the packed cigar + if ( m_isBigEndian ) { + char* cigarData = (char*)calloc(sizeof(char), packedCigarLength); + memcpy(cigarData, packedCigar.data(), packedCigarLength); + if ( m_isBigEndian ) { + for ( unsigned int i = 0; i < packedCigarLength; ++i ) + BamTools::SwapEndian_32p(&cigarData[i]); + } + m_stream.Write(cigarData, packedCigarLength); + free(cigarData); + } + else + m_stream.Write(packedCigar.data(), packedCigarLength); + + // write the encoded query sequence + m_stream.Write(encodedQuery.data(), encodedQueryLength); + + // write the base qualities + char* pBaseQualities = (char*)al.Qualities.data(); + for ( unsigned int i = 0; i < queryLength; ++i ) + pBaseQualities[i] -= 33; // FASTQ conversion + m_stream.Write(pBaseQualities, queryLength); + + // write the read group tag + if ( m_isBigEndian ) { + + char* tagData = (char*)calloc(sizeof(char), tagDataLength); + memcpy(tagData, al.TagData.data(), tagDataLength); + + int i = 0; + while ( (unsigned int)i < tagDataLength ) { + + i += Constants::BAM_TAG_TAGSIZE; // skip tag chars (e.g. "RG", "NM", etc.) + const char type = tagData[i]; // get tag type at position i + ++i; + + switch ( type ) { + + case(Constants::BAM_TAG_TYPE_ASCII) : + case(Constants::BAM_TAG_TYPE_INT8) : + case(Constants::BAM_TAG_TYPE_UINT8) : + ++i; + break; + + case(Constants::BAM_TAG_TYPE_INT16) : + case(Constants::BAM_TAG_TYPE_UINT16) : + BamTools::SwapEndian_16p(&tagData[i]); + i += sizeof(uint16_t); + break; + + case(Constants::BAM_TAG_TYPE_FLOAT) : + case(Constants::BAM_TAG_TYPE_INT32) : + case(Constants::BAM_TAG_TYPE_UINT32) : + BamTools::SwapEndian_32p(&tagData[i]); + i += sizeof(uint32_t); + break; + + case(Constants::BAM_TAG_TYPE_HEX) : + case(Constants::BAM_TAG_TYPE_STRING) : + // no endian swapping necessary for hex-string/string data + while ( tagData[i] ) + ++i; + // increment one more for null terminator + ++i; + break; + + case(Constants::BAM_TAG_TYPE_ARRAY) : + + { + // read array type + const char arrayType = tagData[i]; + ++i; + + // swap endian-ness of number of elements in place, then retrieve for loop + BamTools::SwapEndian_32p(&tagData[i]); + int32_t numElements; + memcpy(&numElements, &tagData[i], sizeof(uint32_t)); + i += sizeof(uint32_t); + + // swap endian-ness of array elements + for ( int j = 0; j < numElements; ++j ) { + switch (arrayType) { + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : + // no endian-swapping necessary + ++i; + break; + case (Constants::BAM_TAG_TYPE_INT16) : + case (Constants::BAM_TAG_TYPE_UINT16) : + BamTools::SwapEndian_16p(&tagData[i]); + i += sizeof(uint16_t); + break; + case (Constants::BAM_TAG_TYPE_FLOAT) : + case (Constants::BAM_TAG_TYPE_INT32) : + case (Constants::BAM_TAG_TYPE_UINT32) : + BamTools::SwapEndian_32p(&tagData[i]); + i += sizeof(uint32_t); + break; + default: + // error case + fprintf(stderr, + "BamWriter ERROR: unknown binary array type encountered: [%c]\n", + arrayType); + exit(1); + } + } + + break; + } + + default : + fprintf(stderr, "BamWriter ERROR: invalid tag value type\n"); // shouldn't get here + free(tagData); + exit(1); + } + } + m_stream.Write(tagData, tagDataLength); + free(tagData); + } + else + m_stream.Write(al.TagData.data(), tagDataLength); + } +} + +void BamWriterPrivate::SetWriteCompressed(bool ok) { + + // warn if BAM file is already open + // modifying compression is not allowed in this case + if ( IsOpen() ) { + cerr << "BamWriter WARNING: attempting to change compression mode on an open BAM file is not allowed. " + << "Ignoring request." << endl; + return; + } + + // set BgzfStream compression mode + m_stream.SetWriteCompressed(ok); +} + +void BamWriterPrivate::WriteMagicNumber(void) { + // write BAM file 'magic number' + m_stream.Write(Constants::BAM_HEADER_MAGIC, Constants::BAM_HEADER_MAGIC_LENGTH); +} + +void BamWriterPrivate::WriteReferences(const BamTools::RefVector& referenceSequences) { + + // write the number of reference sequences + uint32_t numReferenceSequences = referenceSequences.size(); + if ( m_isBigEndian ) BamTools::SwapEndian_32(numReferenceSequences); + m_stream.Write((char*)&numReferenceSequences, Constants::BAM_SIZEOF_INT); + + // foreach reference sequence + RefVector::const_iterator rsIter = referenceSequences.begin(); + RefVector::const_iterator rsEnd = referenceSequences.end(); + for ( ; rsIter != rsEnd; ++rsIter ) { + + // write the reference sequence name length + uint32_t referenceSequenceNameLen = rsIter->RefName.size() + 1; + if ( m_isBigEndian ) BamTools::SwapEndian_32(referenceSequenceNameLen); + m_stream.Write((char*)&referenceSequenceNameLen, Constants::BAM_SIZEOF_INT); + + // write the reference sequence name + m_stream.Write(rsIter->RefName.c_str(), referenceSequenceNameLen); + + // write the reference sequence length + int32_t referenceLength = rsIter->RefLength; + if ( m_isBigEndian ) BamTools::SwapEndian_32(referenceLength); + m_stream.Write((char*)&referenceLength, Constants::BAM_SIZEOF_INT); + } +} + +void BamWriterPrivate::WriteSamHeaderText(const std::string& samHeaderText) { + + // write the SAM header text length + uint32_t samHeaderLen = samHeaderText.size(); + if ( m_isBigEndian ) BamTools::SwapEndian_32(samHeaderLen); + m_stream.Write((char*)&samHeaderLen, Constants::BAM_SIZEOF_INT); + + // write the SAM header text + if ( samHeaderLen > 0 ) + m_stream.Write(samHeaderText.data(), samHeaderLen); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BamWriter_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,67 @@ +// *************************************************************************** +// BamWriter_p.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 24 February 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic functionality for producing BAM files +// *************************************************************************** + +#ifndef BAMWRITER_P_H +#define BAMWRITER_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to +// version without notice, or even be removed. +// +// We mean it. + +#include <api/BamAux.h> +#include <api/internal/BgzfStream_p.h> +#include <string> +#include <vector> + +namespace BamTools { +namespace Internal { + +class BamWriterPrivate { + + // ctor & dtor + public: + BamWriterPrivate(void); + ~BamWriterPrivate(void); + + // interface methods + public: + void Close(void); + bool IsOpen(void) const; + bool Open(const std::string& filename, + const std::string& samHeaderText, + const BamTools::RefVector& referenceSequences); + void SaveAlignment(const BamAlignment& al); + void SetWriteCompressed(bool ok); + + // 'internal' methods + public: + unsigned int CalculateMinimumBin(const int begin, int end) const; + void CreatePackedCigar(const std::vector<BamTools::CigarOp>& cigarOperations, std::string& packedCigar); + void EncodeQuerySequence(const std::string& query, std::string& encodedQuery); + void WriteMagicNumber(void); + void WriteReferences(const BamTools::RefVector& referenceSequences); + void WriteSamHeaderText(const std::string& samHeaderText); + + // data members + private: + BgzfStream m_stream; + bool m_isBigEndian; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMWRITER_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BgzfStream_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,439 @@ +// *************************************************************************** +// BgzfStream_p.cpp (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011(DB) +// --------------------------------------------------------------------------- +// Based on BGZF routines developed at the Broad Institute. +// Provides the basic functionality for reading & writing BGZF files +// Replaces the old BGZF.* files to avoid clashing with other toolkits +// *************************************************************************** + +#include <api/internal/BgzfStream_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <cstring> +#include <algorithm> +using namespace std; + +// constructor +BgzfStream::BgzfStream(void) + : UncompressedBlockSize(Constants::BGZF_DEFAULT_BLOCK_SIZE) + , CompressedBlockSize(Constants::BGZF_MAX_BLOCK_SIZE) + , BlockLength(0) + , BlockOffset(0) + , BlockAddress(0) + , IsOpen(false) + , IsWriteOnly(false) + , IsWriteCompressed(true) + , Stream(NULL) + , UncompressedBlock(NULL) + , CompressedBlock(NULL) +{ + try { + CompressedBlock = new char[CompressedBlockSize]; + UncompressedBlock = new char[UncompressedBlockSize]; + } catch( std::bad_alloc& ba ) { + fprintf(stderr, "BgzfStream ERROR: unable to allocate memory\n"); + exit(1); + } +} + +// destructor +BgzfStream::~BgzfStream(void) { + if( CompressedBlock ) delete[] CompressedBlock; + if( UncompressedBlock ) delete[] UncompressedBlock; +} + +// closes BGZF file +void BgzfStream::Close(void) { + + // skip if file not open + if ( !IsOpen ) return; + + // if writing to file, flush the current BGZF block, + // then write an empty block (as EOF marker) + if ( IsWriteOnly ) { + FlushBlock(); + int blockLength = DeflateBlock(); + fwrite(CompressedBlock, 1, blockLength, Stream); + } + + // flush and close stream + fflush(Stream); + fclose(Stream); + + // reset flags + IsWriteCompressed = true; + IsOpen = false; +} + +// compresses the current block +int BgzfStream::DeflateBlock(void) { + + // initialize the gzip header + char* buffer = CompressedBlock; + memset(buffer, 0, 18); + buffer[0] = Constants::GZIP_ID1; + buffer[1] = (char)Constants::GZIP_ID2; + buffer[2] = Constants::CM_DEFLATE; + buffer[3] = Constants::FLG_FEXTRA; + buffer[9] = (char)Constants::OS_UNKNOWN; + buffer[10] = Constants::BGZF_XLEN; + buffer[12] = Constants::BGZF_ID1; + buffer[13] = Constants::BGZF_ID2; + buffer[14] = Constants::BGZF_LEN; + + // set compression level + const int compressionLevel = ( IsWriteCompressed ? Z_DEFAULT_COMPRESSION : 0 ); + + // loop to retry for blocks that do not compress enough + int inputLength = BlockOffset; + int compressedLength = 0; + unsigned int bufferSize = CompressedBlockSize; + + while ( true ) { + + // initialize zstream values + z_stream zs; + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = (Bytef*)UncompressedBlock; + zs.avail_in = inputLength; + zs.next_out = (Bytef*)&buffer[Constants::BGZF_BLOCK_HEADER_LENGTH]; + zs.avail_out = bufferSize - Constants::BGZF_BLOCK_HEADER_LENGTH - Constants::BGZF_BLOCK_FOOTER_LENGTH; + + // initialize the zlib compression algorithm + if ( deflateInit2(&zs, + compressionLevel, + Z_DEFLATED, + Constants::GZIP_WINDOW_BITS, + Constants::Z_DEFAULT_MEM_LEVEL, + Z_DEFAULT_STRATEGY) != Z_OK ) + { + fprintf(stderr, "BgzfStream ERROR: zlib deflate initialization failed\n"); + exit(1); + } + + // compress the data + int status = deflate(&zs, Z_FINISH); + if ( status != Z_STREAM_END ) { + + deflateEnd(&zs); + + // reduce the input length and try again + if ( status == Z_OK ) { + inputLength -= 1024; + if ( inputLength < 0 ) { + fprintf(stderr, "BgzfStream ERROR: input reduction failed\n"); + exit(1); + } + continue; + } + + fprintf(stderr, "BgzfStream ERROR: zlib::deflateEnd() failed\n"); + exit(1); + } + + // finalize the compression routine + if ( deflateEnd(&zs) != Z_OK ) { + fprintf(stderr, "BgzfStream ERROR: zlib::deflateEnd() failed\n"); + exit(1); + } + + compressedLength = zs.total_out; + compressedLength += Constants::BGZF_BLOCK_HEADER_LENGTH + Constants::BGZF_BLOCK_FOOTER_LENGTH; + if ( compressedLength > Constants::BGZF_MAX_BLOCK_SIZE ) { + fprintf(stderr, "BgzfStream ERROR: deflate overflow\n"); + exit(1); + } + + break; + } + + // store the compressed length + BamTools::PackUnsignedShort(&buffer[16], (unsigned short)(compressedLength - 1)); + + // store the CRC32 checksum + unsigned int crc = crc32(0, NULL, 0); + crc = crc32(crc, (Bytef*)UncompressedBlock, inputLength); + BamTools::PackUnsignedInt(&buffer[compressedLength - 8], crc); + BamTools::PackUnsignedInt(&buffer[compressedLength - 4], inputLength); + + // ensure that we have less than a block of data left + int remaining = BlockOffset - inputLength; + if ( remaining > 0 ) { + if ( remaining > inputLength ) { + fprintf(stderr, "BgzfStream ERROR: after deflate, remainder too large\n"); + exit(1); + } + memcpy(UncompressedBlock, UncompressedBlock + inputLength, remaining); + } + + // update block data + BlockOffset = remaining; + + // return result + return compressedLength; +} + +// flushes the data in the BGZF block +void BgzfStream::FlushBlock(void) { + + // flush all of the remaining blocks + while ( BlockOffset > 0 ) { + + // compress the data block + int blockLength = DeflateBlock(); + + // flush the data to our output stream + int numBytesWritten = fwrite(CompressedBlock, 1, blockLength, Stream); + if ( numBytesWritten != blockLength ) { + fprintf(stderr, "BgzfStream ERROR: expected to write %u bytes during flushing, but wrote %u bytes\n", + blockLength, numBytesWritten); + exit(1); + } + + // update block data + BlockAddress += blockLength; + } +} + +// decompresses the current block +int BgzfStream::InflateBlock(const int& blockLength) { + + // inflate the data from compressed buffer into uncompressed buffer + z_stream zs; + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = (Bytef*)CompressedBlock + 18; + zs.avail_in = blockLength - 16; + zs.next_out = (Bytef*)UncompressedBlock; + zs.avail_out = UncompressedBlockSize; + + int status = inflateInit2(&zs, Constants::GZIP_WINDOW_BITS); + if ( status != Z_OK ) { + fprintf(stderr, "BgzfStream ERROR: could not decompress block - zlib::inflateInit() failed\n"); + return -1; + } + + status = inflate(&zs, Z_FINISH); + if ( status != Z_STREAM_END ) { + inflateEnd(&zs); + fprintf(stderr, "BgzfStream ERROR: could not decompress block - zlib::inflate() failed\n"); + return -1; + } + + status = inflateEnd(&zs); + if ( status != Z_OK ) { + fprintf(stderr, "BgzfStream ERROR: could not decompress block - zlib::inflateEnd() failed\n"); + return -1; + } + + // return result + return zs.total_out; +} + +// opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing) +bool BgzfStream::Open(const string& filename, const char* mode) { + + // close current stream, if necessary, before opening next + if ( IsOpen ) Close(); + + // determine open mode + if ( strcmp(mode, "rb") == 0 ) + IsWriteOnly = false; + else if ( strcmp(mode, "wb") == 0) + IsWriteOnly = true; + else { + fprintf(stderr, "BgzfStream ERROR: unknown file mode: %s\n", mode); + return false; + } + + // open BGZF stream on a file + if ( (filename != "stdin") && (filename != "stdout") && (filename != "-") ) + Stream = fopen(filename.c_str(), mode); + + // open BGZF stream on stdin + else if ( (filename == "stdin" || filename == "-") && (strcmp(mode, "rb") == 0 ) ) + Stream = freopen(NULL, mode, stdin); + + // open BGZF stream on stdout + else if ( (filename == "stdout" || filename == "-") && (strcmp(mode, "wb") == 0) ) + Stream = freopen(NULL, mode, stdout); + + if ( !Stream ) { + fprintf(stderr, "BgzfStream ERROR: unable to open file %s\n", filename.c_str() ); + return false; + } + + // set flag & return success + IsOpen = true; + return true; +} + +// reads BGZF data into a byte buffer +int BgzfStream::Read(char* data, const unsigned int dataLength) { + + // if stream not open for reading (or empty request) + if ( !IsOpen || IsWriteOnly || dataLength == 0 ) + return 0; + + // read blocks as needed until desired data length is retrieved + char* output = data; + unsigned int numBytesRead = 0; + while ( numBytesRead < dataLength ) { + + // determine bytes available in current block + int bytesAvailable = BlockLength - BlockOffset; + + // read (and decompress) next block if needed + if ( bytesAvailable <= 0 ) { + if ( !ReadBlock() ) return -1; + bytesAvailable = BlockLength - BlockOffset; + if ( bytesAvailable <= 0 ) break; + } + + // copy data from uncompressed source buffer into data destination buffer + char* buffer = UncompressedBlock; + int copyLength = min( (int)(dataLength-numBytesRead), bytesAvailable ); + memcpy(output, buffer + BlockOffset, copyLength); + + // update counters + BlockOffset += copyLength; + output += copyLength; + numBytesRead += copyLength; + } + + // update block data + if ( BlockOffset == BlockLength ) { + BlockAddress = ftell64(Stream); + BlockOffset = 0; + BlockLength = 0; + } + + return numBytesRead; +} + +// reads a BGZF block +bool BgzfStream::ReadBlock(void) { + + char header[Constants::BGZF_BLOCK_HEADER_LENGTH]; + int64_t blockAddress = ftell64(Stream); + + // read block header from file + int count = fread(header, 1, sizeof(header), Stream); + + // if block header empty + if ( count == 0 ) { + BlockLength = 0; + return true; + } + + // if block header invalid size + if ( count != sizeof(header) ) { + fprintf(stderr, "BgzfStream ERROR: read block failed - could not read block header\n"); + return false; + } + + // validate block header contents + if ( !BgzfStream::CheckBlockHeader(header) ) { + fprintf(stderr, "BgzfStream ERROR: read block failed - invalid block header\n"); + return false; + } + + // copy header contents to compressed buffer + int blockLength = BamTools::UnpackUnsignedShort(&header[16]) + 1; + char* compressedBlock = CompressedBlock; + memcpy(compressedBlock, header, Constants::BGZF_BLOCK_HEADER_LENGTH); + int remaining = blockLength - Constants::BGZF_BLOCK_HEADER_LENGTH; + + // read remainder of block + count = fread(&compressedBlock[Constants::BGZF_BLOCK_HEADER_LENGTH], 1, remaining, Stream); + if ( count != remaining ) { + fprintf(stderr, "BgzfStream ERROR: read block failed - could not read data from block\n"); + return false; + } + + // decompress block data + count = InflateBlock(blockLength); + if ( count < 0 ) { + fprintf(stderr, "BgzfStream ERROR: read block failed - could not decompress block data\n"); + return false; + } + + // update block data + if ( BlockLength != 0 ) + BlockOffset = 0; + BlockAddress = blockAddress; + BlockLength = count; + + // return success + return true; +} + +// seek to position in BGZF file +bool BgzfStream::Seek(const int64_t& position) { + + // skip if not open + if ( !IsOpen ) return false; + + // determine adjusted offset & address + int blockOffset = (position & 0xFFFF); + int64_t blockAddress = (position >> 16) & 0xFFFFFFFFFFFFLL; + + // attempt seek in file + if ( fseek64(Stream, blockAddress, SEEK_SET) != 0 ) { + fprintf(stderr, "BgzfStream ERROR: unable to seek in file\n"); + return false; + } + + // update block data & return success + BlockLength = 0; + BlockAddress = blockAddress; + BlockOffset = blockOffset; + return true; +} + +void BgzfStream::SetWriteCompressed(bool ok) { + IsWriteCompressed = ok; +} + +// get file position in BGZF file +int64_t BgzfStream::Tell(void) const { + if ( !IsOpen ) + return 0; + return ( (BlockAddress << 16) | (BlockOffset & 0xFFFF) ); +} + +// writes the supplied data into the BGZF buffer +unsigned int BgzfStream::Write(const char* data, const unsigned int dataLen) { + + // skip if file not open for writing + if ( !IsOpen || !IsWriteOnly ) return false; + + // write blocks as needed til all data is written + unsigned int numBytesWritten = 0; + const char* input = data; + unsigned int blockLength = UncompressedBlockSize; + while ( numBytesWritten < dataLen ) { + + // copy data contents to uncompressed output buffer + unsigned int copyLength = min(blockLength - BlockOffset, dataLen - numBytesWritten); + char* buffer = UncompressedBlock; + memcpy(buffer + BlockOffset, input, copyLength); + + // update counter + BlockOffset += copyLength; + input += copyLength; + numBytesWritten += copyLength; + + // flush (& compress) output buffer when full + if ( BlockOffset == blockLength ) FlushBlock(); + } + + // return result + return numBytesWritten; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/BgzfStream_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,109 @@ +// *************************************************************************** +// BgzfStream_p.h (c) 2011 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 April 2011(DB) +// --------------------------------------------------------------------------- +// Based on BGZF routines developed at the Broad Institute. +// Provides the basic functionality for reading & writing BGZF files +// Replaces the old BGZF.* files to avoid clashing with other toolkits +// *************************************************************************** + +#ifndef BGZFSTREAM_P_H +#define BGZFSTREAM_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <api/BamAux.h> +#include <api/BamConstants.h> +#include "zlib.h" +#include <cstdio> +#include <string> + +namespace BamTools { +namespace Internal { + +class BgzfStream { + + // constructor & destructor + public: + BgzfStream(void); + ~BgzfStream(void); + + // main interface methods + public: + // closes BGZF file + void Close(void); + // opens the BGZF file (mode is either "rb" for reading, or "wb" for writing) + bool Open(const std::string& filename, const char* mode); + // reads BGZF data into a byte buffer + int Read(char* data, const unsigned int dataLength); + // seek to position in BGZF file + bool Seek(const int64_t& position); + // enable/disable compressed output + void SetWriteCompressed(bool ok); + // get file position in BGZF file + int64_t Tell(void) const; + // writes the supplied data into the BGZF buffer + unsigned int Write(const char* data, const unsigned int dataLen); + + // internal methods + private: + // compresses the current block + int DeflateBlock(void); + // flushes the data in the BGZF block + void FlushBlock(void); + // de-compresses the current block + int InflateBlock(const int& blockLength); + // reads a BGZF block + bool ReadBlock(void); + + // static 'utility' methods + public: + // checks BGZF block header + static inline bool CheckBlockHeader(char* header); + + // data members + public: + unsigned int UncompressedBlockSize; + unsigned int CompressedBlockSize; + unsigned int BlockLength; + unsigned int BlockOffset; + uint64_t BlockAddress; + bool IsOpen; + bool IsWriteOnly; + bool IsWriteCompressed; + FILE* Stream; + char* UncompressedBlock; + char* CompressedBlock; +}; + +// ------------------------------------------------------------- +// static 'utility' method implementations + +// checks BGZF block header +inline +bool BgzfStream::CheckBlockHeader(char* header) { + return (header[0] == Constants::GZIP_ID1 && + header[1] == (char)Constants::GZIP_ID2 && + header[2] == Z_DEFLATED && + (header[3] & Constants::FLG_FEXTRA) != 0 && + BamTools::UnpackUnsignedShort(&header[10]) == Constants::BGZF_XLEN && + header[12] == Constants::BGZF_ID1 && + header[13] == Constants::BGZF_ID2 && + BamTools::UnpackUnsignedShort(&header[14]) == Constants::BGZF_LEN ); +} + +} // namespace Internal +} // namespace BamTools + +#endif // BGZFSTREAM_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/SamFormatParser_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,231 @@ +// *************************************************************************** +// SamFormatParser.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides functionality for parsing SAM header text into SamHeader object +// *************************************************************************** + +#include <api/SamConstants.h> +#include <api/SamHeader.h> +#include <api/internal/SamFormatParser_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <iostream> +#include <sstream> +#include <vector> +using namespace std; + +SamFormatParser::SamFormatParser(SamHeader& header) + : m_header(header) +{ } + +SamFormatParser::~SamFormatParser(void) { } + +void SamFormatParser::Parse(const string& headerText) { + + // clear header's prior contents + m_header.Clear(); + + // empty header is OK, but skip processing + if ( headerText.empty() ) + return; + + // other wise parse SAM lines + istringstream headerStream(headerText); + string headerLine(""); + while ( getline(headerStream, headerLine) ) + ParseSamLine(headerLine); +} + +void SamFormatParser::ParseSamLine(const string& line) { + + // skip if line is not long enough to contain true values + if (line.length() < 5 ) return; + + // determine token at beginning of line + const string firstToken = line.substr(0,3); + string restOfLine = line.substr(4); + if ( firstToken == Constants::SAM_HD_BEGIN_TOKEN) ParseHDLine(restOfLine); + else if ( firstToken == Constants::SAM_SQ_BEGIN_TOKEN) ParseSQLine(restOfLine); + else if ( firstToken == Constants::SAM_RG_BEGIN_TOKEN) ParseRGLine(restOfLine); + else if ( firstToken == Constants::SAM_PG_BEGIN_TOKEN) ParsePGLine(restOfLine); + else if ( firstToken == Constants::SAM_CO_BEGIN_TOKEN) ParseCOLine(restOfLine); + else + cerr << "SamFormatParser ERROR: unknown token: " << firstToken << endl; +} + +void SamFormatParser::ParseHDLine(const string& line) { + + // split HD lines into tokens + vector<string> tokens = Split(line, Constants::SAM_TAB); + + // iterate over tokens + vector<string>::const_iterator tokenIter = tokens.begin(); + vector<string>::const_iterator tokenEnd = tokens.end(); + for ( ; tokenIter != tokenEnd; ++tokenIter ) { + + // get tag/value + const string tokenTag = (*tokenIter).substr(0,2); + const string tokenValue = (*tokenIter).substr(3); + + // set header contents + if ( tokenTag == Constants::SAM_HD_VERSION_TAG ) m_header.Version = tokenValue; + else if ( tokenTag == Constants::SAM_HD_SORTORDER_TAG ) m_header.SortOrder = tokenValue; + else if ( tokenTag == Constants::SAM_HD_GROUPORDER_TAG ) m_header.GroupOrder = tokenValue; + else + cerr << "SamFormatParser ERROR: unknown HD tag: " << tokenTag << endl; + } + + // if @HD line exists, VN must be provided + if ( !m_header.HasVersion() ) + cerr << "SamFormatParser ERROR: @HD line is missing VN tag" << endl; +} + +void SamFormatParser::ParseSQLine(const string& line) { + + SamSequence seq; + + // split SQ line into tokens + vector<string> tokens = Split(line, Constants::SAM_TAB); + + // iterate over tokens + vector<string>::const_iterator tokenIter = tokens.begin(); + vector<string>::const_iterator tokenEnd = tokens.end(); + for ( ; tokenIter != tokenEnd; ++tokenIter ) { + + // get tag/value + const string tokenTag = (*tokenIter).substr(0,2); + const string tokenValue = (*tokenIter).substr(3); + + // set sequence contents + if ( tokenTag == Constants::SAM_SQ_NAME_TAG ) seq.Name = tokenValue; + else if ( tokenTag == Constants::SAM_SQ_LENGTH_TAG ) seq.Length = tokenValue; + else if ( tokenTag == Constants::SAM_SQ_ASSEMBLYID_TAG ) seq.AssemblyID = tokenValue; + else if ( tokenTag == Constants::SAM_SQ_CHECKSUM_TAG ) seq.Checksum = tokenValue; + else if ( tokenTag == Constants::SAM_SQ_SPECIES_TAG ) seq.Species = tokenValue; + else if ( tokenTag == Constants::SAM_SQ_URI_TAG ) seq.URI = tokenValue; + else + cerr << "SamFormatParser ERROR: unknown SQ tag: " << tokenTag << endl; + } + + bool isMissingRequiredFields = false; + + // if @SQ line exists, SN must be provided + if ( !seq.HasName() ) { + isMissingRequiredFields = true; + cerr << "SamFormatParser ERROR: @SQ line is missing SN tag" << endl; + } + + // if @SQ line exists, LN must be provided + if ( !seq.HasLength() ) { + isMissingRequiredFields = true; + cerr << "SamFormatParser ERROR: @SQ line is missing LN tag" << endl; + } + + // store SAM sequence entry + if ( !isMissingRequiredFields ) + m_header.Sequences.Add(seq); +} + +void SamFormatParser::ParseRGLine(const string& line) { + + SamReadGroup rg; + + // split string into tokens + vector<string> tokens = Split(line, Constants::SAM_TAB); + + // iterate over tokens + vector<string>::const_iterator tokenIter = tokens.begin(); + vector<string>::const_iterator tokenEnd = tokens.end(); + for ( ; tokenIter != tokenEnd; ++tokenIter ) { + + // get token tag/value + const string tokenTag = (*tokenIter).substr(0,2); + const string tokenValue = (*tokenIter).substr(3); + + // set read group contents + if ( tokenTag == Constants::SAM_RG_ID_TAG ) rg.ID = tokenValue; + else if ( tokenTag == Constants::SAM_RG_DESCRIPTION_TAG ) rg.Description = tokenValue; + else if ( tokenTag == Constants::SAM_RG_FLOWORDER_TAG ) rg.FlowOrder = tokenValue; + else if ( tokenTag == Constants::SAM_RG_KEYSEQUENCE_TAG ) rg.KeySequence = tokenValue; + else if ( tokenTag == Constants::SAM_RG_LIBRARY_TAG ) rg.Library = tokenValue; + else if ( tokenTag == Constants::SAM_RG_PLATFORMUNIT_TAG ) rg.PlatformUnit = tokenValue; + else if ( tokenTag == Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG ) rg.PredictedInsertSize = tokenValue; + else if ( tokenTag == Constants::SAM_RG_PRODUCTIONDATE_TAG ) rg.ProductionDate = tokenValue; + else if ( tokenTag == Constants::SAM_RG_PROGRAM_TAG ) rg.Program = tokenValue; + else if ( tokenTag == Constants::SAM_RG_SAMPLE_TAG ) rg.Sample = tokenValue; + else if ( tokenTag == Constants::SAM_RG_SEQCENTER_TAG ) rg.SequencingCenter = tokenValue; + else if ( tokenTag == Constants::SAM_RG_SEQTECHNOLOGY_TAG ) rg.SequencingTechnology = tokenValue; + else + cerr << "SamFormatParser ERROR: unknown RG tag: " << tokenTag << endl; + } + + bool isMissingRequiredFields = false; + + // if @RG line exists, ID must be provided + if ( !rg.HasID() ) { + isMissingRequiredFields = true; + cerr << "SamFormatParser ERROR: @RG line is missing ID tag" << endl; + } + + // store SAM read group entry + if ( !isMissingRequiredFields ) + m_header.ReadGroups.Add(rg); +} + +void SamFormatParser::ParsePGLine(const string& line) { + + SamProgram pg; + + // split string into tokens + vector<string> tokens = Split(line, Constants::SAM_TAB); + + // iterate over tokens + vector<string>::const_iterator tokenIter = tokens.begin(); + vector<string>::const_iterator tokenEnd = tokens.end(); + for ( ; tokenIter != tokenEnd; ++tokenIter ) { + + // get token tag/value + const string tokenTag = (*tokenIter).substr(0,2); + const string tokenValue = (*tokenIter).substr(3); + + // set program record contents + if ( tokenTag == Constants::SAM_PG_ID_TAG ) pg.ID = tokenValue; + else if ( tokenTag == Constants::SAM_PG_NAME_TAG ) pg.Name = tokenValue; + else if ( tokenTag == Constants::SAM_PG_COMMANDLINE_TAG ) pg.CommandLine = tokenValue; + else if ( tokenTag == Constants::SAM_PG_PREVIOUSPROGRAM_TAG ) pg.PreviousProgramID = tokenValue; + else if ( tokenTag == Constants::SAM_PG_VERSION_TAG ) pg.Version = tokenValue; + else + cerr << "SamFormatParser ERROR: unknown PG tag: " << tokenTag << endl; + } + + bool isMissingRequiredFields = false; + + // if @PG line exists, ID must be provided + if ( !pg.HasID() ) { + isMissingRequiredFields = true; + cerr << "SamFormatParser ERROR: @PG line is missing ID tag" << endl; + } + + // store SAM program record + if ( !isMissingRequiredFields ) + m_header.Programs.Add(pg); +} + +void SamFormatParser::ParseCOLine(const string& line) { + // simply add line to comments list + m_header.Comments.push_back(line); +} + +const vector<string> SamFormatParser::Split(const string& line, const char delim) { + vector<string> tokens; + stringstream lineStream(line); + string token; + while ( getline(lineStream, token, delim) ) + tokens.push_back(token); + return tokens; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/SamFormatParser_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,62 @@ +// *************************************************************************** +// SamFormatParser.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 23 December 2010 (DB) +// --------------------------------------------------------------------------- +// Provides functionality for parsing SAM header text into SamHeader object +// *************************************************************************** + +#ifndef SAM_FORMAT_PARSER_H +#define SAM_FORMAT_PARSER_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <string> +#include <vector> + +namespace BamTools { + +class SamHeader; + +namespace Internal { + +class SamFormatParser { + + // ctor & dtor + public: + SamFormatParser(BamTools::SamHeader& header); + ~SamFormatParser(void); + + // parse text & populate header data + public: + void Parse(const std::string& headerText); + + // internal methods + private: + void ParseSamLine(const std::string& line); + void ParseHDLine(const std::string& line); + void ParseSQLine(const std::string& line); + void ParseRGLine(const std::string& line); + void ParsePGLine(const std::string& line); + void ParseCOLine(const std::string& line); + const std::vector<std::string> Split(const std::string& line, const char delim); + + // data members + private: + SamHeader& m_header; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // SAM_FORMAT_PARSER_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/SamFormatPrinter_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,211 @@ +// *************************************************************************** +// SamFormatPrinter.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides functionality for printing formatted SAM header to string +// *************************************************************************** + +#include <api/SamConstants.h> +#include <api/SamHeader.h> +#include <api/internal/SamFormatPrinter_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <iostream> +#include <sstream> +#include <vector> +using namespace std; + +SamFormatPrinter::SamFormatPrinter(const SamHeader& header) + : m_header(header) +{ } + +SamFormatPrinter::~SamFormatPrinter(void) { } + +const string SamFormatPrinter::FormatTag(const string &tag, const string &value) const { + return string(Constants::SAM_TAB + tag + Constants::SAM_COLON + value); +} + +const string SamFormatPrinter::ToString(void) const { + + // clear out stream + stringstream out(""); + + // generate formatted header text + PrintHD(out); + PrintSQ(out); + PrintRG(out); + PrintPG(out); + PrintCO(out); + + // return result + return out.str(); +} + +void SamFormatPrinter::PrintHD(std::stringstream& out) const { + + // if header has @HD data + if ( m_header.HasVersion() ) { + + // @HD VN:<Version> + out << Constants::SAM_HD_BEGIN_TOKEN + << FormatTag(Constants::SAM_HD_VERSION_TAG, m_header.Version); + + // SO:<SortOrder> + if ( m_header.HasSortOrder() ) + out << FormatTag(Constants::SAM_HD_SORTORDER_TAG, m_header.SortOrder); + + // GO:<GroupOrder> + if ( m_header.HasGroupOrder() ) + out << FormatTag(Constants::SAM_HD_GROUPORDER_TAG, m_header.GroupOrder); + + // newline + out << endl; + } +} + +void SamFormatPrinter::PrintSQ(std::stringstream& out) const { + + // iterate over sequence entries + SamSequenceConstIterator seqIter = m_header.Sequences.ConstBegin(); + SamSequenceConstIterator seqEnd = m_header.Sequences.ConstEnd(); + for ( ; seqIter != seqEnd; ++seqIter ) { + const SamSequence& seq = (*seqIter); + + // @SQ SN:<Name> LN:<Length> + out << Constants::SAM_SQ_BEGIN_TOKEN + << FormatTag(Constants::SAM_SQ_NAME_TAG, seq.Name) + << FormatTag(Constants::SAM_SQ_LENGTH_TAG, seq.Length); + + // AS:<AssemblyID> + if ( seq.HasAssemblyID() ) + out << FormatTag(Constants::SAM_SQ_ASSEMBLYID_TAG, seq.AssemblyID); + + // M5:<Checksum> + if ( seq.HasChecksum() ) + out << FormatTag(Constants::SAM_SQ_CHECKSUM_TAG, seq.Checksum); + + // SP:<Species> + if ( seq.HasSpecies() ) + out << FormatTag(Constants::SAM_SQ_SPECIES_TAG, seq.Species); + + // UR:<URI> + if ( seq.HasURI() ) + out << FormatTag(Constants::SAM_SQ_URI_TAG, seq.URI); + + // newline + out << endl; + } +} + +void SamFormatPrinter::PrintRG(std::stringstream& out) const { + + // iterate over read group entries + SamReadGroupConstIterator rgIter = m_header.ReadGroups.ConstBegin(); + SamReadGroupConstIterator rgEnd = m_header.ReadGroups.ConstEnd(); + for ( ; rgIter != rgEnd; ++rgIter ) { + const SamReadGroup& rg = (*rgIter); + + // @RG ID:<ID> + out << Constants::SAM_RG_BEGIN_TOKEN + << FormatTag(Constants::SAM_RG_ID_TAG, rg.ID); + + // CN:<SequencingCenter> + if ( rg.HasSequencingCenter() ) + out << FormatTag(Constants::SAM_RG_SEQCENTER_TAG, rg.SequencingCenter); + + // DS:<Description> + if ( rg.HasDescription() ) + out << FormatTag(Constants::SAM_RG_DESCRIPTION_TAG, rg.Description); + + // DT:<ProductionDate> + if ( rg.HasProductionDate() ) + out << FormatTag(Constants::SAM_RG_PRODUCTIONDATE_TAG, rg.ProductionDate); + + // FO:<FlowOrder> + if ( rg.HasFlowOrder() ) + out << FormatTag(Constants::SAM_RG_FLOWORDER_TAG, rg.FlowOrder); + + // KS:<KeySequence> + if ( rg.HasKeySequence() ) + out << FormatTag(Constants::SAM_RG_KEYSEQUENCE_TAG, rg.KeySequence); + + // LB:<Library> + if ( rg.HasLibrary() ) + out << FormatTag(Constants::SAM_RG_LIBRARY_TAG, rg.Library); + + // PG:<Program> + if ( rg.HasProgram() ) + out << FormatTag(Constants::SAM_RG_PROGRAM_TAG, rg.Program); + + // PI:<PredictedInsertSize> + if ( rg.HasPredictedInsertSize() ) + out << FormatTag(Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG, rg.PredictedInsertSize); + + // PL:<SequencingTechnology> + if ( rg.HasSequencingTechnology() ) + out << FormatTag(Constants::SAM_RG_SEQTECHNOLOGY_TAG, rg.SequencingTechnology); + + // PU:<PlatformUnit> + if ( rg.HasPlatformUnit() ) + out << FormatTag(Constants::SAM_RG_PLATFORMUNIT_TAG, rg.PlatformUnit); + + // SM:<Sample> + if ( rg.HasSample() ) + out << FormatTag(Constants::SAM_RG_SAMPLE_TAG, rg.Sample); + + // newline + out << endl; + } +} + +void SamFormatPrinter::PrintPG(std::stringstream& out) const { + + // iterate over program record entries + SamProgramConstIterator pgIter = m_header.Programs.ConstBegin(); + SamProgramConstIterator pgEnd = m_header.Programs.ConstEnd(); + for ( ; pgIter != pgEnd; ++pgIter ) { + const SamProgram& pg = (*pgIter); + + // @PG ID:<ID> + out << Constants::SAM_PG_BEGIN_TOKEN + << FormatTag(Constants::SAM_PG_ID_TAG, pg.ID); + + // PN:<Name> + if ( pg.HasName() ) + out << FormatTag(Constants::SAM_PG_NAME_TAG, pg.Name); + + // CL:<CommandLine> + if ( pg.HasCommandLine() ) + out << FormatTag(Constants::SAM_PG_COMMANDLINE_TAG, pg.CommandLine); + + // PP:<PreviousProgramID> + if ( pg.HasPreviousProgramID() ) + out << FormatTag(Constants::SAM_PG_PREVIOUSPROGRAM_TAG, pg.PreviousProgramID); + + // VN:<Version> + if ( pg.HasVersion() ) + out << FormatTag(Constants::SAM_PG_VERSION_TAG, pg.Version); + + // newline + out << endl; + } +} + +void SamFormatPrinter::PrintCO(std::stringstream& out) const { + + // iterate over comments + vector<string>::const_iterator commentIter = m_header.Comments.begin(); + vector<string>::const_iterator commentEnd = m_header.Comments.end(); + for ( ; commentIter != commentEnd; ++commentIter ) { + + // @CO <Comment> + out << Constants::SAM_CO_BEGIN_TOKEN + << Constants::SAM_TAB + << (*commentIter) + << endl; + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/SamFormatPrinter_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,61 @@ +// *************************************************************************** +// SamFormatPrinter.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 23 December 2010 (DB) +// --------------------------------------------------------------------------- +// Provides functionality for printing formatted SAM header to string +// *************************************************************************** + +#ifndef SAM_FORMAT_PRINTER_H +#define SAM_FORMAT_PRINTER_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <sstream> +#include <string> + +namespace BamTools { + +class SamHeader; + +namespace Internal { + +class SamFormatPrinter { + + // ctor & dtor + public: + SamFormatPrinter(const BamTools::SamHeader& header); + ~SamFormatPrinter(void); + + // generates SAM-formatted string from header data + public: + const std::string ToString(void) const; + + // internal methods + private: + const std::string FormatTag(const std::string& tag, const std::string& value) const; + void PrintHD(std::stringstream& out) const; + void PrintSQ(std::stringstream& out) const; + void PrintRG(std::stringstream& out) const; + void PrintPG(std::stringstream& out) const; + void PrintCO(std::stringstream& out) const; + + // data members + private: + const SamHeader& m_header; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // SAM_FORMAT_PRINTER_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/SamHeaderValidator_p.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,511 @@ +// *************************************************************************** +// SamHeaderValidator.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 18 April 2011 (DB) +// --------------------------------------------------------------------------- +// Provides functionality for validating SamHeader data +// *************************************************************************** + +#include <api/SamConstants.h> +#include <api/SamHeader.h> +#include <api/internal/SamHeaderValidator_p.h> +#include <api/internal/SamHeaderVersion_p.h> +using namespace BamTools; +using namespace BamTools::Internal; + +#include <cctype> +#include <iostream> +#include <set> +#include <sstream> +using namespace std; + +namespace BamTools { +namespace Internal { + +bool caseInsensitiveCompare(const string& lhs, const string& rhs) { + + // can omit checking chars if lengths not equal + const int lhsLength = lhs.length(); + const int rhsLength = rhs.length(); + if ( lhsLength != rhsLength ) + return false; + + // do *basic* toupper checks on each string char's + for ( int i = 0; i < lhsLength; ++i ) { + if ( toupper( (int)lhs.at(i)) != toupper( (int)rhs.at(i)) ) + return false; + } + + // otherwise OK + return true; +} + +} // namespace Internal +} // namespace BamTools + +// ------------------------------------------------------------------------ +// Allow validation rules to vary, as needed, between SAM header versions +// +// use SAM_VERSION_X_Y to tag important changes +// +// Together, they will allow for comparisons like: +// if ( m_version < SAM_VERSION_2_0 ) { +// // use some older rule +// else +// // use rule introduced with version 2.0 + +static const SamHeaderVersion SAM_VERSION_1_0 = SamHeaderVersion(1,0); +static const SamHeaderVersion SAM_VERSION_1_1 = SamHeaderVersion(1,1); +static const SamHeaderVersion SAM_VERSION_1_2 = SamHeaderVersion(1,2); +static const SamHeaderVersion SAM_VERSION_1_3 = SamHeaderVersion(1,3); +static const SamHeaderVersion SAM_VERSION_1_4 = SamHeaderVersion(1,4); + +// TODO: This functionality is currently unused. +// Make validation "version-aware." +// +// ------------------------------------------------------------------------ + +const string SamHeaderValidator::ERROR_PREFIX = "ERROR: "; +const string SamHeaderValidator::WARN_PREFIX = "WARNING: "; +const string SamHeaderValidator::NEWLINE = "\n"; + +SamHeaderValidator::SamHeaderValidator(const SamHeader& header) + : m_header(header) +{ } + +SamHeaderValidator::~SamHeaderValidator(void) { } + +bool SamHeaderValidator::Validate(bool verbose) { + + // validate header components + bool isValid = true; + isValid &= ValidateMetadata(); + isValid &= ValidateSequenceDictionary(); + isValid &= ValidateReadGroupDictionary(); + isValid &= ValidateProgramChain(); + + // report errors if desired + if ( verbose ) { + PrintErrorMessages(); + PrintWarningMessages(); + } + + // return validation status + return isValid; +} + +bool SamHeaderValidator::ValidateMetadata(void) { + bool isValid = true; + isValid &= ValidateVersion(); + isValid &= ValidateSortOrder(); + isValid &= ValidateGroupOrder(); + return isValid; +} + +bool SamHeaderValidator::ValidateVersion(void) { + + const string& version = m_header.Version; + + // warn if version not present + if ( version.empty() ) { + AddWarning("Version (VN) missing. Not required, but strongly recommended"); + return true; + } + + // invalid if version does not contain a period + const size_t periodFound = version.find(Constants::SAM_PERIOD); + if ( periodFound == string::npos ) { + AddError("Invalid version (VN) format: " + version); + return false; + } + + // invalid if major version is empty or contains non-digits + const string majorVersion = version.substr(0, periodFound); + if ( majorVersion.empty() || !ContainsOnlyDigits(majorVersion) ) { + AddError("Invalid version (VN) format: " + version); + return false; + } + + // invalid if major version is empty or contains non-digits + const string minorVersion = version.substr(periodFound + 1); + if ( minorVersion.empty() || !ContainsOnlyDigits(minorVersion) ) { + AddError("Invalid version (VN) format: " + version); + return false; + } + + // TODO: check if version is not just syntactically OK, + // but is also a valid SAM version ( 1.0 .. CURRENT ) + + // all checked out this far, then version is OK + return true; +} + +// assumes non-empty input string +bool SamHeaderValidator::ContainsOnlyDigits(const string& s) { + const size_t nonDigitPosition = s.find_first_not_of(Constants::SAM_DIGITS); + return ( nonDigitPosition == string::npos ) ; +} + +bool SamHeaderValidator::ValidateSortOrder(void) { + + const string& sortOrder = m_header.SortOrder; + + // warn if sort order not present + if ( sortOrder.empty() ) { + AddWarning("Sort order (SO) missing. Not required, but strongly recommended"); + return true; + } + + // if sort order is valid keyword + if ( sortOrder == Constants::SAM_HD_SORTORDER_COORDINATE || + sortOrder == Constants::SAM_HD_SORTORDER_QUERYNAME || + sortOrder == Constants::SAM_HD_SORTORDER_UNSORTED + ) + { + return true; + } + + // otherwise + AddError("Invalid sort order (SO): " + sortOrder); + return false; +} + +bool SamHeaderValidator::ValidateGroupOrder(void) { + + const string& groupOrder = m_header.GroupOrder; + + // if no group order, no problem, just return OK + if ( groupOrder.empty() ) + return true; + + // if group order is valid keyword + if ( groupOrder == Constants::SAM_HD_GROUPORDER_NONE || + groupOrder == Constants::SAM_HD_GROUPORDER_QUERY || + groupOrder == Constants::SAM_HD_GROUPORDER_REFERENCE + ) + { + return true; + } + + // otherwise + AddError("Invalid group order (GO): " + groupOrder); + return false; +} + +bool SamHeaderValidator::ValidateSequenceDictionary(void) { + + bool isValid = true; + + // check for unique sequence names + isValid &= ContainsUniqueSequenceNames(); + + // iterate over sequences + const SamSequenceDictionary& sequences = m_header.Sequences; + SamSequenceConstIterator seqIter = sequences.ConstBegin(); + SamSequenceConstIterator seqEnd = sequences.ConstEnd(); + for ( ; seqIter != seqEnd; ++seqIter ) { + const SamSequence& seq = (*seqIter); + isValid &= ValidateSequence(seq); + } + + // return validation state + return isValid; +} + +bool SamHeaderValidator::ContainsUniqueSequenceNames(void) { + + bool isValid = true; + set<string> sequenceNames; + set<string>::iterator nameIter; + + // iterate over sequences + const SamSequenceDictionary& sequences = m_header.Sequences; + SamSequenceConstIterator seqIter = sequences.ConstBegin(); + SamSequenceConstIterator seqEnd = sequences.ConstEnd(); + for ( ; seqIter != seqEnd; ++seqIter ) { + const SamSequence& seq = (*seqIter); + + // lookup sequence name + const string& name = seq.Name; + nameIter = sequenceNames.find(name); + + // error if found (duplicate entry) + if ( nameIter != sequenceNames.end() ) { + AddError("Sequence name (SN): " + name + " is not unique"); + isValid = false; + } + + // otherwise ok, store name + sequenceNames.insert(name); + } + + // return validation state + return isValid; +} + +bool SamHeaderValidator::ValidateSequence(const SamSequence& seq) { + bool isValid = true; + isValid &= CheckNameFormat(seq.Name); + isValid &= CheckLengthInRange(seq.Length); + return isValid; +} + +bool SamHeaderValidator::CheckNameFormat(const string& name) { + + // invalid if name is empty + if ( name.empty() ) { + AddError("Sequence entry (@SQ) is missing SN tag"); + return false; + } + + // invalid if first character is a reserved char + const char firstChar = name.at(0); + if ( firstChar == Constants::SAM_EQUAL || firstChar == Constants::SAM_STAR ) { + AddError("Invalid sequence name (SN): " + name); + return false; + } + // otherwise OK + return true; +} + +bool SamHeaderValidator::CheckLengthInRange(const string& length) { + + // invalid if empty + if ( length.empty() ) { + AddError("Sequence entry (@SQ) is missing LN tag"); + return false; + } + + // convert string length to numeric + stringstream lengthStream(length); + unsigned int sequenceLength; + lengthStream >> sequenceLength; + + // invalid if length outside accepted range + if ( sequenceLength < Constants::SAM_SQ_LENGTH_MIN || sequenceLength > Constants::SAM_SQ_LENGTH_MAX ) { + AddError("Sequence length (LN): " + length + " out of range"); + return false; + } + + // otherwise OK + return true; +} + +bool SamHeaderValidator::ValidateReadGroupDictionary(void) { + + bool isValid = true; + + // check for unique read group IDs & platform units + isValid &= ContainsUniqueIDsAndPlatformUnits(); + + // iterate over read groups + const SamReadGroupDictionary& readGroups = m_header.ReadGroups; + SamReadGroupConstIterator rgIter = readGroups.ConstBegin(); + SamReadGroupConstIterator rgEnd = readGroups.ConstEnd(); + for ( ; rgIter != rgEnd; ++rgIter ) { + const SamReadGroup& rg = (*rgIter); + isValid &= ValidateReadGroup(rg); + } + + // return validation state + return isValid; +} + +bool SamHeaderValidator::ContainsUniqueIDsAndPlatformUnits(void) { + + bool isValid = true; + set<string> readGroupIds; + set<string> platformUnits; + set<string>::iterator idIter; + set<string>::iterator puIter; + + // iterate over sequences + const SamReadGroupDictionary& readGroups = m_header.ReadGroups; + SamReadGroupConstIterator rgIter = readGroups.ConstBegin(); + SamReadGroupConstIterator rgEnd = readGroups.ConstEnd(); + for ( ; rgIter != rgEnd; ++rgIter ) { + const SamReadGroup& rg = (*rgIter); + + // -------------------------------- + // check for unique ID + + // lookup read group ID + const string& id = rg.ID; + idIter = readGroupIds.find(id); + + // error if found (duplicate entry) + if ( idIter != readGroupIds.end() ) { + AddError("Read group ID (ID): " + id + " is not unique"); + isValid = false; + } + + // otherwise ok, store id + readGroupIds.insert(id); + + // -------------------------------- + // check for unique platform unit + + // lookup platform unit + const string& pu = rg.PlatformUnit; + puIter = platformUnits.find(pu); + + // error if found (duplicate entry) + if ( puIter != platformUnits.end() ) { + AddError("Platform unit (PU): " + pu + " is not unique"); + isValid = false; + } + + // otherwise ok, store platform unit + platformUnits.insert(pu); + } + + // return validation state + return isValid; +} + +bool SamHeaderValidator::ValidateReadGroup(const SamReadGroup& rg) { + bool isValid = true; + isValid &= CheckReadGroupID(rg.ID); + isValid &= CheckSequencingTechnology(rg.SequencingTechnology); + return isValid; +} + +bool SamHeaderValidator::CheckReadGroupID(const string& id) { + + // invalid if empty + if ( id.empty() ) { + AddError("Read group entry (@RG) is missing ID tag"); + return false; + } + + // otherwise OK + return true; +} + +bool SamHeaderValidator::CheckSequencingTechnology(const string& technology) { + + // if no technology provided, no problem, just return OK + if ( technology.empty() ) + return true; + + // if technology is valid keyword + if ( caseInsensitiveCompare(technology, Constants::SAM_RG_SEQTECHNOLOGY_CAPILLARY) || + caseInsensitiveCompare(technology, Constants::SAM_RG_SEQTECHNOLOGY_HELICOS) || + caseInsensitiveCompare(technology, Constants::SAM_RG_SEQTECHNOLOGY_ILLUMINA) || + caseInsensitiveCompare(technology, Constants::SAM_RG_SEQTECHNOLOGY_IONTORRENT) || + caseInsensitiveCompare(technology, Constants::SAM_RG_SEQTECHNOLOGY_LS454) || + caseInsensitiveCompare(technology, Constants::SAM_RG_SEQTECHNOLOGY_PACBIO) || + caseInsensitiveCompare(technology, Constants::SAM_RG_SEQTECHNOLOGY_SOLID) + ) + { + return true; + } + + // otherwise + AddError("Invalid read group sequencing platform (PL): " + technology); + return false; +} + +bool SamHeaderValidator::ValidateProgramChain(void) { + bool isValid = true; + isValid &= ContainsUniqueProgramIds(); + isValid &= ValidatePreviousProgramIds(); + return isValid; +} + +bool SamHeaderValidator::ContainsUniqueProgramIds(void) { + + bool isValid = true; + set<string> programIds; + set<string>::iterator pgIdIter; + + // iterate over program records + const SamProgramChain& programs = m_header.Programs; + SamProgramConstIterator pgIter = programs.ConstBegin(); + SamProgramConstIterator pgEnd = programs.ConstEnd(); + for ( ; pgIter != pgEnd; ++pgIter ) { + const SamProgram& pg = (*pgIter); + + // lookup program ID + const string& pgId = pg.ID; + pgIdIter = programIds.find(pgId); + + // error if found (duplicate entry) + if ( pgIdIter != programIds.end() ) { + AddError("Program ID (ID): " + pgId + " is not unique"); + isValid = false; + } + + // otherwise ok, store ID + programIds.insert(pgId); + } + + // return validation state + return isValid; +} + +bool SamHeaderValidator::ValidatePreviousProgramIds(void) { + + bool isValid = true; + + // iterate over program records + const SamProgramChain& programs = m_header.Programs; + SamProgramConstIterator pgIter = programs.ConstBegin(); + SamProgramConstIterator pgEnd = programs.ConstEnd(); + for ( ; pgIter != pgEnd; ++pgIter ) { + const SamProgram& pg = (*pgIter); + + // ignore record for validation if PreviousProgramID is empty + const string& ppId = pg.PreviousProgramID; + if ( ppId.empty() ) + continue; + + // see if program "chain" contains an entry for ppId + if ( !programs.Contains(ppId) ) { + AddError("PreviousProgramID (PP): " + ppId + " is not a known ID"); + isValid = false; + } + } + + // return validation state + return isValid; +} +void SamHeaderValidator::AddError(const string& message) { + m_errorMessages.push_back(ERROR_PREFIX + message + NEWLINE); +} + +void SamHeaderValidator::AddWarning(const string& message) { + m_warningMessages.push_back(WARN_PREFIX + message + NEWLINE); +} + +void SamHeaderValidator::PrintErrorMessages(void) { + + // skip if no error messages + if ( m_errorMessages.empty() ) return; + + // print error header line + cerr << "* SAM header has " << m_errorMessages.size() << " errors:" << endl; + + // print each error message + vector<string>::const_iterator errorIter = m_errorMessages.begin(); + vector<string>::const_iterator errorEnd = m_errorMessages.end(); + for ( ; errorIter != errorEnd; ++errorIter ) + cerr << (*errorIter); +} + +void SamHeaderValidator::PrintWarningMessages(void) { + + // skip if no warning messages + if ( m_warningMessages.empty() ) return; + + // print warning header line + cerr << "* SAM header has " << m_warningMessages.size() << " warnings:" << endl; + + // print each warning message + vector<string>::const_iterator warnIter = m_warningMessages.begin(); + vector<string>::const_iterator warnEnd = m_warningMessages.end(); + for ( ; warnIter != warnEnd; ++warnIter ) + cerr << (*warnIter); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/SamHeaderValidator_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,102 @@ +// *************************************************************************** +// SamHeaderValidator.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 13 January 2011 (DB) +// --------------------------------------------------------------------------- +// Provides functionality for validating SamHeader data +// *************************************************************************** + +#ifndef SAM_HEADER_VALIDATOR_P_H +#define SAM_HEADER_VALIDATOR_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <string> +#include <vector> + +namespace BamTools { + +class SamHeader; +class SamReadGroup; +class SamSequence; + +namespace Internal { + +class SamHeaderValidator { + + // ctor & dtor + public: + SamHeaderValidator(const SamHeader& header); + ~SamHeaderValidator(void); + + // SamHeaderValidator interface + public: + // validates SamHeader data, returns true/false accordingly + // prints error & warning messages to stderr when @verbose is true + bool Validate(bool verbose = false); + + // internal methods + private: + + // validate header metadata + bool ValidateMetadata(void); + bool ValidateVersion(void); + bool ContainsOnlyDigits(const std::string& s); + bool ValidateSortOrder(void); + bool ValidateGroupOrder(void); + + // validate sequence dictionary + bool ValidateSequenceDictionary(void); + bool ContainsUniqueSequenceNames(void); + bool CheckNameFormat(const std::string& name); + bool ValidateSequence(const SamSequence& seq); + bool CheckLengthInRange(const std::string& length); + + // validate read group dictionary + bool ValidateReadGroupDictionary(void); + bool ContainsUniqueIDsAndPlatformUnits(void); + bool ValidateReadGroup(const SamReadGroup& rg); + bool CheckReadGroupID(const std::string& id); + bool CheckSequencingTechnology(const std::string& technology); + + // validate program data + bool ValidateProgramChain(void); + bool ContainsUniqueProgramIds(void); + bool ValidatePreviousProgramIds(void); + + // error reporting + void AddError(const std::string& message); + void AddWarning(const std::string& message); + void PrintErrorMessages(void); + void PrintWarningMessages(void); + + // data members + private: + + // SamHeader being validated + const SamHeader& m_header; + + // error reporting helpers + static const std::string ERROR_PREFIX; + static const std::string WARN_PREFIX; + static const std::string NEWLINE; + + // error reporting messages + std::vector<std::string> m_errorMessages; + std::vector<std::string> m_warningMessages; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // SAM_HEADER_VALIDATOR_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/api/internal/SamHeaderVersion_p.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,135 @@ +// *************************************************************************** +// SamHeaderVersion.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 24 February 2011 (DB) +// --------------------------------------------------------------------------- +// Provides functionality for comparing SAM header versions +// ************************************************************************* + +#ifndef SAM_HEADERVERSION_P_H +#define SAM_HEADERVERSION_P_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to version +// without notice, or even be removed. +// +// We mean it. + +#include <api/SamConstants.h> +#include <sstream> +#include <string> + +namespace BamTools { +namespace Internal { + +class SamHeaderVersion { + + // ctors & dtor + public: + SamHeaderVersion(void) + : m_majorVersion(0) + , m_minorVersion(0) + { } + + explicit SamHeaderVersion(const std::string& version) + : m_majorVersion(0) + , m_minorVersion(0) + { + SetVersion(version); + } + + SamHeaderVersion(const unsigned int& major, const unsigned int& minor) + : m_majorVersion(major) + , m_minorVersion(minor) + { } + + ~SamHeaderVersion(void) { + m_majorVersion = 0; + m_minorVersion = 0; + } + + // acess data + public: + unsigned int MajorVersion(void) const { return m_majorVersion; } + unsigned int MinorVersion(void) const { return m_minorVersion; } + + void SetVersion(const std::string& version); + std::string ToString(void) const; + + // data members + private: + unsigned int m_majorVersion; + unsigned int m_minorVersion; +}; + +inline +void SamHeaderVersion::SetVersion(const std::string& version) { + + // do nothing if version is empty + if ( !version.empty() ) { + + std::stringstream versionStream(""); + + // do nothing if period not found + const size_t periodFound = version.find(Constants::SAM_PERIOD); + if ( periodFound != std::string::npos ) { + + // store major version if non-empty and contains only digits + const std::string& majorVersion = version.substr(0, periodFound); + versionStream.str(majorVersion); + if ( !majorVersion.empty() ) { + const size_t nonDigitFound = majorVersion.find_first_not_of(Constants::SAM_DIGITS); + if ( nonDigitFound == std::string::npos ) + versionStream >> m_majorVersion; + } + + // store minor version if non-empty and contains only digits + const std::string& minorVersion = version.substr(periodFound + 1); + versionStream.str(minorVersion); + if ( !minorVersion.empty() ) { + const size_t nonDigitFound = minorVersion.find_first_not_of(Constants::SAM_DIGITS); + if ( nonDigitFound == std::string::npos ) + versionStream >> m_minorVersion; + } + } + } +} + +// ----------------------------------------------------- +// printing + +inline std::string SamHeaderVersion::ToString(void) const { + std::stringstream version; + version << m_majorVersion << Constants::SAM_PERIOD << m_minorVersion; + return version.str(); +} + +// ----------------------------------------------------- +// comparison operators + +inline bool operator==(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { + return (lhs.MajorVersion() == rhs.MajorVersion()) && + (lhs.MinorVersion() == rhs.MinorVersion()); +} + +inline bool operator<(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { + if ( lhs.MajorVersion() == rhs.MajorVersion() ) + return lhs.MinorVersion() < rhs.MinorVersion(); + else + return lhs.MajorVersion() < rhs.MajorVersion(); +} + +inline bool operator> (const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { return rhs < lhs; } +inline bool operator<=(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { return !(lhs>rhs); } +inline bool operator>=(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { return !(lhs<rhs); } + +} // namespace Internal +} // namespace BamTools + +#endif // SAM_HEADERVERSION_P_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/BamTools/src/shared/bamtools_global.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,79 @@ +// *************************************************************************** +// bamtools_global.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 3 March 2011 (DB) +// --------------------------------------------------------------------------- +// Provides the basic definitions for exporting & importing library symbols. +// Also provides some platform-specific rules for definitions. +// *************************************************************************** + +#ifndef BAMTOOLS_GLOBAL_H +#define BAMTOOLS_GLOBAL_H + +/*! \brief Library export macro + \internal +*/ +#ifndef BAMTOOLS_LIBRARY_EXPORT +# if defined(WIN32) +# define BAMTOOLS_LIBRARY_EXPORT __declspec(dllexport) +# else +# define BAMTOOLS_LIBRARY_EXPORT __attribute__((visibility("default"))) +# endif +#endif // BAMTOOLS_LIBRARY_EXPORT + +/*! \brief Library import macro + \internal +*/ +#ifndef BAMTOOLS_LIBRARY_IMPORT +# if defined(WIN32) +# define BAMTOOLS_LIBRARY_IMPORT __declspec(dllimport) +# else +# define BAMTOOLS_LIBRARY_IMPORT +# endif +#endif // BAMTOOLS_LIBRARY_IMPORT + +/*! \brief Platform-specific type definitions + \internal +*/ +#ifndef BAMTOOLS_LFS +#define BAMTOOLS_LFS + #ifdef WIN32 + #define ftell64(a) _ftelli64(a) + #define fseek64(a,b,c) _fseeki64(a,b,c) + #else + #define ftell64(a) ftello(a) + #define fseek64(a,b,c) fseeko(a,b,c) + #endif +#endif // BAMTOOLS_LFS + +/*! \def ftell64(a) + \brief Platform-independent tell() operation. + \internal +*/ +/*! \def fseek64(a,b,c) + \brief Platform-independent seek() operation. + \internal +*/ + +/*! \brief Platform-specific type definitions + \internal +*/ +#ifndef BAMTOOLS_TYPES +#define BAMTOOLS_TYPES + #ifdef _MSC_VER + typedef char int8_t; + typedef unsigned char uint8_t; + typedef short int16_t; + typedef unsigned short uint16_t; + typedef int int32_t; + typedef unsigned int uint32_t; + typedef long long int64_t; + typedef unsigned long long uint64_t; + #else + #include <stdint.h> + #endif +#endif // BAMTOOLS_TYPES + +#endif // BAMTOOLS_GLOBAL_H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/Fasta/Fasta.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,325 @@ +// *************************************************************************** +// FastaIndex.cpp (c) 2010 Erik Garrison <erik.garrison@bc.edu> +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 9 February 2010 (EG) +// --------------------------------------------------------------------------- + +#include "Fasta.h" + +FastaIndexEntry::FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len) + : name(name) + , length(length) + , offset(offset) + , line_blen(line_blen) + , line_len(line_len) +{} + +FastaIndexEntry::FastaIndexEntry(void) // empty constructor +{ clear(); } + +FastaIndexEntry::~FastaIndexEntry(void) +{} + +void FastaIndexEntry::clear(void) +{ + name = ""; + length = NULL; + offset = -1; // no real offset will ever be below 0, so this allows us to + // check if we have already recorded a real offset + line_blen = NULL; + line_len = NULL; +} + +ostream& operator<<(ostream& output, const FastaIndexEntry& e) { + // just write the first component of the name, for compliance with other tools + output << split(e.name, ' ').at(0) << "\t" << e.length << "\t" << e.offset << "\t" << + e.line_blen << "\t" << e.line_len; + return output; // for multiple << operators. +} + +FastaIndex::FastaIndex(void) +{} + +void FastaIndex::readIndexFile(string fname) { + string line; + long long linenum = 0; + indexFile.open(fname.c_str(), ifstream::in); + if (indexFile.is_open()) { + while (getline (indexFile, line)) { + ++linenum; + // the fai format defined in samtools is tab-delimited, every line being: + // fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len + vector<string> fields = split(line, '\t'); + if (fields.size() == 5) { // if we don't get enough fields then there is a problem with the file + // note that fields[0] is the sequence name + char* end; + string name = split(fields[0], " \t").at(0); // key by first token of name + sequenceNames.push_back(name); + this->insert(make_pair(name, FastaIndexEntry(fields[0], atoi(fields[1].c_str()), + strtoll(fields[2].c_str(), &end, 10), + atoi(fields[3].c_str()), + atoi(fields[4].c_str())))); + } else { + cerr << "Warning: malformed fasta index file " << fname << + "does not have enough fields @ line " << linenum << endl; + cerr << line << endl; + exit(1); + } + } + } else { + cerr << "could not open index file " << fname << endl; + exit(1); + } +} + +// for consistency this should be a class method +bool fastaIndexEntryCompare ( FastaIndexEntry a, FastaIndexEntry b) { return (a.offset<b.offset); } + +ostream& operator<<(ostream& output, FastaIndex& fastaIndex) { + vector<FastaIndexEntry> sortedIndex; + for(vector<string>::const_iterator it = fastaIndex.sequenceNames.begin(); it != fastaIndex.sequenceNames.end(); ++it) + { + sortedIndex.push_back(fastaIndex[*it]); + } + sort(sortedIndex.begin(), sortedIndex.end(), fastaIndexEntryCompare); + for( vector<FastaIndexEntry>::iterator fit = sortedIndex.begin(); fit != sortedIndex.end(); ++fit) { + output << *fit << endl; + } + return output; +} + +void FastaIndex::indexReference(string refname) { + // overview: + // for line in the reference fasta file + // track byte offset from the start of the file + // if line is a fasta header, take the name and dump the last sequnece to the index + // if line is a sequence, add it to the current sequence + //cerr << "indexing fasta reference " << refname << endl; + string line; + FastaIndexEntry entry; // an entry buffer used in processing + entry.clear(); + int line_length = 0; + long long offset = 0; // byte offset from start of file + long long line_number = 0; // current line number + bool mismatchedLineLengths = false; // flag to indicate if our line length changes mid-file + // this will be used to raise an error + // if we have a line length change at + // any line other than the last line in + // the sequence + bool emptyLine = false; // flag to catch empty lines, which we allow for + // index generation only on the last line of the sequence + ifstream refFile; + refFile.open(refname.c_str()); + if (refFile.is_open()) { + while (getline(refFile, line)) { + ++line_number; + line_length = line.length(); + if (line[0] == ';') { + // fasta comment, skip + } else if (line[0] == '+') { + // fastq quality header + getline(refFile, line); + line_length = line.length(); + offset += line_length + 1; + // get and don't handle the quality line + getline(refFile, line); + line_length = line.length(); + } else if (line[0] == '>' || line[0] == '@') { // fasta /fastq header + // if we aren't on the first entry, push the last sequence into the index + if (entry.name != "") { + mismatchedLineLengths = false; // reset line length error tracker for every new sequence + emptyLine = false; + flushEntryToIndex(entry); + entry.clear(); + } + entry.name = line.substr(1, line_length - 1); + } else { // we assume we have found a sequence line + if (entry.offset == -1) // NB initially the offset is -1 + entry.offset = offset; + entry.length += line_length; + if (entry.line_len) { + //entry.line_len = entry.line_len ? entry.line_len : line_length + 1; + if (mismatchedLineLengths || emptyLine) { + if (line_length == 0) { + emptyLine = true; // flag empty lines, raise error only if this is embedded in the sequence + } else { + if (emptyLine) { + cerr << "ERROR: embedded newline"; + } else { + cerr << "ERROR: mismatched line lengths"; + } + cerr << " at line " << line_number << " within sequence " << entry.name << + endl << "File not suitable for fasta index generation." << endl; + exit(1); + } + } + // this flag is set here and checked on the next line + // because we may have reached the end of the sequence, in + // which case a mismatched line length is OK + if (entry.line_len != line_length + 1) { + mismatchedLineLengths = true; + if (line_length == 0) { + emptyLine = true; // flag empty lines, raise error only if this is embedded in the sequence + } + } + } else { + entry.line_len = line_length + 1; // first line + } + entry.line_blen = entry.line_len - 1; + } + offset += line_length + 1; + } + // we've hit the end of the fasta file! + // flush the last entry + flushEntryToIndex(entry); + } else { + cerr << "could not open reference file " << refname << " for indexing!" << endl; + exit(1); + } +} + +void FastaIndex::flushEntryToIndex(FastaIndexEntry& entry) { + string name = split(entry.name, " \t").at(0); // key by first token of name + sequenceNames.push_back(name); + this->insert(make_pair(name, FastaIndexEntry(entry.name, entry.length, + entry.offset, entry.line_blen, + entry.line_len))); + +} + +void FastaIndex::writeIndexFile(string fname) { + //cerr << "writing fasta index file " << fname << endl; + ofstream file; + file.open(fname.c_str()); + if (file.is_open()) { + file << *this; + } else { + cerr << "could not open index file " << fname << " for writing!" << endl; + exit(1); + } +} + +FastaIndex::~FastaIndex(void) { + indexFile.close(); +} + +FastaIndexEntry FastaIndex::entry(string name) { + FastaIndex::iterator e = this->find(name); + if (e == this->end()) { + cerr << "unable to find FASTA index entry for '" << name << "'" << endl; + exit(1); + } else { + return e->second; + } +} + +string FastaIndex::indexFileExtension() { return ".fai"; } + +void FastaReference::open(string reffilename, bool usemmap) { + filename = reffilename; + if (!(file = fopen(filename.c_str(), "r"))) { + cerr << "could not open " << filename << endl; + exit(1); + } + index = new FastaIndex(); + struct stat stFileInfo; + string indexFileName = filename + index->indexFileExtension(); + // if we can find an index file, use it + if(stat(indexFileName.c_str(), &stFileInfo) == 0) { + index->readIndexFile(indexFileName); + } else { // otherwise, read the reference and generate the index file in the cwd + cerr << "index file " << indexFileName << " not found, generating..." << endl; + index->indexReference(filename); + index->writeIndexFile(indexFileName); + } + if (usemmap) { + usingmmap = true; + int fd = fileno(file); + struct stat sb; + if (fstat(fd, &sb) == -1) + cerr << "could not stat file" << filename << endl; + filesize = sb.st_size; + // map the whole file + filemm = mmap(NULL, filesize, PROT_READ, MAP_SHARED, fd, 0); + } +} + +FastaReference::~FastaReference(void) { + fclose(file); + if (usingmmap) { + munmap(filemm, filesize); + } + delete index; +} + +string FastaReference::getSequence(string seqname) { + FastaIndexEntry entry = index->entry(seqname); + int newlines_in_sequence = entry.length / entry.line_blen; + int seqlen = newlines_in_sequence + entry.length; + char* seq = (char*) calloc (seqlen + 1, sizeof(char)); + if (usingmmap) { + memcpy(seq, (char*) filemm + entry.offset, seqlen); + } else { + fseek64(file, entry.offset, SEEK_SET); + fread(seq, sizeof(char), seqlen, file); + } + seq[seqlen] = '\0'; + char* pbegin = seq; + char* pend = seq + (seqlen/sizeof(char)); + pend = remove(pbegin, pend, '\n'); + pend = remove(pbegin, pend, '\0'); + string s = seq; + free(seq); + s.resize((pend - pbegin)/sizeof(char)); + return s; +} + +// TODO cleanup; odd function. use a map +string FastaReference::sequenceNameStartingWith(string seqnameStart) { + try { + return (*index)[seqnameStart].name; + } catch (exception& e) { + cerr << e.what() << ": unable to find index entry for " << seqnameStart << endl; + exit(1); + } +} + +string FastaReference::getSubSequence(string seqname, int start, int length) { + FastaIndexEntry entry = index->entry(seqname); + if (start < 0 || length < 1) { + cerr << "Error: cannot construct subsequence with negative offset or length < 1" << endl; + exit(1); + } + // we have to handle newlines + // approach: count newlines before start + // count newlines by end of read + // subtracting newlines before start find count of embedded newlines + int newlines_before = start > 0 ? (start - 1) / entry.line_blen : 0; + int newlines_by_end = (start + length - 1) / entry.line_blen; + int newlines_inside = newlines_by_end - newlines_before; + int seqlen = length + newlines_inside; + char* seq = (char*) calloc (seqlen + 1, sizeof(char)); + if (usingmmap) { + memcpy(seq, (char*) filemm + entry.offset + newlines_before + start, seqlen); + } else { + fseek64(file, (off_t) (entry.offset + newlines_before + start), SEEK_SET); + fread(seq, sizeof(char), (off_t) seqlen, file); + } + seq[seqlen] = '\0'; + char* pbegin = seq; + char* pend = seq + (seqlen/sizeof(char)); + pend = remove(pbegin, pend, '\n'); + pend = remove(pbegin, pend, '\0'); + string s = seq; + free(seq); + s.resize((pend - pbegin)/sizeof(char)); + return s; +} + +long unsigned int FastaReference::sequenceLength(string seqname) { + FastaIndexEntry entry = index->entry(seqname); + return entry.length; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/Fasta/Fasta.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,78 @@ +// *************************************************************************** +// FastaIndex.h (c) 2010 Erik Garrison <erik.garrison@bc.edu> +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 5 February 2010 (EG) +// --------------------------------------------------------------------------- + +#ifndef _FASTA_H +#define _FASTA_H + +#include <map> +#include <iostream> +#include <fstream> +#include <vector> +#include <stdint.h> +#include <stdio.h> +#include <algorithm> +#include "LargeFileSupport.h" +#include <sys/stat.h> +#include <sys/mman.h> +#include "split.h" +#include <stdlib.h> +#include <ctype.h> +#include <unistd.h> + +using namespace std; + +class FastaIndexEntry { + friend ostream& operator<<(ostream& output, const FastaIndexEntry& e); + public: + FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len); + FastaIndexEntry(void); + ~FastaIndexEntry(void); + string name; // sequence name + int length; // length of sequence + long long offset; // bytes offset of sequence from start of file + int line_blen; // line length in bytes, sequence characters + int line_len; // line length including newline + void clear(void); +}; + +class FastaIndex : public map<string, FastaIndexEntry> { + friend ostream& operator<<(ostream& output, FastaIndex& i); + public: + FastaIndex(void); + ~FastaIndex(void); + vector<string> sequenceNames; + void indexReference(string refName); + void readIndexFile(string fname); + void writeIndexFile(string fname); + ifstream indexFile; + FastaIndexEntry entry(string key); + void flushEntryToIndex(FastaIndexEntry& entry); + string indexFileExtension(void); +}; + +class FastaReference { + public: + void open(string reffilename, bool usemmap = false); + bool usingmmap; + string filename; + FastaReference(void) : usingmmap(false) { } + ~FastaReference(void); + FILE* file; + void* filemm; + size_t filesize; + FastaIndex* index; + vector<FastaIndexEntry> findSequencesStartingWith(string seqnameStart); + string getSequence(string seqname); + // potentially useful for performance, investigate + // void getSequence(string seqname, string& sequence); + string getSubSequence(string seqname, int start, int length); + string sequenceNameStartingWith(string seqnameStart); + long unsigned int sequenceLength(string seqname); +}; + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/Fasta/LargeFileSupport.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,13 @@ +#pragma once + +#define _FILE_OFFSET_BITS 64 + +#ifdef WIN32 +#define ftell64(a) _ftelli64(a) +#define fseek64(a,b,c) _fseeki64(a,b,c) +typedef __int64_t off_type; +#else +#define ftell64(a) ftello(a) +#define fseek64(a,b,c) fseeko(a,b,c) +typedef off_t off_type; +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/Fasta/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,26 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= Fasta.cpp split.cpp +OBJECTS= $(SOURCES:.cpp=.o) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +all: $(BUILT_OBJECTS) + +.PHONY: all + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/Fasta/split.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,33 @@ +#include "split.h" + +std::vector<std::string> &split(const std::string &s, char delim, std::vector<std::string> &elems) { + std::stringstream ss(s); + std::string item; + while(std::getline(ss, item, delim)) { + elems.push_back(item); + } + return elems; +} + +std::vector<std::string> split(const std::string &s, char delim) { + std::vector<std::string> elems; + return split(s, delim, elems); +} + +std::vector<std::string> &split(const std::string &s, const std::string& delims, std::vector<std::string> &elems) { + char* tok; + char cchars [s.size()+1]; + char* cstr = &cchars[0]; + strcpy(cstr, s.c_str()); + tok = strtok(cstr, delims.c_str()); + while (tok != NULL) { + elems.push_back(tok); + tok = strtok(NULL, delims.c_str()); + } + return elems; +} + +std::vector<std::string> split(const std::string &s, const std::string& delims) { + std::vector<std::string> elems; + return split(s, delims, elems); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/Fasta/split.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,20 @@ +#ifndef __SPLIT_H +#define __SPLIT_H + +// functions to split a string by a specific delimiter +#include <string> +#include <vector> +#include <sstream> +#include <string.h> + +// thanks to Evan Teran, http://stackoverflow.com/questions/236129/how-to-split-a-string/236803#236803 + +// split a string on a single delimiter character (delim) +std::vector<std::string>& split(const std::string &s, char delim, std::vector<std::string> &elems); +std::vector<std::string> split(const std::string &s, char delim); + +// split a string on any character found in the string of delimiters (delims) +std::vector<std::string>& split(const std::string &s, const std::string& delims, std::vector<std::string> &elems); +std::vector<std::string> split(const std::string &s, const std::string& delims); + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedFile/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,29 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ -I$(UTILITIES_DIR)/stringUtilities/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= bedFile.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedFile/bedFile.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,720 @@ +/***************************************************************************** + bedFile.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedFile.h" + + +/************************************************ +Helper functions +*************************************************/ +void splitBedIntoBlocks(const BED &bed, int lineNum, bedVector &bedBlocks) { + + if (bed.otherFields.size() < 6) { + cerr << "Input error: Cannot split into blocks. Found interval with fewer than 12 columns on line " << lineNum << "." << endl; + exit(1); + } + + int blockCount = atoi(bed.otherFields[3].c_str()); + if ( blockCount <= 0 ) { + cerr << "Input error: found interval having <= 0 blocks on line " << lineNum << "." << endl; + exit(1); + } + else if ( blockCount == 1 ) { + //take a short-cut for single blocks + bedBlocks.push_back(bed); + } + else { + // get the comma-delimited strings for the BED12 block starts and block ends. + string blockSizes(bed.otherFields[4]); + string blockStarts(bed.otherFields[5]); + + vector<int> sizes; + vector<int> starts; + Tokenize(blockSizes, sizes, ","); + Tokenize(blockStarts, starts, ","); + + if ( sizes.size() != (size_t) blockCount || starts.size() != (size_t) blockCount ) { + cerr << "Input error: found interval with block-counts not matching starts/sizes on line " << lineNum << "." << endl; + exit(1); + } + + // add each BED block to the bedBlocks vector + for (UINT i = 0; i < (UINT) blockCount; ++i) { + CHRPOS blockStart = bed.start + starts[i]; + CHRPOS blockEnd = bed.start + starts[i] + sizes[i]; + BED currBedBlock(bed.chrom, blockStart, blockEnd, bed.name, bed.score, bed.strand, bed.otherFields); + bedBlocks.push_back(currBedBlock); + } + } +} + + +/*********************************************** +Sorting comparison functions +************************************************/ +bool sortByChrom(BED const &a, BED const &b) { + if (a.chrom < b.chrom) return true; + else return false; +}; + +bool sortByStart(const BED &a, const BED &b) { + if (a.start < b.start) return true; + else return false; +}; + +bool sortBySizeAsc(const BED &a, const BED &b) { + + CHRPOS aLen = a.end - a.start; + CHRPOS bLen = b.end - b.start; + + if (aLen < bLen) return true; + else return false; +}; + +bool sortBySizeDesc(const BED &a, const BED &b) { + + CHRPOS aLen = a.end - a.start; + CHRPOS bLen = b.end - b.start; + + if (aLen > bLen) return true; + else return false; +}; + +bool sortByScoreAsc(const BED &a, const BED &b) { + if (a.score < b.score) return true; + else return false; +}; + +bool sortByScoreDesc(const BED &a, const BED &b) { + if (a.score > b.score) return true; + else return false; +}; + +bool byChromThenStart(BED const &a, BED const &b) { + + if (a.chrom < b.chrom) return true; + else if (a.chrom > b.chrom) return false; + + if (a.start < b.start) return true; + else if (a.start >= b.start) return false; + + return false; +}; + + +/******************************************* +Class methods +*******************************************/ + +// Constructor +BedFile::BedFile(string &bedFile) +: bedFile(bedFile), + _isGff(false), + _isVcf(false), + _typeIsKnown(false), + _merged_start(-1), + _merged_end(-1), + _merged_chrom(""), + _prev_start(-1), + _prev_chrom("") +{} + +// Destructor +BedFile::~BedFile(void) { +} + + +void BedFile::Open(void) { + + _bedFields.reserve(12); + + if (bedFile == "stdin" || bedFile == "-") { + _bedStream = &cin; + } + else { + _bedStream = new ifstream(bedFile.c_str(), ios::in); + + if( isGzipFile(_bedStream) ) { + delete _bedStream; + _bedStream = new igzstream(bedFile.c_str(), ios::in); + } + if ( !(_bedStream->good()) ) { + cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + } +} + +// Rewind the pointer back to the beginning of the file +void BedFile::Rewind(void) { + _bedStream->seekg(0, ios::beg); +} + +// Jump to a specific byte in the file +void BedFile::Seek(unsigned long offset) { + _bedStream->seekg(offset); +} + +// Jump to a specific byte in the file +bool BedFile::Empty() { + return _bedStream->eof(); +} + + +// Close the BED file +void BedFile::Close(void) { + if (bedFile != "stdin" && bedFile != "-") delete _bedStream; +} + + +BedLineStatus BedFile::GetNextBed(BED &bed, int &lineNum, bool forceSorted) { + + // make sure there are still lines to process. + // if so, tokenize, validate and return the BED entry. + _bedFields.clear(); + // clear out the previous bed's data + if (_bedStream->good()) { + // parse the bedStream pointer + getline(*_bedStream, _bedLine); + lineNum++; + + // split into a string vector. + Tokenize(_bedLine, _bedFields); + + // load the BED struct as long as it's a valid BED entry. + BedLineStatus status = parseLine(bed, _bedFields, lineNum); + if (!forceSorted) { + return status; + } + else if (status == BED_VALID) { + if (bed.chrom == _prev_chrom) { + if ((int) bed.start >= _prev_start) { + _prev_chrom = bed.chrom; + _prev_start = bed.start; + return status; + } + else { + cerr << "ERROR: input file: (" << bedFile << ") is not sorted by chrom then start" << endl; + exit(1); + } + } + else if (bed.chrom > _prev_chrom) { + _prev_chrom = bed.chrom; + _prev_start = bed.start; + return status; + } + else if (bed.chrom < _prev_chrom) { + cerr << "ERROR: input file: (" << bedFile << ") is not sorted by chrom then start" << endl; + exit(1); + } + } + } + + // default if file is closed or EOF + return BED_INVALID; +} + + +bool BedFile::GetNextMergedBed(BED &merged_bed, int &lineNum) { + + if (_bedStream->good()) { + BED bed; + BedLineStatus bedStatus; + // force sorting; hence third param = true + while ((bedStatus = GetNextBed(bed, lineNum, true)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + if (((int) bed.start - _merged_end > 0) || + (_merged_end < 0) || + (bed.chrom != _merged_chrom)) + { + if (_merged_start >= 0) { + merged_bed.chrom = _merged_chrom; + merged_bed.start = _merged_start; + merged_bed.end = _merged_end; + + _merged_chrom = bed.chrom; + _merged_start = bed.start; + _merged_end = bed.end; + + return true; + } + else { + _merged_start = bed.start; + _merged_chrom = bed.chrom; + _merged_end = bed.end; + } + } + else if ((int) bed.end > _merged_end) + { + _merged_end = bed.end; + } + } + } + // handle the last merged block in the file. + if (bedStatus == BED_INVALID) + { + merged_bed.chrom = _merged_chrom; + merged_bed.start = _merged_start; + merged_bed.end = _merged_end; + return true; + } + } + return false; +} + + +void BedFile::FindOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, + string strand, vector<BED> &hits, bool sameStrand, bool diffStrand) { + + BIN startBin, endBin; + startBin = (start >> _binFirstShift); + endBin = ((end-1) >> _binFirstShift); + + // loop through each bin "level" in the binning hierarchy + for (BINLEVEL i = 0; i < _binLevels; ++i) { + + // loop through each bin at this level of the hierarchy + BIN offset = _binOffsetsExtended[i]; + for (BIN j = (startBin+offset); j <= (endBin+offset); ++j) { + + // loop through each feature in this chrom/bin and see if it overlaps + // with the feature that was passed in. if so, add the feature to + // the list of hits. + vector<BED>::const_iterator bedItr = bedMap[chrom][j].begin(); + vector<BED>::const_iterator bedEnd = bedMap[chrom][j].end(); + + for (; bedItr != bedEnd; ++bedItr) { + // do we have sufficient overlap? + if (overlaps(bedItr->start, bedItr->end, start, end) > 0) { + + bool strands_are_same = (strand == bedItr->strand); + + // test for necessary strandedness + if ( (sameStrand == false && diffStrand == false) + || + (sameStrand == true && strands_are_same == true) + || + (diffStrand == true && strands_are_same == false) + ) + { + hits.push_back(*bedItr); + } + } + } + } + startBin >>= _binNextShift; + endBin >>= _binNextShift; + } +} + + +bool BedFile::FindOneOrMoreOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, + bool sameStrand, bool diffStrand, float overlapFraction) { + + BIN startBin, endBin; + startBin = (start >> _binFirstShift); + endBin = ((end-1) >> _binFirstShift); + + CHRPOS aLength = (end - start); + + // loop through each bin "level" in the binning hierarchy + for (BINLEVEL i = 0; i < _binLevels; ++i) { + + // loop through each bin at this level of the hierarchy + BIN offset = _binOffsetsExtended[i]; + for (BIN j = (startBin+offset); j <= (endBin+offset); ++j) { + + // loop through each feature in this chrom/bin and see if it overlaps + // with the feature that was passed in. if so, add the feature to + // the list of hits. + vector<BED>::const_iterator bedItr = bedMap[chrom][j].begin(); + vector<BED>::const_iterator bedEnd = bedMap[chrom][j].end(); + for (; bedItr != bedEnd; ++bedItr) { + + CHRPOS s = max(start, bedItr->start); + CHRPOS e = min(end, bedItr->end); + // the number of overlapping bases b/w a and b + int overlapBases = (e - s); + + // do we have sufficient overlap? + if ( (float) overlapBases / (float) aLength >= overlapFraction) { + + bool strands_are_same = (strand == bedItr->strand); + // test for necessary strandedness + if ( (sameStrand == false && diffStrand == false) + || + (sameStrand == true && strands_are_same == true) + || + (diffStrand == true && strands_are_same == false) + ) + { + return true; + } + } + } + } + startBin >>= _binNextShift; + endBin >>= _binNextShift; + } + return false; +} + + +bool BedFile::FindOneOrMoreReciprocalOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, + bool sameStrand, bool diffStrand, float overlapFraction) { + + BIN startBin, endBin; + startBin = (start >> _binFirstShift); + endBin = ((end-1) >> _binFirstShift); + + CHRPOS aLength = (end - start); + + // loop through each bin "level" in the binning hierarchy + for (BINLEVEL i = 0; i < _binLevels; ++i) { + + // loop through each bin at this level of the hierarchy + BIN offset = _binOffsetsExtended[i]; + for (BIN j = (startBin+offset); j <= (endBin+offset); ++j) { + + // loop through each feature in this chrom/bin and see if it overlaps + // with the feature that was passed in. if so, add the feature to + // the list of hits. + vector<BED>::const_iterator bedItr = bedMap[chrom][j].begin(); + vector<BED>::const_iterator bedEnd = bedMap[chrom][j].end(); + for (; bedItr != bedEnd; ++bedItr) { + CHRPOS s = max(start, bedItr->start); + CHRPOS e = min(end, bedItr->end); + + // the number of overlapping bases b/w a and b + int overlapBases = (e - s); + + // do we have sufficient overlap? + if ( (float) overlapBases / (float) aLength >= overlapFraction) { + CHRPOS bLength = (bedItr->end - bedItr->start); + float bOverlap = ( (float) overlapBases / (float) bLength ); + bool strands_are_same = (strand == bedItr->strand); + + // test for sufficient reciprocal overlap and strandedness + if ( (bOverlap >= overlapFraction) && + ((sameStrand == false && diffStrand == false) + || + (sameStrand == true && strands_are_same == true) + || + (diffStrand == true && strands_are_same == false)) + ) + { + return true; + } + } + } + } + startBin >>= _binNextShift; + endBin >>= _binNextShift; + } + return false; +} + + +void BedFile::countHits(const BED &a, bool sameStrand, bool diffStrand, bool countsOnly) { + + BIN startBin, endBin; + startBin = (a.start >> _binFirstShift); + endBin = ((a.end-1) >> _binFirstShift); + + // loop through each bin "level" in the binning hierarchy + for (BINLEVEL i = 0; i < _binLevels; ++i) { + + // loop through each bin at this level of the hierarchy + BIN offset = _binOffsetsExtended[i]; + for (BIN j = (startBin+offset); j <= (endBin+offset); ++j) { + + // loop through each feature in this chrom/bin and see if it overlaps + // with the feature that was passed in. if so, add the feature to + // the list of hits. + vector<BEDCOV>::iterator bedItr = bedCovMap[a.chrom][j].begin(); + vector<BEDCOV>::iterator bedEnd = bedCovMap[a.chrom][j].end(); + for (; bedItr != bedEnd; ++bedItr) { + + bool strands_are_same = (a.strand == bedItr->strand); + // skip the hit if not on the same strand (and we care) + if ((sameStrand == true && strands_are_same == false) || + (diffStrand == true && strands_are_same == true) + ) + { + continue; + } + else if (overlaps(bedItr->start, bedItr->end, a.start, a.end) > 0) { + + bedItr->count++; + if (countsOnly == false) { + if (a.zeroLength == false) { + bedItr->depthMap[a.start+1].starts++; + bedItr->depthMap[a.end].ends++; + } + else { + // correct for the fact that we artificially expanded the zeroLength feature + bedItr->depthMap[a.start+2].starts++; + bedItr->depthMap[a.end-1].ends++; + } + + if (a.start < bedItr->minOverlapStart) { + bedItr->minOverlapStart = a.start; + } + } + } + } + } + startBin >>= _binNextShift; + endBin >>= _binNextShift; + } +} + + +void BedFile::countSplitHits(const vector<BED> &bedBlocks, bool sameStrand, bool diffStrand, bool countsOnly) { + + // set to track the distinct B features that had coverage. + // we'll update the counts of coverage for these features by one + // at the end of this function to avoid over-counting. + set< vector<BEDCOV>::iterator > validHits; + + vector<BED>::const_iterator blockItr = bedBlocks.begin(); + vector<BED>::const_iterator blockEnd = bedBlocks.end(); + for (; blockItr != blockEnd; ++blockItr) { + + BIN startBin, endBin; + startBin = (blockItr->start >> _binFirstShift); + endBin = ((blockItr->end-1) >> _binFirstShift); + + // loop through each bin "level" in the binning hierarchy + for (BINLEVEL i = 0; i < _binLevels; ++i) { + + // loop through each bin at this level of the hierarchy + BIN offset = _binOffsetsExtended[i]; + for (BIN j = (startBin+offset); j <= (endBin+offset); ++j) { + + // loop through each feature in this chrom/bin and see if it overlaps + // with the feature that was passed in. if so, add the feature to + // the list of hits. + vector<BEDCOV>::iterator bedItr = bedCovMap[blockItr->chrom][j].begin(); + vector<BEDCOV>::iterator bedEnd = bedCovMap[blockItr->chrom][j].end(); + for (; bedItr != bedEnd; ++bedItr) { + + bool strands_are_same = (blockItr->strand == bedItr->strand); + // skip the hit if not on the same strand (and we care) + if ((sameStrand == true && strands_are_same == false) || + (diffStrand == true && strands_are_same == true) + ) + { + continue; + } + else if (overlaps(bedItr->start, bedItr->end, blockItr->start, blockItr->end) > 0) { + if (countsOnly == false) { + if (blockItr->zeroLength == false) { + bedItr->depthMap[blockItr->start+1].starts++; + bedItr->depthMap[blockItr->end].ends++; + } + else { + // correct for the fact that we artificially expanded the zeroLength feature + bedItr->depthMap[blockItr->start+2].starts++; + bedItr->depthMap[blockItr->end-1].ends++; + } + } + + validHits.insert(bedItr); + if (blockItr->start < bedItr->minOverlapStart) + bedItr->minOverlapStart = blockItr->start; + } + } + } + startBin >>= _binNextShift; + endBin >>= _binNextShift; + } + } + // incrment the count of overlap by one for each B feature that overlapped + // the current passed hit. This is necessary to prevent over-counting for + // each "split"" of a single read. + set< vector<BEDCOV>::iterator >::iterator validHitsItr = validHits.begin(); + set< vector<BEDCOV>::iterator >::iterator validHitsEnd = validHits.end(); + for (; validHitsItr != validHitsEnd; ++validHitsItr) + // the validHitsItr points to another itr, hence the (*itr)-> dereferencing. + // ugly, but that's C++. + (*validHitsItr)->count++; +} + + +void BedFile::countListHits(const BED &a, int index, bool sameStrand, bool diffStrand) { + + BIN startBin, endBin; + startBin = (a.start >> _binFirstShift); + endBin = ((a.end-1) >> _binFirstShift); + + // loop through each bin "level" in the binning hierarchy + for (BINLEVEL i = 0; i < _binLevels; ++i) { + + // loop through each bin at this level of the hierarchy + BIN offset = _binOffsetsExtended[i]; + for (BIN j = (startBin+offset); j <= (endBin+offset); ++j) { + + // loop through each feature in this chrom/bin and see if it overlaps + // with the feature that was passed in. if so, add the feature to + // the list of hits. + vector<BEDCOVLIST>::iterator bedItr = bedCovListMap[a.chrom][j].begin(); + vector<BEDCOVLIST>::iterator bedEnd = bedCovListMap[a.chrom][j].end(); + for (; bedItr != bedEnd; ++bedItr) { + + bool strands_are_same = (a.strand == bedItr->strand); + // skip the hit if not on the same strand (and we care) + if ((sameStrand == true && strands_are_same == false) || + (diffStrand == true && strands_are_same == true) + ) + { + continue; + } + else if (overlaps(bedItr->start, bedItr->end, a.start, a.end) > 0) { + bedItr->counts[index]++; + if (a.zeroLength == false) { + bedItr->depthMapList[index][a.start+1].starts++; + bedItr->depthMapList[index][a.end].ends++; + } + else { + // correct for the fact that we artificially expanded the zeroLength feature + bedItr->depthMapList[index][a.start+2].starts++; + bedItr->depthMapList[index][a.end-1].ends++; + } + + if (a.start < bedItr->minOverlapStarts[index]) { + bedItr->minOverlapStarts[index] = a.start; + } + } + } + } + startBin >>= _binNextShift; + endBin >>= _binNextShift; + } +} + +void BedFile::setZeroBased(bool zeroBased) { this->isZeroBased = zeroBased; } + +void BedFile::setGff (bool gff) { this->_isGff = gff; } + + +void BedFile::setVcf (bool vcf) { this->_isVcf = vcf; } + + +void BedFile::setFileType (FileType type) { + _fileType = type; + _typeIsKnown = true; +} + + +void BedFile::setBedType (int colNums) { + bedType = colNums; +} + + +void BedFile::loadBedFileIntoMap() { + + BED bedEntry, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + + Open(); + while ((bedStatus = GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + BIN bin = getBin(bedEntry.start, bedEntry.end); + bedMap[bedEntry.chrom][bin].push_back(bedEntry); + bedEntry = nullBed; + } + } + Close(); +} + + +void BedFile::loadBedCovFileIntoMap() { + + BED bedEntry, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + + Open(); + while ((bedStatus = GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + BIN bin = getBin(bedEntry.start, bedEntry.end); + + BEDCOV bedCov; + bedCov.chrom = bedEntry.chrom; + bedCov.start = bedEntry.start; + bedCov.end = bedEntry.end; + bedCov.name = bedEntry.name; + bedCov.score = bedEntry.score; + bedCov.strand = bedEntry.strand; + bedCov.otherFields = bedEntry.otherFields; + bedCov.zeroLength = bedEntry.zeroLength; + bedCov.count = 0; + bedCov.minOverlapStart = INT_MAX; + + bedCovMap[bedEntry.chrom][bin].push_back(bedCov); + bedEntry = nullBed; + } + } + Close(); +} + +void BedFile::loadBedCovListFileIntoMap() { + + BED bedEntry, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + + Open(); + while ((bedStatus = GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + BIN bin = getBin(bedEntry.start, bedEntry.end); + + BEDCOVLIST bedCovList; + bedCovList.chrom = bedEntry.chrom; + bedCovList.start = bedEntry.start; + bedCovList.end = bedEntry.end; + bedCovList.name = bedEntry.name; + bedCovList.score = bedEntry.score; + bedCovList.strand = bedEntry.strand; + bedCovList.otherFields = bedEntry.otherFields; + bedCovList.zeroLength = bedEntry.zeroLength; + + bedCovListMap[bedEntry.chrom][bin].push_back(bedCovList); + bedEntry = nullBed; + } + } + Close(); +} + + +void BedFile::loadBedFileIntoMapNoBin() { + + BED bedEntry, nullBed; + int lineNum = 0; + BedLineStatus bedStatus; + + Open(); + while ((bedStatus = this->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + bedMapNoBin[bedEntry.chrom].push_back(bedEntry); + bedEntry = nullBed; + } + } + Close(); + + // sort the BED entries for each chromosome + // in ascending order of start position + for (masterBedMapNoBin::iterator m = this->bedMapNoBin.begin(); m != this->bedMapNoBin.end(); ++m) { + sort(m->second.begin(), m->second.end(), sortByStart); + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedFile/bedFile.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,1167 @@ +/***************************************************************************** + bedFile.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef BEDFILE_H +#define BEDFILE_H + +// "local" includes +#include "gzstream.h" +#include "lineFileUtilities.h" +#include "fileType.h" + +// standard includes +#include <vector> +#include <map> +#include <set> +#include <string> +#include <iostream> +#include <fstream> +#include <sstream> +#include <cstring> +#include <algorithm> +#include <limits.h> +#include <stdint.h> +#include <cstdio> +//#include <tr1/unordered_map> // Experimental. +using namespace std; + + +//************************************************* +// Data type tydedef +//************************************************* +typedef uint32_t CHRPOS; +typedef uint16_t BINLEVEL; +typedef uint32_t BIN; +typedef uint16_t USHORT; +typedef uint32_t UINT; + +//************************************************* +// Genome binning constants +//************************************************* + +const BIN _numBins = 37450; +const BINLEVEL _binLevels = 7; + +// bins range in size from 16kb to 512Mb +// Bin 0 spans 512Mbp, # Level 1 +// Bins 1-8 span 64Mbp, # Level 2 +// Bins 9-72 span 8Mbp, # Level 3 +// Bins 73-584 span 1Mbp # Level 4 +// Bins 585-4680 span 128Kbp # Level 5 +// Bins 4681-37449 span 16Kbp # Level 6 +const BIN _binOffsetsExtended[] = {32678+4096+512+64+8+1, 4096+512+64+8+1, 512+64+8+1, 64+8+1, 8+1, 1, 0}; +//const BIN _binOffsetsExtended[] = {4096+512+64+8+1, 4096+512+64+8+1, 512+64+8+1, 64+8+1, 8+1, 1, 0}; + +const USHORT _binFirstShift = 14; /* How much to shift to get to finest bin. */ +const USHORT _binNextShift = 3; /* How much to shift to get to next larger bin. */ + + +//************************************************* +// Common data structures +//************************************************* + +struct DEPTH { + UINT starts; + UINT ends; +}; + + +/* + Structure for regular BED records +*/ +struct BED { + + // Regular BED fields + string chrom; + CHRPOS start; + CHRPOS end; + string name; + string score; + string strand; + + // Add'l fields for BED12 and/or custom BED annotations + vector<string> otherFields; + + // experimental fields for the FJOIN approach. + bool zeroLength; + bool added; + bool finished; + // list of hits from another file. + vector<BED> overlaps; + +public: + // constructors + + // Null + BED() + : chrom(""), + start(0), + end(0), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BED3 + BED(string chrom, CHRPOS start, CHRPOS end) + : chrom(chrom), + start(start), + end(end), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BED4 + BED(string chrom, CHRPOS start, CHRPOS end, string strand) + : chrom(chrom), + start(start), + end(end), + name(""), + score(""), + strand(strand), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BED6 + BED(string chrom, CHRPOS start, CHRPOS end, string name, + string score, string strand) + : chrom(chrom), + start(start), + end(end), + name(name), + score(score), + strand(strand), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BEDALL + BED(string chrom, CHRPOS start, CHRPOS end, string name, + string score, string strand, vector<string> otherFields) + : chrom(chrom), + start(start), + end(end), + name(name), + score(score), + strand(strand), + otherFields(otherFields), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + int size() { + return end-start; + } + +}; // BED + + +/* + Structure for each end of a paired BED record + mate points to the other end. +*/ +struct MATE { + BED bed; + int lineNum; + MATE *mate; +}; + + +/* + Structure for regular BED COVERAGE records +*/ +struct BEDCOV { + + string chrom; + + // Regular BED fields + CHRPOS start; + CHRPOS end; + string name; + string score; + string strand; + + // Add'l fields for BED12 and/or custom BED annotations + vector<string> otherFields; + + // flag a zero-length feature + bool zeroLength; + + // Additional fields specific to computing coverage + map<unsigned int, DEPTH> depthMap; + unsigned int count; + CHRPOS minOverlapStart; + + + public: + // constructors + // Null + BEDCOV() + : chrom(""), + start(0), + end(0), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + depthMap(), + count(0), + minOverlapStart(0) + {} +}; + + +/* + Structure for BED COVERAGE records having lists of + multiple coverages +*/ +struct BEDCOVLIST { + + // Regular BED fields + string chrom; + CHRPOS start; + CHRPOS end; + string name; + string score; + string strand; + + // Add'l fields for BED12 and/or custom BED annotations + vector<string> otherFields; + + // flag a zero-length feature + bool zeroLength; + + // Additional fields specific to computing coverage + vector< map<unsigned int, DEPTH> > depthMapList; + vector<unsigned int> counts; + vector<CHRPOS> minOverlapStarts; + + + public: + // constructors + // Null + BEDCOVLIST() + : chrom(""), + start(0), + end(0), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + depthMapList(), + counts(0), + minOverlapStarts(0) + {} +}; + + +// enum to flag the state of a given line in a BED file. +enum BedLineStatus +{ + BED_INVALID = -1, + BED_HEADER = 0, + BED_BLANK = 1, + BED_VALID = 2 +}; + +// enum to indicate the type of file we are dealing with +enum FileType +{ + BED_FILETYPE, + GFF_FILETYPE, + VCF_FILETYPE +}; + +//************************************************* +// Data structure typedefs +//************************************************* +typedef vector<BED> bedVector; +typedef vector<BEDCOV> bedCovVector; +typedef vector<MATE> mateVector; +typedef vector<BEDCOVLIST> bedCovListVector; + +typedef map<BIN, bedVector, std::less<BIN> > binsToBeds; +typedef map<BIN, bedCovVector, std::less<BIN> > binsToBedCovs; +typedef map<BIN, mateVector, std::less<BIN> > binsToMates; +typedef map<BIN, bedCovListVector, std::less<BIN> > binsToBedCovLists; + +typedef map<string, binsToBeds, std::less<string> > masterBedMap; +typedef map<string, binsToBedCovs, std::less<string> > masterBedCovMap; +typedef map<string, binsToMates, std::less<string> > masterMateMap; +typedef map<string, binsToBedCovLists, std::less<string> > masterBedCovListMap; +typedef map<string, bedVector, std::less<string> > masterBedMapNoBin; + + +// EXPERIMENTAL - wait for TR1 +// typedef vector<BED> bedVector; +// typedef vector<BEDCOV> bedCovVector; +// +// typedef tr1::unordered_map<BIN, bedVector> binsToBeds; +// typedef tr1::unordered_map<BIN, bedCovVector> binsToBedCovs; +// +// typedef tr1::unordered_map<string, binsToBeds> masterBedMap; +// typedef tr1::unordered_map<string, binsToBedCovs> masterBedCovMap; +// typedef tr1::unordered_map<string, bedVector> masterBedMapNoBin; + + + +// return the genome "bin" for a feature with this start and end +inline +BIN getBin(CHRPOS start, CHRPOS end) { + --end; + start >>= _binFirstShift; + end >>= _binFirstShift; + + for (register short i = 0; i < _binLevels; ++i) { + if (start == end) return _binOffsetsExtended[i] + start; + start >>= _binNextShift; + end >>= _binNextShift; + } + cerr << "start " << start << ", end " << end << " out of range in findBin (max is 512M)" << endl; + return 0; +} + +/**************************************************** +// isInteger(s): Tests if string s is a valid integer +*****************************************************/ +inline bool isInteger(const std::string& s) { + int len = s.length(); + for (int i = 0; i < len; i++) { + if (!std::isdigit(s[i])) return false; + } + return true; +} + + +// return the amount of overlap between two features. Negative if none and the the +// number of negative bases is the distance between the two. +inline +int overlaps(CHRPOS aS, CHRPOS aE, CHRPOS bS, CHRPOS bE) { + return min(aE, bE) - max(aS, bS); +} + +// is A after (to the right of) B? +inline +bool after(const BED &a, const BED &b) { + return (a.start >= b.end); +} + + +// Ancillary functions +void splitBedIntoBlocks(const BED &bed, int lineNum, bedVector &bedBlocks); + + +// BED Sorting Methods +bool sortByChrom(const BED &a, const BED &b); +bool sortByStart(const BED &a, const BED &b); +bool sortBySizeAsc(const BED &a, const BED &b); +bool sortBySizeDesc(const BED &a, const BED &b); +bool sortByScoreAsc(const BED &a, const BED &b); +bool sortByScoreDesc(const BED &a, const BED &b); +bool byChromThenStart(BED const &a, BED const &b); + + + +//************************************************ +// BedFile Class methods and elements +//************************************************ +class BedFile { + +public: + + // Constructor + BedFile(string &); + + // Destructor + ~BedFile(void); + + // Open a BED file for reading (creates an istream pointer) + void Open(void); + + // Rewind the pointer back to the beginning of the file + void Rewind(void); + + // Jump to a specific byte in the file + void Seek(unsigned long offset); + + bool Empty(); + + // Close an opened BED file. + void Close(void); + + // Get the next BED entry in an opened BED file. + BedLineStatus GetNextBed (BED &bed, int &lineNum, bool forceSorted = false); + + // Returns the next MERGED (i.e., non-overlapping) interval in an opened BED file + // NOTE: assumes input file is sorted by chrom then start + bool GetNextMergedBed(BED &merged_bed, int &lineNum); + + // load a BED file into a map keyed by chrom, then bin. value is vector of BEDs + void loadBedFileIntoMap(); + + // load a BED file into a map keyed by chrom, then bin. value is vector of BEDCOVs + void loadBedCovFileIntoMap(); + + // load a BED file into a map keyed by chrom, then bin. value is vector of BEDCOVLISTs + void loadBedCovListFileIntoMap(); + + // load a BED file into a map keyed by chrom. value is vector of BEDs + void loadBedFileIntoMapNoBin(); + + // Given a chrom, start, end and strand for a single feature, + // search for all overlapping features in another BED file. + // Searches through each relevant genome bin on the same chromosome + // as the single feature. Note: Adapted from kent source "binKeeperFind" + void FindOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, vector<BED> &hits, bool sameStrand, bool diffStrand); + + // return true if at least one overlap was found. otherwise, return false. + bool FindOneOrMoreOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, + bool sameStrand, bool diffStrand, float overlapFraction = 0.0); + + // return true if at least one __reciprocal__ overlap was found. otherwise, return false. + bool FindOneOrMoreReciprocalOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, + bool sameStrand, bool diffStrand, float overlapFraction = 0.0); + + // Given a chrom, start, end and strand for a single feature, + // increment a the number of hits for each feature in B file + // that the feature overlaps + void countHits(const BED &a, bool sameStrand = false, bool diffStrand = false, bool countsOnly = false); + + // same as above, but has special logic that processes a set of + // BED "blocks" from a single entry so as to avoid over-counting + // each "block" of a single BAM/BED12 as distinct coverage. That is, + // if one read has four block, we only want to count the coverage as + // coming from one read, not four. + void countSplitHits(const vector<BED> &bedBlock, bool sameStrand = false, bool diffStrand = false, bool countsOnly = false); + + // Given a chrom, start, end and strand for a single feature, + // increment a the number of hits for each feature in B file + // that the feature overlaps + void countListHits(const BED &a, int index, bool sameStrand, bool diffStrand); + + // the bedfile with which this instance is associated + string bedFile; + unsigned int bedType; // 3-6, 12 for BED + // 9 for GFF + bool isZeroBased; + + // Main data structires used by BEDTools + masterBedCovMap bedCovMap; + masterBedCovListMap bedCovListMap; + masterBedMap bedMap; + masterBedMapNoBin bedMapNoBin; + +private: + + // data + bool _isGff; + bool _isVcf; + bool _typeIsKnown; // do we know the type? (i.e., BED, GFF, VCF) + FileType _fileType; // what is the file type? (BED? GFF? VCF?) + istream *_bedStream; + string _bedLine; + vector<string> _bedFields; + int _merged_start; + int _merged_end; + string _merged_chrom; + int _prev_start; + string _prev_chrom; + + void setZeroBased(bool zeroBased); + void setGff (bool isGff); + void setVcf (bool isVcf); + void setFileType (FileType type); + void setBedType (int colNums); + + /****************************************************** + Private definitions to circumvent linker issues with + templated member functions. + *******************************************************/ + + /* + parseLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline BedLineStatus parseLine (T &bed, const vector<string> &lineVector, int &lineNum) { + + //char *p2End, *p3End, *p4End, *p5End; + //long l2, l3, l4, l5; + unsigned int numFields = lineVector.size(); + + // bail out if we have a blank line + if (numFields == 0) { + return BED_BLANK; + } + + if ((lineVector[0].find("track") == string::npos) && (lineVector[0].find("browser") == string::npos) && (lineVector[0].find("#") == string::npos) ) { + + if (numFields >= 3) { + // line parsing for all lines after the first non-header line + if (_typeIsKnown == true) { + switch(_fileType) { + case BED_FILETYPE: + if (parseBedLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + case VCF_FILETYPE: + if (parseVcfLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + case GFF_FILETYPE: + if (parseGffLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + default: + printf("ERROR: file type encountered. Exiting\n"); + exit(1); + } + } + // line parsing for first non-header line: figure out file contents + else { + // it's BED format if columns 2 and 3 are integers + if (isInteger(lineVector[1]) && isInteger(lineVector[2])) { + setGff(false); + setZeroBased(true); + setFileType(BED_FILETYPE); + setBedType(numFields); // we now expect numFields columns in each line + if (parseBedLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + } + // it's VCF, assuming the second column is numeric and there are at least 8 fields. + else if (isInteger(lineVector[1]) && numFields >= 8) { + setGff(false); + setVcf(true); + setZeroBased(false); + setFileType(VCF_FILETYPE); + setBedType(numFields); // we now expect numFields columns in each line + if (parseVcfLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + } + // it's GFF, assuming columns columns 4 and 5 are numeric and we have 9 fields total. + else if ((numFields >= 8) && isInteger(lineVector[3]) && isInteger(lineVector[4])) { + setGff(true); + setZeroBased(false); + setFileType(GFF_FILETYPE); + setBedType(numFields); // we now expect numFields columns in each line + if (parseGffLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + } + else { + cerr << "Unexpected file format. Please use tab-delimited BED, GFF, or VCF. " << + "Perhaps you have non-integer starts or ends at line " << lineNum << "?" << endl; + exit(1); + } + } + } + else { + cerr << "It looks as though you have less than 3 columns at line: " << lineNum << ". Are you sure your files are tab-delimited?" << endl; + exit(1); + } + } + else { + lineNum--; + return BED_HEADER; + } + // default + return BED_INVALID; + } + + + /* + parseBedLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline bool parseBedLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) { + + // process as long as the number of fields in this + // line matches what we expect for this file. + if (numFields == this->bedType) { + bed.chrom = lineVector[0]; + int i; + i = atoi(lineVector[1].c_str()); + if (i<0) { + cerr << "Error: malformed BED entry at line " << lineNum << ". Start Coordinate detected that is < 0. Exiting." << endl; + exit(1); + } + bed.start = (CHRPOS)i; + i = atoi(lineVector[2].c_str()); + if (i<0) { + cerr << "Error: malformed BED entry at line " << lineNum << ". End Coordinate detected that is < 0. Exiting." << endl; + exit(1); + } + bed.end = (CHRPOS)i; + + // handle starts == end (e.g., insertions in reference genome) + if (bed.start == bed.end) { + bed.start--; + bed.end++; + bed.zeroLength = true; + } + + if (this->bedType == 4) { + bed.name = lineVector[3]; + } + else if (this->bedType == 5) { + bed.name = lineVector[3]; + bed.score = lineVector[4]; + } + else if (this->bedType == 6) { + bed.name = lineVector[3]; + bed.score = lineVector[4]; + bed.strand = lineVector[5]; + } + else if (this->bedType > 6) { + bed.name = lineVector[3]; + bed.score = lineVector[4]; + bed.strand = lineVector[5]; + for (unsigned int i = 6; i < lineVector.size(); ++i) { + bed.otherFields.push_back(lineVector[i]); + } + } + else if (this->bedType != 3) { + cerr << "Error: unexpected number of fields at line: " << lineNum + << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + + // sanity checks. + if (bed.start <= bed.end) { + return true; + } + else { + cerr << "Error: malformed BED entry at line " << lineNum << ". Start was greater than end. Exiting." << endl; + exit(1); + } + } + else if (numFields == 1) { + cerr << "Only one BED field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + else if ((numFields != this->bedType) && (numFields != 0)) { + cerr << "Differing number of BED fields encountered at line: " << lineNum << ". Exiting..." << endl; + exit(1); + } + else if ((numFields < 3) && (numFields != 0)) { + cerr << "TAB delimited BED file with at least 3 fields (chrom, start, end) is required at line: "<< lineNum << ". Exiting..." << endl; + exit(1); + } + return false; + } + + + /* + parseVcfLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline bool parseVcfLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) { + if (numFields == this->bedType) { + bed.chrom = lineVector[0]; + bed.start = atoi(lineVector[1].c_str()) - 1; // VCF is one-based + bed.end = bed.start + lineVector[3].size(); // VCF 4.0 stores the size of the affected REF allele. + bed.strand = "+"; + // construct the name from the ref and alt alleles. + // if it's an annotated variant, add the rsId as well. + bed.name = lineVector[3] + "/" + lineVector[4]; + if (lineVector[2] != ".") { + bed.name += "_" + lineVector[2]; + } + + if (this->bedType > 2) { + for (unsigned int i = 2; i < numFields; ++i) + bed.otherFields.push_back(lineVector[i]); + } + + if ((bed.start <= bed.end) && (bed.start >= 0) && (bed.end >= 0)) { + return true; + } + else if (bed.start > bed.end) { + cerr << "Error: malformed VCF entry at line " << lineNum << ". Start was greater than end. Exiting." << endl; + exit(1); + } + else if ( (bed.start < 0) || (bed.end < 0) ) { + cerr << "Error: malformed VCF entry at line " << lineNum << ". Coordinate detected that is < 0. Exiting." << endl; + exit(1); + } + } + else if (numFields == 1) { + cerr << "Only one VCF field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + else if ((numFields != this->bedType) && (numFields != 0)) { + cerr << "Differing number of VCF fields encountered at line: " << lineNum << ". Exiting..." << endl; + exit(1); + } + else if ((numFields < 2) && (numFields != 0)) { + cerr << "TAB delimited VCF file with at least 2 fields (chrom, pos) is required at line: "<< lineNum << ". Exiting..." << endl; + exit(1); + } + return false; + } + + + + /* + parseGffLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline bool parseGffLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) { + if (numFields == this->bedType) { + if (this->bedType >= 8 && _isGff) { + bed.chrom = lineVector[0]; + if (isInteger(lineVector[3])) + bed.start = atoi(lineVector[3].c_str()); + if (isInteger(lineVector[4])) + bed.end = atoi(lineVector[4].c_str()); + bed.name = lineVector[2]; + bed.score = lineVector[5]; + bed.strand = lineVector[6].c_str(); + bed.otherFields.push_back(lineVector[1]); // add GFF "source". unused in BED + bed.otherFields.push_back(lineVector[7]); // add GFF "fname". unused in BED + // handle the optional 9th field. + if (this->bedType == 9) + bed.otherFields.push_back(lineVector[8]); // add GFF "group". unused in BED + bed.start--; + } + else { + cerr << "Error: unexpected number of fields at line: " << lineNum << + ". Verify that your files are TAB-delimited and that your GFF file has 8 or 9 fields. Exiting..." << endl; + exit(1); + } + if (bed.start > bed.end) { + cerr << "Error: malformed GFF entry at line " << lineNum << ". Start was greater than end. Exiting." << endl; + exit(1); + } + if ( (bed.start < 0) || (bed.end < 0) ) { + cerr << "Error: malformed GFF entry at line " << lineNum << ". Coordinate detected that is < 1. Exiting." << endl; + exit(1); + } + return true; + } + else if (numFields == 1) { + cerr << "Only one GFF field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + else if ((numFields != this->bedType) && (numFields != 0)) { + cerr << "Differing number of GFF fields encountered at line: " << lineNum << ". Exiting..." << endl; + exit(1); + } + else if ((numFields < 8) && (numFields != 0)) { + cerr << "TAB delimited GFF file with 8 or 9 fields is required at line: "<< lineNum << ". Exiting..." << endl; + exit(1); + } + return false; + } + + +public: + + /* + reportBedTab + + Writes the _original_ BED entry with a TAB + at the end of the line. + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedTab(const T &bed) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + CHRPOS start = bed.start; + CHRPOS end = bed.end; + if (bed.zeroLength) { + if (_isGff == false) + start++; + end--; + } + + // BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\t", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + // GFF + else if (_isGff == true) { + // "GFF-8" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-9" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + + /* + reportBedNewLine + + Writes the _original_ BED entry with a NEWLINE + at the end of the line. + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedNewLine(const T &bed) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + CHRPOS start = bed.start; + CHRPOS end = bed.end; + if (bed.zeroLength) { + if (_isGff == false) + start++; + end--; + } + + //BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\n", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("\t%s", othIt->c_str()); + } + printf("\n"); + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + printf("\n"); + } + // GFF + else if (_isGff == true) { + // "GFF-8" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-9" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + + /* + reportBedRangeNewLine + + Writes a custom start->end for a BED entry + with a NEWLINE at the end of the line. + + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedRangeTab(const T &bed, CHRPOS start, CHRPOS end) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + if (bed.zeroLength) { + start = bed.start + 1; + end = bed.end - 1; + } + // BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\t", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), bed.start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + // GFF + else if (_isGff == true) { + // "GFF-8" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-9" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + + /* + reportBedRangeTab + + Writes a custom start->end for a BED entry + with a TAB at the end of the line. + + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedRangeNewLine(const T &bed, CHRPOS start, CHRPOS end) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + if (bed.zeroLength) { + start = bed.start + 1; + end = bed.end - 1; + } + // BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\n", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("\t%s", othIt->c_str()); + } + printf("\n"); + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), bed.start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + printf("\n"); + } + // GFF + else if (_isGff == true) { + // "GFF-9" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-8" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + /* + reportNullBedTab + */ + void reportNullBedTab() { + + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf (".\t-1\t-1\t"); + } + else if (this->bedType == 4) { + printf (".\t-1\t-1\t.\t"); + } + else if (this->bedType == 5) { + printf (".\t-1\t-1\t.\t-1\t"); + } + else if (this->bedType == 6) { + printf (".\t-1\t-1\t.\t-1\t.\t"); + } + else if (this->bedType > 6) { + printf (".\t-1\t-1\t.\t-1\t.\t"); + for (unsigned int i = 6; i < this->bedType; ++i) { + printf(".\t"); + } + } + } + else if (_isGff == true && _isVcf == false) { + if (this->bedType == 8) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t"); + } + else if (this->bedType == 9) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\t"); + } + } + } + + + /* + reportNullBedTab + */ + void reportNullBedNewLine() { + + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf (".\t-1\t-1\n"); + } + else if (this->bedType == 4) { + printf (".\t-1\t-1\t.\n"); + } + else if (this->bedType == 5) { + printf (".\t-1\t-1\t.\t-1\n"); + } + else if (this->bedType == 6) { + printf (".\t-1\t-1\t.\t-1\t.\n"); + } + else if (this->bedType > 6) { + printf (".\t-1\t-1\t.\t-1\t."); + for (unsigned int i = 6; i < this->bedType; ++i) { + printf("\t."); + } + printf("\n"); + } + } + else if (_isGff == true && _isVcf == false) { + if (this->bedType == 8) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\n"); + } + else if (this->bedType == 9) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\n"); + } + } + } + + +}; + +#endif /* BEDFILE_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedFile/bedFile.h.orig Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,1144 @@ +/***************************************************************************** + bedFile.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef BEDFILE_H +#define BEDFILE_H + +// "local" includes +#include "gzstream.h" +#include "lineFileUtilities.h" +#include "fileType.h" + +// standard includes +#include <vector> +#include <map> +#include <set> +#include <string> +#include <iostream> +#include <fstream> +#include <sstream> +#include <cstring> +#include <algorithm> +#include <limits.h> +#include <stdint.h> +#include <cstdio> +//#include <tr1/unordered_map> // Experimental. +using namespace std; + + +//************************************************* +// Data type tydedef +//************************************************* +typedef uint32_t CHRPOS; +typedef uint16_t BINLEVEL; +typedef uint32_t BIN; +typedef uint16_t USHORT; +typedef uint32_t UINT; + +//************************************************* +// Genome binning constants +//************************************************* + +const BIN _numBins = 37450; +const BINLEVEL _binLevels = 7; + +// bins range in size from 16kb to 512Mb +// Bin 0 spans 512Mbp, # Level 1 +// Bins 1-8 span 64Mbp, # Level 2 +// Bins 9-72 span 8Mbp, # Level 3 +// Bins 73-584 span 1Mbp # Level 4 +// Bins 585-4680 span 128Kbp # Level 5 +// Bins 4681-37449 span 16Kbp # Level 6 +const BIN _binOffsetsExtended[] = {32678+4096+512+64+8+1, 4096+512+64+8+1, 512+64+8+1, 64+8+1, 8+1, 1, 0}; +//const BIN _binOffsetsExtended[] = {4096+512+64+8+1, 4096+512+64+8+1, 512+64+8+1, 64+8+1, 8+1, 1, 0}; + +const USHORT _binFirstShift = 14; /* How much to shift to get to finest bin. */ +const USHORT _binNextShift = 3; /* How much to shift to get to next larger bin. */ + + +//************************************************* +// Common data structures +//************************************************* + +struct DEPTH { + UINT starts; + UINT ends; +}; + + +/* + Structure for regular BED records +*/ +struct BED { + + // Regular BED fields + string chrom; + CHRPOS start; + CHRPOS end; + string name; + string score; + string strand; + + // Add'l fields for BED12 and/or custom BED annotations + vector<string> otherFields; + + // experimental fields for the FJOIN approach. + bool zeroLength; + bool added; + bool finished; + // list of hits from another file. + vector<BED> overlaps; + +public: + // constructors + + // Null + BED() + : chrom(""), + start(0), + end(0), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BED3 + BED(string chrom, CHRPOS start, CHRPOS end) + : chrom(chrom), + start(start), + end(end), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BED4 + BED(string chrom, CHRPOS start, CHRPOS end, string strand) + : chrom(chrom), + start(start), + end(end), + name(""), + score(""), + strand(strand), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BED6 + BED(string chrom, CHRPOS start, CHRPOS end, string name, + string score, string strand) + : chrom(chrom), + start(start), + end(end), + name(name), + score(score), + strand(strand), + otherFields(), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + // BEDALL + BED(string chrom, CHRPOS start, CHRPOS end, string name, + string score, string strand, vector<string> otherFields) + : chrom(chrom), + start(start), + end(end), + name(name), + score(score), + strand(strand), + otherFields(otherFields), + zeroLength(false), + added(false), + finished(false), + overlaps() + {} + + int size() { + return end-start; + } + +}; // BED + + +/* + Structure for each end of a paired BED record + mate points to the other end. +*/ +struct MATE { + BED bed; + int lineNum; + MATE *mate; +}; + + +/* + Structure for regular BED COVERAGE records +*/ +struct BEDCOV { + + string chrom; + + // Regular BED fields + CHRPOS start; + CHRPOS end; + string name; + string score; + string strand; + + // Add'l fields for BED12 and/or custom BED annotations + vector<string> otherFields; + + // flag a zero-length feature + bool zeroLength; + + // Additional fields specific to computing coverage + map<unsigned int, DEPTH> depthMap; + unsigned int count; + CHRPOS minOverlapStart; + + + public: + // constructors + // Null + BEDCOV() + : chrom(""), + start(0), + end(0), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + depthMap(), + count(0), + minOverlapStart(0) + {} +}; + + +/* + Structure for BED COVERAGE records having lists of + multiple coverages +*/ +struct BEDCOVLIST { + + // Regular BED fields + string chrom; + CHRPOS start; + CHRPOS end; + string name; + string score; + string strand; + + // Add'l fields for BED12 and/or custom BED annotations + vector<string> otherFields; + + // flag a zero-length feature + bool zeroLength; + + // Additional fields specific to computing coverage + vector< map<unsigned int, DEPTH> > depthMapList; + vector<unsigned int> counts; + vector<CHRPOS> minOverlapStarts; + + + public: + // constructors + // Null + BEDCOVLIST() + : chrom(""), + start(0), + end(0), + name(""), + score(""), + strand(""), + otherFields(), + zeroLength(false), + depthMapList(), + counts(0), + minOverlapStarts(0) + {} +}; + + +// enum to flag the state of a given line in a BED file. +enum BedLineStatus +{ + BED_INVALID = -1, + BED_HEADER = 0, + BED_BLANK = 1, + BED_VALID = 2 +}; + +// enum to indicate the type of file we are dealing with +enum FileType +{ + BED_FILETYPE, + GFF_FILETYPE, + VCF_FILETYPE +}; + +//************************************************* +// Data structure typedefs +//************************************************* +typedef vector<BED> bedVector; +typedef vector<BEDCOV> bedCovVector; +typedef vector<MATE> mateVector; +typedef vector<BEDCOVLIST> bedCovListVector; + +typedef map<BIN, bedVector, std::less<BIN> > binsToBeds; +typedef map<BIN, bedCovVector, std::less<BIN> > binsToBedCovs; +typedef map<BIN, mateVector, std::less<BIN> > binsToMates; +typedef map<BIN, bedCovListVector, std::less<BIN> > binsToBedCovLists; + +typedef map<string, binsToBeds, std::less<string> > masterBedMap; +typedef map<string, binsToBedCovs, std::less<string> > masterBedCovMap; +typedef map<string, binsToMates, std::less<string> > masterMateMap; +typedef map<string, binsToBedCovLists, std::less<string> > masterBedCovListMap; +typedef map<string, bedVector, std::less<string> > masterBedMapNoBin; + + +// EXPERIMENTAL - wait for TR1 +// typedef vector<BED> bedVector; +// typedef vector<BEDCOV> bedCovVector; +// +// typedef tr1::unordered_map<BIN, bedVector> binsToBeds; +// typedef tr1::unordered_map<BIN, bedCovVector> binsToBedCovs; +// +// typedef tr1::unordered_map<string, binsToBeds> masterBedMap; +// typedef tr1::unordered_map<string, binsToBedCovs> masterBedCovMap; +// typedef tr1::unordered_map<string, bedVector> masterBedMapNoBin; + + + +// return the genome "bin" for a feature with this start and end +inline +BIN getBin(CHRPOS start, CHRPOS end) { + --end; + start >>= _binFirstShift; + end >>= _binFirstShift; + + for (register short i = 0; i < _binLevels; ++i) { + if (start == end) return _binOffsetsExtended[i] + start; + start >>= _binNextShift; + end >>= _binNextShift; + } + cerr << "start " << start << ", end " << end << " out of range in findBin (max is 512M)" << endl; + return 0; +} + +/**************************************************** +// isInteger(s): Tests if string s is a valid integer +*****************************************************/ +inline bool isInteger(const std::string& s) { + int len = s.length(); + for (int i = 0; i < len; i++) { + if (!std::isdigit(s[i])) return false; + } + return true; +} + + +// return the amount of overlap between two features. Negative if none and the the +// number of negative bases is the distance between the two. +inline +int overlaps(CHRPOS aS, CHRPOS aE, CHRPOS bS, CHRPOS bE) { + return min(aE, bE) - max(aS, bS); +} + + +// Ancillary functions +void splitBedIntoBlocks(const BED &bed, int lineNum, bedVector &bedBlocks); + + +// BED Sorting Methods +bool sortByChrom(const BED &a, const BED &b); +bool sortByStart(const BED &a, const BED &b); +bool sortBySizeAsc(const BED &a, const BED &b); +bool sortBySizeDesc(const BED &a, const BED &b); +bool sortByScoreAsc(const BED &a, const BED &b); +bool sortByScoreDesc(const BED &a, const BED &b); +bool byChromThenStart(BED const &a, BED const &b); + + + +//************************************************ +// BedFile Class methods and elements +//************************************************ +class BedFile { + +public: + + // Constructor + BedFile(string &); + + // Destructor + ~BedFile(void); + + // Open a BED file for reading (creates an istream pointer) + void Open(void); + + // Close an opened BED file. + void Close(void); + + // Get the next BED entry in an opened BED file. + BedLineStatus GetNextBed (BED &bed, int &lineNum); + + // load a BED file into a map keyed by chrom, then bin. value is vector of BEDs + void loadBedFileIntoMap(); + + // load a BED file into a map keyed by chrom, then bin. value is vector of BEDCOVs + void loadBedCovFileIntoMap(); + + // load a BED file into a map keyed by chrom, then bin. value is vector of BEDCOVLISTs + void loadBedCovListFileIntoMap(); + + // load a BED file into a map keyed by chrom. value is vector of BEDs + void loadBedFileIntoMapNoBin(); + + // Given a chrom, start, end and strand for a single feature, + // search for all overlapping features in another BED file. + // Searches through each relevant genome bin on the same chromosome + // as the single feature. Note: Adapted from kent source "binKeeperFind" + void FindOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, vector<BED> &hits, bool forceStrand); + + // return true if at least one overlap was found. otherwise, return false. + bool FindOneOrMoreOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, + bool forceStrand, float overlapFraction = 0.0); + + // return true if at least one __reciprocal__ overlap was found. otherwise, return false. + bool FindOneOrMoreReciprocalOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end, string strand, + bool forceStrand, float overlapFraction = 0.0); + + // Given a chrom, start, end and strand for a single feature, + // increment a the number of hits for each feature in B file + // that the feature overlaps + void countHits(const BED &a, bool forceStrand = false, bool countsOnly = false); + + // same as above, but has special logic that processes a set of + // BED "blocks" from a single entry so as to avoid over-counting + // each "block" of a single BAM/BED12 as distinct coverage. That is, + // if one read has four block, we only want to count the coverage as + // coming from one read, not four. + void countSplitHits(const vector<BED> &bedBlock, bool forceStrand = false, bool countsOnly = false); + + // Given a chrom, start, end and strand for a single feature, + // increment a the number of hits for each feature in B file + // that the feature overlaps + void countListHits(const BED &a, int index, bool forceStrand); + + // the bedfile with which this instance is associated + string bedFile; + unsigned int bedType; // 3-6, 12 for BED + // 9 for GFF + bool isZeroBased; + + // Main data structires used by BEDTools + masterBedCovMap bedCovMap; + masterBedCovListMap bedCovListMap; + masterBedMap bedMap; + masterBedMapNoBin bedMapNoBin; + +private: + + // data + bool _isGff; + bool _isVcf; + bool _typeIsKnown; // do we know the type? (i.e., BED, GFF, VCF) + FileType _fileType; // what is the file type? (BED? GFF? VCF?) + istream *_bedStream; + string _bedLine; + vector<string> _bedFields; + + void setZeroBased(bool zeroBased); + void setGff (bool isGff); + void setVcf (bool isVcf); + void setFileType (FileType type); + void setBedType (int colNums); + + /****************************************************** + Private definitions to circumvent linker issues with + templated member functions. + *******************************************************/ + + /* + parseLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline BedLineStatus parseLine (T &bed, const vector<string> &lineVector, int &lineNum) { + + //char *p2End, *p3End, *p4End, *p5End; + //long l2, l3, l4, l5; + unsigned int numFields = lineVector.size(); + + // bail out if we have a blank line + if (numFields == 0) { + return BED_BLANK; + } + + if ((lineVector[0].find("track") == string::npos) && (lineVector[0].find("browser") == string::npos) && (lineVector[0].find("#") == string::npos) ) { + + if (numFields >= 3) { + // line parsing for all lines after the first non-header line + if (_typeIsKnown == true) { + switch(_fileType) { + case BED_FILETYPE: + if (parseBedLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + case VCF_FILETYPE: + if (parseVcfLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + case GFF_FILETYPE: + if (parseGffLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + default: + printf("ERROR: file type encountered. Exiting\n"); + exit(1); + } + } + // line parsing for first non-header line: figure out file contents + else { + // it's BED format if columns 2 and 3 are integers + if (isInteger(lineVector[1]) && isInteger(lineVector[2])) { + setGff(false); + setZeroBased(true); + setFileType(BED_FILETYPE); + setBedType(numFields); // we now expect numFields columns in each line + if (parseBedLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + } + // it's VCF, assuming the second column is numeric and there are at least 8 fields. + else if (isInteger(lineVector[1]) && numFields >= 8) { + setGff(false); + setVcf(true); + setZeroBased(false); + setFileType(VCF_FILETYPE); + setBedType(numFields); // we now expect numFields columns in each line + if (parseVcfLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + } + // it's GFF, assuming columns columns 4 and 5 are numeric and we have 9 fields total. + else if ((numFields >= 8) && isInteger(lineVector[3]) && isInteger(lineVector[4])) { + setGff(true); + setZeroBased(false); + setFileType(GFF_FILETYPE); + setBedType(numFields); // we now expect numFields columns in each line + if (parseGffLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID; + } + else { + cerr << "Unexpected file format. Please use tab-delimited BED, GFF, or VCF. " << + "Perhaps you have non-integer starts or ends at line " << lineNum << "?" << endl; + exit(1); + } + } + } + else { + cerr << "It looks as though you have less than 3 columns at line: " << lineNum << ". Are you sure your files are tab-delimited?" << endl; + exit(1); + } + } + else { + lineNum--; + return BED_HEADER; + } + // default + return BED_INVALID; + } + + + /* + parseBedLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline bool parseBedLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) { + + // process as long as the number of fields in this + // line matches what we expect for this file. + if (numFields == this->bedType) { + bed.chrom = lineVector[0]; + bed.start = atoi(lineVector[1].c_str()); + bed.end = atoi(lineVector[2].c_str()); + + // handle starts == end (e.g., insertions in reference genome) + if (bed.start == bed.end) { + bed.start--; + bed.end++; + bed.zeroLength = true; + } + + if (this->bedType == 4) { + bed.name = lineVector[3]; + } + else if (this->bedType == 5) { + bed.name = lineVector[3]; + bed.score = lineVector[4]; + } + else if (this->bedType == 6) { + bed.name = lineVector[3]; + bed.score = lineVector[4]; + bed.strand = lineVector[5]; + } + else if (this->bedType > 6) { + bed.name = lineVector[3]; + bed.score = lineVector[4]; + bed.strand = lineVector[5]; + for (unsigned int i = 6; i < lineVector.size(); ++i) { + bed.otherFields.push_back(lineVector[i]); + } + } + else if (this->bedType != 3) { + cerr << "Error: unexpected number of fields at line: " << lineNum + << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + + // sanity checks. + if ((bed.start <= bed.end) && (bed.start >= 0) && (bed.end >= 0)) { + return true; + } + else if (bed.start > bed.end) { + cerr << "Error: malformed BED entry at line " << lineNum << ". Start was greater than end. Exiting." << endl; + exit(1); + } + else if ( (bed.start < 0) || (bed.end < 0) ) { + cerr << "Error: malformed BED entry at line " << lineNum << ". Coordinate detected that is < 0. Exiting." << endl; + exit(1); + } + } + else if (numFields == 1) { + cerr << "Only one BED field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + else if ((numFields != this->bedType) && (numFields != 0)) { + cerr << "Differing number of BED fields encountered at line: " << lineNum << ". Exiting..." << endl; + exit(1); + } + else if ((numFields < 3) && (numFields != 0)) { + cerr << "TAB delimited BED file with at least 3 fields (chrom, start, end) is required at line: "<< lineNum << ". Exiting..." << endl; + exit(1); + } + return false; + } + + + /* + parseVcfLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline bool parseVcfLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) { + if (numFields == this->bedType) { + bed.chrom = lineVector[0]; + bed.start = atoi(lineVector[1].c_str()) - 1; // VCF is one-based + bed.end = bed.start + lineVector[3].size(); // VCF 4.0 stores the size of the affected REF allele. + bed.strand = "+"; + // construct the name from the ref and alt alleles. + // if it's an annotated variant, add the rsId as well. + bed.name = lineVector[3] + "/" + lineVector[4]; + if (lineVector[2] != ".") { + bed.name += "_" + lineVector[2]; + } + + if (this->bedType > 2) { + for (unsigned int i = 2; i < numFields; ++i) + bed.otherFields.push_back(lineVector[i]); + } + + if ((bed.start <= bed.end) && (bed.start > 0) && (bed.end > 0)) { + return true; + } + else if (bed.start > bed.end) { + cerr << "Error: malformed VCF entry at line " << lineNum << ". Start was greater than end. Exiting." << endl; + exit(1); + } + else if ( (bed.start < 0) || (bed.end < 0) ) { + cerr << "Error: malformed VCF entry at line " << lineNum << ". Coordinate detected that is < 0. Exiting." << endl; + exit(1); + } + } + else if (numFields == 1) { + cerr << "Only one VCF field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + else if ((numFields != this->bedType) && (numFields != 0)) { + cerr << "Differing number of VCF fields encountered at line: " << lineNum << ". Exiting..." << endl; + exit(1); + } + else if ((numFields < 2) && (numFields != 0)) { + cerr << "TAB delimited VCF file with at least 2 fields (chrom, pos) is required at line: "<< lineNum << ". Exiting..." << endl; + exit(1); + } + return false; + } + + + + /* + parseGffLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.) + */ + template <typename T> + inline bool parseGffLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) { + if (numFields == this->bedType) { + if (this->bedType >= 8 && _isGff) { + bed.chrom = lineVector[0]; + bed.start = atoi(lineVector[3].c_str()); + bed.end = atoi(lineVector[4].c_str()); + bed.name = lineVector[2]; + bed.score = lineVector[5]; + bed.strand = lineVector[6].c_str(); + bed.otherFields.push_back(lineVector[1]); // add GFF "source". unused in BED + bed.otherFields.push_back(lineVector[7]); // add GFF "fname". unused in BED + // handle the optional 9th field. + if (this->bedType == 9) + bed.otherFields.push_back(lineVector[8]); // add GFF "group". unused in BED + + // handle starts == end (e.g., insertions in reference genome) + if (bed.start == bed.end) { + bed.end++; + bed.zeroLength = true; + } + // GFF uses 1-based starts, covert to zero-based + bed.start--; + } + else { + cerr << "Error: unexpected number of fields at line: " << lineNum << + ". Verify that your files are TAB-delimited and that your GFF file has 8 or 9 fields. Exiting..." << endl; + exit(1); + } + if (bed.start > bed.end) { + cerr << "Error: malformed GFF entry at line " << lineNum << ". Start was greater than end. Exiting." << endl; + exit(1); + } + else if ( (bed.start < 0) || (bed.end < 0) ) { + cerr << "Error: malformed GFF entry at line " << lineNum << ". Coordinate detected that is < 1. Exiting." << endl; + exit(1); + } + else return true; + } + else if (numFields == 1) { + cerr << "Only one GFF field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + else if ((numFields != this->bedType) && (numFields != 0)) { + cerr << "Differing number of GFF fields encountered at line: " << lineNum << ". Exiting..." << endl; + exit(1); + } + else if ((numFields < 8) && (numFields != 0)) { + cerr << "TAB delimited GFF file with 8 or 9 fields is required at line: "<< lineNum << ". Exiting..." << endl; + exit(1); + } + return false; + } + + +public: + + /* + reportBedTab + + Writes the _original_ BED entry with a TAB + at the end of the line. + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedTab(const T &bed) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + CHRPOS start = bed.start; + CHRPOS end = bed.end; + if (bed.zeroLength) { + if (_isGff == false) + start++; + end--; + } + + // BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\t", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + // GFF + else if (_isGff == true) { + // "GFF-8" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-9" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + + /* + reportBedNewLine + + Writes the _original_ BED entry with a NEWLINE + at the end of the line. + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedNewLine(const T &bed) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + CHRPOS start = bed.start; + CHRPOS end = bed.end; + if (bed.zeroLength) { + if (_isGff == false) + start++; + end--; + } + + //BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\n", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("\t%s", othIt->c_str()); + } + printf("\n"); + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + printf("\n"); + } + // GFF + else if (_isGff == true) { + // "GFF-8" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-9" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + + /* + reportBedRangeNewLine + + Writes a custom start->end for a BED entry + with a NEWLINE at the end of the line. + + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedRangeTab(const T &bed, CHRPOS start, CHRPOS end) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + if (bed.zeroLength) { + start = bed.start + 1; + end = bed.end - 1; + } + + // BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\t", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), bed.start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + } + // GFF + else if (_isGff == true) { + // "GFF-8" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-9" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + + /* + reportBedRangeTab + + Writes a custom start->end for a BED entry + with a TAB at the end of the line. + + Works for BED3 - BED6. + */ + template <typename T> + inline void reportBedRangeNewLine(const T &bed, CHRPOS start, CHRPOS end) { + + // if it is azeroLength feature, we need to + // correct the start and end coords to what they were + // in the original file + if (bed.zeroLength) { + start = bed.start + 1; + end = bed.end - 1; + } + + // BED + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf ("%s\t%d\t%d\n", bed.chrom.c_str(), start, end); + } + else if (this->bedType == 4) { + printf ("%s\t%d\t%d\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str()); + } + else if (this->bedType == 5) { + printf ("%s\t%d\t%d\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str()); + } + else if (this->bedType == 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + } + else if (this->bedType > 6) { + printf ("%s\t%d\t%d\t%s\t%s\t%s", bed.chrom.c_str(), start, end, bed.name.c_str(), + bed.score.c_str(), bed.strand.c_str()); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("\t%s", othIt->c_str()); + } + printf("\n"); + } + } + // VCF + else if (_isGff == false && _isVcf == true) { + printf ("%s\t%d\t", bed.chrom.c_str(), bed.start+1); + + vector<string>::const_iterator othIt = bed.otherFields.begin(); + vector<string>::const_iterator othEnd = bed.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("%s\t", othIt->c_str()); + } + printf("\n"); + } + // GFF + else if (_isGff == true) { + // "GFF-9" + if (this->bedType == 8) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str()); + } + // "GFF-8" + else if (this->bedType == 9) { + printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(), + bed.name.c_str(), start+1, end, + bed.score.c_str(), bed.strand.c_str(), + bed.otherFields[1].c_str(), bed.otherFields[2].c_str()); + } + } + } + + + /* + reportNullBedTab + */ + void reportNullBedTab() { + + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf (".\t-1\t-1\t"); + } + else if (this->bedType == 4) { + printf (".\t-1\t-1\t.\t"); + } + else if (this->bedType == 5) { + printf (".\t-1\t-1\t.\t-1\t"); + } + else if (this->bedType == 6) { + printf (".\t-1\t-1\t.\t-1\t.\t"); + } + else if (this->bedType > 6) { + printf (".\t-1\t-1\t.\t-1\t.\t"); + for (unsigned int i = 6; i < this->bedType; ++i) { + printf(".\t"); + } + } + } + else if (_isGff == true && _isVcf == false) { + if (this->bedType == 8) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t"); + } + else if (this->bedType == 9) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\t"); + } + } + } + + + /* + reportNullBedTab + */ + void reportNullBedNewLine() { + + if (_isGff == false && _isVcf == false) { + if (this->bedType == 3) { + printf (".\t-1\t-1\n"); + } + else if (this->bedType == 4) { + printf (".\t-1\t-1\t.\n"); + } + else if (this->bedType == 5) { + printf (".\t-1\t-1\t.\t-1\n"); + } + else if (this->bedType == 6) { + printf (".\t-1\t-1\t.\t-1\t.\n"); + } + else if (this->bedType > 6) { + printf (".\t-1\t-1\t.\t-1\t."); + for (unsigned int i = 6; i < this->bedType; ++i) { + printf("\t."); + } + printf("\n"); + } + } + else if (_isGff == true && _isVcf == false) { + if (this->bedType == 8) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\n"); + } + else if (this->bedType == 9) { + printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\n"); + } + } + } + + +}; + +#endif /* BEDFILE_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedFilePE/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,29 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= bedFilePE.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=lineFileUtilities.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedFilePE/bedFilePE.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,530 @@ +// +// bedFilePE.cpp +// BEDTools +// +// Created by Aaron Quinlan Spring 2009. +// Copyright 2009 Aaron Quinlan. All rights reserved. +// +// Summary: Contains common functions for finding BED overlaps. +// +// Acknowledgments: Much of the code herein is taken from Jim Kent's +// BED processing code. I am grateful for his elegant +// genome binning algorithm and therefore use it extensively. + + +#include "bedFilePE.h" + + +// Constructor +BedFilePE::BedFilePE(string &bedFile) { + this->bedFile = bedFile; +} + +// Destructor +BedFilePE::~BedFilePE(void) { +} + +void BedFilePE::Open(void) { + if (bedFile == "stdin" || bedFile == "-") { + _bedStream = &cin; + } + else { + _bedStream = new ifstream(bedFile.c_str(), ios::in); + + if (isGzipFile(_bedStream) == true) { + delete _bedStream; + _bedStream = new igzstream(bedFile.c_str(), ios::in); + } + // can we open the file? + if ( !(_bedStream->good()) ) { + cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + } +} + + + +// Close the BEDPE file +void BedFilePE::Close(void) { + if (bedFile != "stdin" && bedFile != "-") delete _bedStream; +} + + +BedLineStatus BedFilePE::GetNextBedPE (BEDPE &bedpe, int &lineNum) { + + // make sure there are still lines to process. + // if so, tokenize, validate and return the BEDPE entry. + if (_bedStream->good()) { + string bedPELine; + vector<string> bedPEFields; + bedPEFields.reserve(10); + + // parse the bedStream pointer + getline(*_bedStream, bedPELine); + lineNum++; + + // split into a string vector. + Tokenize(bedPELine,bedPEFields); + + // load the BEDPE struct as long as it's a valid BEDPE entry. + return parseLine(bedpe, bedPEFields, lineNum); + } + // default if file is closed or EOF + return BED_INVALID; +} + + +/* + reportBedPETab + + Writes the _original_ BED entry for A. + Works for BEDPE only. +*/ +void BedFilePE::reportBedPETab(const BEDPE &a) { + + if (this->bedType == 6) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2); + } + else if (this->bedType == 7) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str()); + } + else if (this->bedType == 8) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str(), a.score.c_str()); + } + else if (this->bedType == 10) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str()); + } + else if (this->bedType > 10) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str()); + + vector<string>::const_iterator othIt = a.otherFields.begin(); + vector<string>::const_iterator othEnd = a.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("\t%s", othIt->c_str()); + } + printf("\t"); + } +} + + + +/* + reportBedPENewLine + + Writes the _original_ BED entry for A. + Works for BEDPE only. +*/ +void BedFilePE::reportBedPENewLine(const BEDPE &a) { + + if (this->bedType == 6) { + printf("%s\t%d\t%d\t%s\t%d\t%d\n", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2); + } + else if (this->bedType == 7) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\n", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str()); + } + else if (this->bedType == 8) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\n", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str(), a.score.c_str()); + } + else if (this->bedType == 10) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str()); + } + else if (this->bedType > 10) { + printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", a.chrom1.c_str(), a.start1, a.end1, + a.chrom2.c_str(), a.start2, a.end2, + a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str()); + + vector<string>::const_iterator othIt = a.otherFields.begin(); + vector<string>::const_iterator othEnd = a.otherFields.end(); + for ( ; othIt != othEnd; ++othIt) { + printf("\t%s", othIt->c_str()); + } + printf("\n"); + } +} + + +BedLineStatus BedFilePE::parseLine (BEDPE &bedpe, const vector<string> &lineVector, int &lineNum) { + + // bail out if we have a blank line + if (lineVector.empty()) + return BED_BLANK; + + if ((lineVector[0].find("track") == string::npos) && (lineVector[0].find("browser") == string::npos) && (lineVector[0].find("#") == string::npos) ) { + // we need at least 6 columns + if (lineVector.size() >= 6) { + if (parseBedPELine(bedpe, lineVector, lineNum) == true) + return BED_VALID; + else return BED_INVALID; + } + else { + cerr << "It looks as though you have less than 6 columns. Are you sure your files are tab-delimited?" << endl; + exit(1); + } + } + else { + lineNum--; + return BED_HEADER; + } + + // default + return BED_INVALID; +} + + +bool BedFilePE::parseBedPELine (BEDPE &bed, const vector<string> &lineVector, const int &lineNum) { + + if ((lineNum == 1) && (lineVector.size() >= 6)) { + + this->bedType = lineVector.size(); + + if (this->bedType == 6) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + return true; + } + else if (this->bedType == 7) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + return true; + } + else if (this->bedType == 8) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + bed.score = lineVector[7].c_str(); + return true; + } + else if (this->bedType == 10) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + bed.score = lineVector[7].c_str(); + + bed.strand1 = lineVector[8]; + bed.strand2 = lineVector[9]; + + return true; + } + else if (this->bedType > 10) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + bed.score = lineVector[7].c_str(); + + bed.strand1 = lineVector[8]; + bed.strand2 = lineVector[9]; + + for (unsigned int i = 10; i < lineVector.size(); ++i) { + bed.otherFields.push_back(lineVector[i]); + } + return true; + } + else { + cerr << "Unexpected number of fields: " << lineNum << ". Verify that your files are TAB-delimited and that your BEDPE file has 6,7,8 or 10 fields. Exiting..." << endl; + exit(1); + } + + if (bed.start1 > bed.end1) { + cerr << "Error: malformed BEDPE entry at line " << lineNum << ". Start1 was greater than End1. Ignoring it and moving on." << endl; + return false; + } + else if (bed.start2 > bed.end2) { + cerr << "Error: malformed BEDPE entry at line " << lineNum << ". Start2 was greater than End2. Ignoring it and moving on." << endl; + return false; + } + else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { + cerr << "Error: malformed BEDPE entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl; + return false; + } + } + else if ( (lineNum > 1) && (lineVector.size() == this->bedType)) { + + if (this->bedType == 6) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + return true; + } + else if (this->bedType == 7) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + return true; + } + else if (this->bedType == 8) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + bed.score = lineVector[7].c_str(); + return true; + } + else if (this->bedType == 10) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + bed.score = lineVector[7].c_str(); + + bed.strand1 = lineVector[8]; + bed.strand2 = lineVector[9]; + + return true; + } + else if (this->bedType > 10) { + bed.chrom1 = lineVector[0]; + bed.start1 = atoi(lineVector[1].c_str()); + bed.end1 = atoi(lineVector[2].c_str()); + + bed.chrom2 = lineVector[3]; + bed.start2 = atoi(lineVector[4].c_str()); + bed.end2 = atoi(lineVector[5].c_str()); + + bed.name = lineVector[6]; + bed.score = lineVector[7].c_str(); + + bed.strand1 = lineVector[8]; + bed.strand2 = lineVector[9]; + + for (unsigned int i = 10; i < lineVector.size(); ++i) { + bed.otherFields.push_back(lineVector[i]); + } + return true; + } + else { + cerr << "Unexpected number of fields: " << lineNum << ". Verify that your files are TAB-delimited and that your BEDPE file has 6,7,8 or 10 fields. Exiting..." << endl; + exit(1); + } + + if (bed.start1 > bed.end1) { + cerr << "Error: malformed BED entry at line " << lineNum << ". Start1 was greater than End1. Ignoring it and moving on." << endl; + return false; + } + else if (bed.start2 > bed.end2) { + cerr << "Error: malformed BED entry at line " << lineNum << ". Start2 was greater than End2. Ignoring it and moving on." << endl; + return false; + } + else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { + cerr << "Error: malformed BED entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl; + return false; + } + } + else if (lineVector.size() == 1) { + cerr << "Only one BED field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl; + exit(1); + } + else if ((lineVector.size() != this->bedType) && (lineVector.size() != 0)) { + cerr << "Differing number of BEDPE fields encountered at line: " << lineNum << ". Exiting..." << endl; + exit(1); + } + else if ((lineVector.size() < 6) && (lineVector.size() != 0)) { + cerr << "TAB delimited BEDPE file with at least 6 fields (chrom1, start1, end1, chrom2, start2, end2) is required at line: "<< lineNum << ". Exiting..." << endl; + exit(1); + } + return false; +} + + +/* + Adapted from kent source "binKeeperFind" +*/ +void BedFilePE::FindOverlapsPerBin(int bEnd, string chrom, CHRPOS start, CHRPOS end, string name, string strand, + vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames) { + + int startBin, endBin; + startBin = (start >> _binFirstShift); + endBin = ((end-1) >> _binFirstShift); + + // loop through each bin "level" in the binning hierarchy + for (int i = 0; i < _binLevels; ++i) { + + // loop through each bin at this level of the hierarchy + int offset = _binOffsetsExtended[i]; + for (int j = (startBin+offset); j <= (endBin+offset); ++j) { + + // loop through each feature in this chrom/bin and see if it overlaps + // with the feature that was passed in. if so, add the feature to + // the list of hits. + vector<MATE>::const_iterator bedItr; + vector<MATE>::const_iterator bedEnd; + if (bEnd == 1) { + bedItr = bedMapEnd1[chrom][j].begin(); + bedEnd = bedMapEnd1[chrom][j].end(); + } + else if (bEnd == 2) { + bedItr = bedMapEnd2[chrom][j].begin(); + bedEnd = bedMapEnd2[chrom][j].end(); + } + else { + cerr << "Unexpected end of B requested" << endl; + } + for (; bedItr != bedEnd; ++bedItr) { + float overlap = overlaps(bedItr->bed.start, bedItr->bed.end, start, end); + float size = end - start; + + if ( (overlap / size) >= overlapFraction ) { + + // skip the hit if not on the same strand (and we care) + if ((forceStrand == false) && (enforceDiffNames == false)) { + hits.push_back(*bedItr); // it's a hit, add it. + } + else if ((forceStrand == true) && (enforceDiffNames == false)) { + if (strand == bedItr->bed.strand) + hits.push_back(*bedItr); // it's a hit, add it. + } + else if ((forceStrand == true) && (enforceDiffNames == true)) { + if ((strand == bedItr->bed.strand) && (name != bedItr->bed.name)) + hits.push_back(*bedItr); // it's a hit, add it. + } + else if ((forceStrand == false) && (enforceDiffNames == true)) { + if (name != bedItr->bed.name) + hits.push_back(*bedItr); // it's a hit, add it. + } + } + + } + } + startBin >>= _binNextShift; + endBin >>= _binNextShift; + } +} + + +void BedFilePE::loadBedPEFileIntoMap() { + + int lineNum = 0; + int bin1, bin2; + BedLineStatus bedStatus; + BEDPE bedpeEntry, nullBedPE; + + Open(); + bedStatus = this->GetNextBedPE(bedpeEntry, lineNum); + while (bedStatus != BED_INVALID) { + + if (bedStatus == BED_VALID) { + MATE *bedEntry1 = new MATE(); + MATE *bedEntry2 = new MATE(); + // separate the BEDPE entry into separate + // BED entries + splitBedPEIntoBeds(bedpeEntry, lineNum, bedEntry1, bedEntry2); + + // load end1 into a UCSC bin map + bin1 = getBin(bedEntry1->bed.start, bedEntry1->bed.end); + this->bedMapEnd1[bedEntry1->bed.chrom][bin1].push_back(*bedEntry1); + + // load end2 into a UCSC bin map + bin2 = getBin(bedEntry2->bed.start, bedEntry2->bed.end); + this->bedMapEnd2[bedEntry2->bed.chrom][bin2].push_back(*bedEntry2); + + bedpeEntry = nullBedPE; + } + bedStatus = this->GetNextBedPE(bedpeEntry, lineNum); + } + Close(); +} + + +void BedFilePE::splitBedPEIntoBeds(const BEDPE &bedpeEntry, const int &lineNum, MATE *bedEntry1, MATE *bedEntry2) { + + /* + Split the BEDPE entry into separate BED entries + + NOTE: I am using a trick here where I store + the lineNum of the BEDPE from the original file + in the "count" column. This allows me to later + resolve whether the hits found on both ends of BEDPE A + came from the same entry in BEDPE B. Tracking by "name" + alone with fail when there are multiple mappings for a given + read-pair. + */ + + bedEntry1->bed.chrom = bedpeEntry.chrom1; + bedEntry1->bed.start = bedpeEntry.start1; + bedEntry1->bed.end = bedpeEntry.end1; + bedEntry1->bed.name = bedpeEntry.name; + bedEntry1->bed.score = bedpeEntry.score; // only store the score in end1 to save memory + bedEntry1->bed.strand = bedpeEntry.strand1; + bedEntry1->bed.otherFields = bedpeEntry.otherFields; // only store the otherFields in end1 to save memory + bedEntry1->lineNum = lineNum; + bedEntry1->mate = bedEntry2; // keep a pointer to end2 + + bedEntry2->bed.chrom = bedpeEntry.chrom2; + bedEntry2->bed.start = bedpeEntry.start2; + bedEntry2->bed.end = bedpeEntry.end2; + bedEntry2->bed.name = bedpeEntry.name; + bedEntry2->bed.strand = bedpeEntry.strand2; + bedEntry2->lineNum = lineNum; + bedEntry2->mate = bedEntry1; // keep a pointer to end1 +} + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedFilePE/bedFilePE.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,93 @@ +#ifndef BEDFILEPE_H +#define BEDFILEPE_H + +#include <vector> +#include <map> +#include <string> +#include <iostream> +#include <fstream> +#include <sstream> +#include <cstring> +#include <algorithm> +#include "bedFile.h" +#include "lineFileUtilities.h" + +using namespace std; + + +/* + Structure for paired-end records +*/ +struct BEDPE { + + // UCSC BED fields + string chrom1; + CHRPOS start1; + CHRPOS end1; + + string chrom2; + CHRPOS start2; + CHRPOS end2; + + string name; + string score; + + string strand1; + string strand2; + + vector<string> otherFields; +}; + + + + +//************************************************ +// BedFile Class methods and elements +//************************************************ +class BedFilePE { + +public: + + // Constructor + BedFilePE(string &); + + // Destructor + ~BedFilePE(void); + + // Open a BEDPE file for reading (creates an istream pointer) + void Open(void); + + // Close an opened BEDPE file. + void Close(void); + + // Get the next BED entry in an opened BED file. + BedLineStatus GetNextBedPE (BEDPE &bedpe, int &lineNum); + + + // Methods + + void reportBedPETab(const BEDPE &a); + void reportBedPENewLine(const BEDPE &a); + void loadBedPEFileIntoMap(); + void splitBedPEIntoBeds(const BEDPE &a, const int &lineNum, MATE *bedEntry1, MATE *bedEntry2); + + + void FindOverlapsPerBin(int bEnd, string chrom, CHRPOS start, CHRPOS end, string name, string strand, + vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames); + + + string bedFile; + unsigned int bedType; + + masterMateMap bedMapEnd1; + masterMateMap bedMapEnd2; + +private: + istream *_bedStream; + + // methods + BedLineStatus parseLine (BEDPE &bedpe, const vector<string> &lineVector, int &lineNum); + bool parseBedPELine (BEDPE &bed, const vector<string> &lineVector, const int &lineNum); +}; + +#endif /* BEDFILEPE_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedGraphFile/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,31 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= bedGraphFile.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedGraphFile/bedGraphFile.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,58 @@ +/***************************************************************************** + bedGraphFile.cpp + + (c) 2010 - Assaf Gordon + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "bedGraphFile.h" +#include <sstream> + +// Constructor +BedGraphFile::BedGraphFile(string &_file) : + bedGraphFile(_file), + _bedGraphStream(NULL) +{} + + +// Destructor +BedGraphFile::~BedGraphFile() { + Close(); +} + + +// Open the BEDGRAPH file +void BedGraphFile::Open() { + if (bedGraphFile == "stdin" || bedGraphFile == "-") { + _bedGraphStream = &cin; + } + else { + _bedGraphStream = new ifstream(bedGraphFile.c_str(), ios::in); + + if (isGzipFile(_bedGraphStream) == true) { + delete _bedGraphStream; + _bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in); + } + // can we open the file? + if ( !(_bedGraphStream->good()) ) { + cerr << "Error: The requested bed file (" << bedGraphFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + } +} + + +// Close the BEDGRAPH file +void BedGraphFile::Close() { + if (bedGraphFile != "stdin" && bedGraphFile != "-") { + if (_bedGraphStream) { + delete _bedGraphStream; + _bedGraphStream = NULL ; + } + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/bedGraphFile/bedGraphFile.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,199 @@ +/***************************************************************************** + bedGraphFile.cpp + + (c) 2010 - Assaf Gordon + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef BEDGRAPHFILE_H +#define BEDGRAPHFILE_H + +#include "gzstream.h" +#include "lineFileUtilities.h" +#include "fileType.h" +#include <vector> +#include <map> +#include <set> +#include <string> +#include <iostream> +#include <fstream> +#include <sstream> +#include <cstring> +#include <algorithm> +#include <limits.h> +#include <stdint.h> +#include <cstdio> + +using namespace std; + +//************************************************* +// Data type tydedef +//************************************************* +#ifndef CHRPOS +typedef uint32_t CHRPOS; +#endif + +#ifndef DEPTH +typedef uint32_t DEPTH; +#endif + +/* + Structure for regular BedGraph records + */ +template <typename T> +class BEDGRAPH +{ +public: + std::string chrom; + CHRPOS start; + CHRPOS end; + T depth; + +public: + typedef T DEPTH_TYPE; + // constructors + + // Null + BEDGRAPH() : + start(0), + end(0), + depth(T()) + {} + + // BEDGraph + BEDGRAPH(string _chrom, CHRPOS _start, CHRPOS _end, T _depth) : + chrom(_chrom), + start(_start), + end(_end), + depth(_depth) + {} +}; // BEDGraph + +typedef BEDGRAPH<int32_t> BEDGRAPH_INT; +typedef BEDGRAPH<std::string> BEDGRAPH_STR; +typedef BEDGRAPH<double> BEDGRAPH_FLOAT; + +template <typename T> +std::ostream& operator<< (std::ostream& strm, const BEDGRAPH<T>& bg) +{ + strm << bg.chrom << "\t" + << bg.start << "\t" + << bg.end << "\t" + << bg.depth; + return strm; +} + +// enum to flag the state of a given line in a BEDGraph file. +enum BedGraphLineStatus +{ + BEDGRAPH_INVALID = -1, + BEDGRAPH_HEADER = 0, + BEDGRAPH_BLANK = 1, + BEDGRAPH_VALID = 2 +}; + + +//************************************************ +// BedGraphFile Class methods and elements +//************************************************ +class BedGraphFile { + +public: + + // Constructor + BedGraphFile(string &); + + // Destructor + ~BedGraphFile(void); + + // Open a BEDGraph file for reading (creates an istream pointer) + void Open(void); + + // Close an opened BED file. + void Close(void); + + // Get the next BED entry in an opened BED file. + template <typename T> + BedGraphLineStatus GetNextBedGraph (BEDGRAPH<T> &bedgraph, int &lineNum) + { + // make sure there are still lines to process. + // if so, tokenize, validate and return the BED entry. + if (_bedGraphStream->good()) { + string bedGraphLine; + vector<string> bedGraphFields; + + // parse the bedStream pointer + getline(*_bedGraphStream, bedGraphLine); + if (_bedGraphStream->eof()) + return BEDGRAPH_INVALID; + if (_bedGraphStream->bad()) { + cerr << "Error while reading file '" << bedGraphFile << "' : " + << strerror(errno) << endl; + exit(1); + } + lineNum++; + + // split into a string vector. + Tokenize(bedGraphLine,bedGraphFields); + + // load the BED struct as long as it's a valid BED entry. + return parseLine(bedgraph, bedGraphFields, lineNum); + } + + // default if file is closed or EOF + return BEDGRAPH_INVALID; + } + + // the bedfile with which this instance is associated + string bedGraphFile; + +private: + // data + istream *_bedGraphStream; + + template <typename T> + BedGraphLineStatus parseLine (BEDGRAPH<T> &bg, const vector<string> &lineVector, int &lineNum) + { + if (lineVector.size() == 0) + return BEDGRAPH_BLANK; + + if (lineVector[0].find("track") != string::npos || + lineVector[0].find("browser") != string::npos || + lineVector[0].find("#") != string::npos) + return BEDGRAPH_HEADER; + + if (lineVector.size() != 4) + return BEDGRAPH_INVALID; + + bg.chrom = lineVector[0]; + + stringstream str_start(lineVector[1]); + if (! (str_start >> bg.start) ) { + cerr << "Input error, failed to extract start value from '" << lineVector[1] + << "' (column 2) in " << bedGraphFile << " line " << lineNum << endl; + exit(1); + } + + stringstream str_end(lineVector[2]); + if (! (str_end >> bg.end) ) { + cerr << "Input error, failed to extract end value from '" << lineVector[2] + << "' (column 3) in " << bedGraphFile << " line " << lineNum << endl; + exit(1); + } + + stringstream str_depth(lineVector[3]); + if (! (str_depth >> bg.depth) ) { + cerr << "Input error, failed to extract depth value from '" << lineVector[3] + << "' (column 4) in " << bedGraphFile << " line " << lineNum << endl; + exit(1); + } + + return BEDGRAPH_VALID; + } +}; + +#endif /* BEDFILE_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/chromsweep/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,32 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= chromsweep.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=lineFileUtilities.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/chromsweep/chromsweep.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,180 @@ +/***************************************************************************** + chromsweep.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "chromsweep.h" +#include <queue> + +bool after(const BED &a, const BED &b); +void report_hits(const BED &curr_qy, const vector<BED> &hits); +vector<BED> scan_cache(const BED &curr_qy, BedLineStatus qy_status, const vector<BED> &db_cache, vector<BED> &hits); + + +/* + // constructor using existing BedFile pointers +*/ +ChromSweep::ChromSweep(BedFile *bedA, BedFile *bedB, bool sameStrand, bool diffStrand) +: _bedA(bedA) +, _bedB(bedB) +, _sameStrand(sameStrand) +, _diffStrand(diffStrand) +{ + // prime the results pump. + _qy_lineNum = 0; + _db_lineNum = 0; + + _hits.reserve(1000); + _cache.reserve(1000); + + _bedA->Open(); + _bedB->Open(); + _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum); + _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum); +} + +/* + Constructor with filenames +*/ +ChromSweep::ChromSweep(string &bedAFile, string &bedBFile) +{ + // prime the results pump. + _qy_lineNum = 0; + _db_lineNum = 0; + + _hits.reserve(100000); + _cache.reserve(100000); + + _bedA = new BedFile(bedAFile); + _bedB = new BedFile(bedBFile); + + _bedA->Open(); + _bedB->Open(); + + _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum); + _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum); +} + + +/* + Destructor +*/ +ChromSweep::~ChromSweep(void) { +} + + +void ChromSweep::ScanCache() { + if (_qy_status != BED_INVALID) { + vector<BED>::iterator c = _cache.begin(); + while (c != _cache.end()) + { + if ((_curr_qy.chrom == c->chrom) && !(after(_curr_qy, *c))) { + if (IsValidHit(_curr_qy, *c)) { + _hits.push_back(*c); + } + ++c; + } + else { + c = _cache.erase(c); + } + } + } +} + + +bool ChromSweep::ChromChange() +{ + // the files are on the same chrom + if ((_curr_qy.chrom == _curr_db.chrom) || (_db_status == BED_INVALID) || (_qy_status == BED_INVALID)) { + return false; + } + // the query is ahead of the database. fast-forward the database to catch-up. + else if (_curr_qy.chrom > _curr_db.chrom) { + while (!_bedB->Empty() && _curr_db.chrom < _curr_qy.chrom) + { + _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum); + } + _cache.clear(); + return false; + } + // the database is ahead of the query. + else { + // 1. scan the cache for remaining hits on the query's current chrom. + if (_curr_qy.chrom == _curr_chrom) + { + ScanCache(); + _results.push(make_pair(_curr_qy, _hits)); + _hits.clear(); + } + // 2. fast-forward until we catch up and report 0 hits until we do. + else if (_curr_qy.chrom < _curr_db.chrom) + { + _results.push(make_pair(_curr_qy, _no_hits)); + _cache.clear(); + } + _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum); + _curr_chrom = _curr_qy.chrom; + return true; + } +} + +bool ChromSweep::IsValidHit(const BED &query, const BED &db) { + // do we have an overlap in the DB? + if (overlaps(query.start, query.end, db.start, db.end) > 0) { + // Now test for necessary strandedness. + bool strands_are_same = (query.strand == db.strand); + if ( (_sameStrand == false && _diffStrand == false) + || + (_sameStrand == true && strands_are_same == true) + || + (_diffStrand == true && strands_are_same == false) + ) + { + return true; + } + } + return false; +} + + +bool ChromSweep::Next(pair<BED, vector<BED> > &next) { + if (!_bedA->Empty()) { + // have we changed chromosomes? + if (ChromChange() == false) { + // scan the database cache for hits + ScanCache(); + // advance the db until we are ahead of the query. update hits and cache as necessary + while (!_bedB->Empty() && _curr_qy.chrom == _curr_db.chrom && !(after(_curr_db, _curr_qy))) + { + if (IsValidHit(_curr_qy, _curr_db)) { + _hits.push_back(_curr_db); + } + _cache.push_back(_curr_db); + _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum); + } + // add the hits for this query to the pump + _results.push(make_pair(_curr_qy, _hits)); + // reset for the next query + _hits.clear(); + _curr_qy = _nullBed; + _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum); + _curr_chrom = _curr_qy.chrom; + } + } + // report the next set if hits if there are still overlaps in the pump + if (!_results.empty()) { + next = _results.front(); + _results.pop(); + return true; + } + // otherwise, the party is over. + else {return false;} +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/chromsweep/chromsweep.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,89 @@ +/***************************************************************************** + chromsweepBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef CHROMSWEEP_H +#define CHROMSWEEP_H + +#include "bedFile.h" +#include <vector> +#include <queue> +#include <iostream> +#include <fstream> +#include <stdlib.h> +using namespace std; + + + +class ChromSweep { + +// public interface. +public: + + // A is the query and B is the database + + // constructor using existing BedFile pointers + ChromSweep(BedFile *bedA, BedFile *bedB, bool sameStrand = false, bool diffStrand = false); + + // constructor using filenames + ChromSweep(string &bedAFile, string &bedBFile); + + // destructor + ~ChromSweep(void); + + // loads next (a pair) with the current query and it's overlaps + // next.first is the current query interval + // next.second is a vector of the current query's hits. + // returns true if overlap + bool Next(pair<BED, vector<BED> > &next); + + // Usage: + // ChromSweep sweep = ChromSweep(_bedA, _bedB); + // pair<BED, vector<BED> > hit_set; + // while (sweep.Next(hit_set)) + // { + // // magic happens here! + // processHits(hit_set.first, hit_set.second); + // } + +// private variables. +private: + + // instances of a bed file class. + BedFile *_bedA, *_bedB; + // do we care about strandedness. + bool _sameStrand, _diffStrand; + // a cache of still active features from the database file + vector<BED> _cache; + // the set of hits in the database for the current query + vector<BED> _hits; + // a queue from which we retrieve overlap results. used by Next() + queue< pair<BED, vector<BED> > > _results; + BED _nullBed; + // an empty BED vector for returning no hits for a given query + vector<BED> _no_hits; + // the current query and db features. + BED _curr_qy, _curr_db; + // a cache of the current chrom from the query. used to handle chrom changes. + string _curr_chrom; + // the current line status in the database and query files + BedLineStatus _qy_status, _db_status; + // the current line numbers in the database and query files + int _qy_lineNum, _db_lineNum; + +// private methods. +private: + + void ScanCache(); + bool ChromChange(); + bool IsValidHit(const BED &query, const BED &db); +}; + +#endif /* CHROMSWEEP_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/fileType/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,29 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= fileType.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS= +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/fileType/fileType.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,71 @@ +/***************************************************************************** +fileType.cpp + +(c) 2009 - Aaron Quinlan +Hall Laboratory +Department of Biochemistry and Molecular Genetics +University of Virginia +aaronquinlan@gmail.com + +Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ + +#include "fileType.h" + + +/* +returns TRUE if the file is a regular file: +not a pipe/device. + +This implies that the file can be opened/closed/seek'd multiple times without losing information +*/ +bool isRegularFile(const string& filename) { + struct stat buf ; + int i; + + i = stat(filename.c_str(), &buf); + if (i!=0) { + cerr << "Error: can't determine file type of '" << filename << "': " << strerror(errno) << endl; + exit(1); + } + if (S_ISREG(buf.st_mode)) + return true; + + return false; +} + +/* +returns TRUE if the file has a GZIP header. +Should only be run on regular files. +*/ +bool isGzipFile(istream *file) { + //see http://www.gzip.org/zlib/rfc-gzip.html#file-format + + /* + 11-Sep-2011: + We now only peek at the first byte and test for GZIPiness. + This is because I can only putback() one byte into an istream + without triggering the "fail" bit. This was necessary to support + FIFOs, per version 2.13.0 + */ + struct { + unsigned char id1; +// unsigned char id2; +// unsigned char cm; + } gzip_header; + + if (!file->read((char*)&gzip_header, sizeof(gzip_header))) { + return false; + } + + if ( gzip_header.id1 == 0x1f ) +// && +// gzip_header.id2 == 0x8b +// && +// gzip_header.cm == 8 ) + { + return true; + } + file->putback(gzip_header.id1); + return false; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/fileType/fileType.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,38 @@ +/***************************************************************************** + fileType.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef FILETYPE_H +#define FILETYPE_H + +#include <string> +#include <iostream> +#include <fstream> +#include <stdlib.h> +#include <string.h> +#include <errno.h> +#include <sys/stat.h> +#include <sys/types.h> +#include <unistd.h> +#include <sstream> + +using namespace std; + +/***************************************************************************** + Convenience functions to detect whether a given file is + "regular" and/or "gzipped". + + Kindly contributed by Assaf Gordon. +******************************************************************************/ +string string_error(int errnum); +bool isRegularFile(const string& filename); +bool isGzipFile(istream *file); + +#endif /* FILETYPE_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/genomeFile/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,32 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../ +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= genomeFile.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=lineFileUtilities.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/genomeFile/genomeFile.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,103 @@ +/***************************************************************************** + genomeFile.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "genomeFile.h" + + +GenomeFile::GenomeFile(const string &genomeFile) { + _genomeFile = genomeFile; + loadGenomeFileIntoMap(); +} + +GenomeFile::GenomeFile(const RefVector &genome) { + for (size_t i = 0; i < genome.size(); ++i) { + string chrom = genome[i].RefName; + int length = genome[i].RefLength; + + _chromSizes[chrom] = length; + _chromList.push_back(chrom); + } +} + +// Destructor +GenomeFile::~GenomeFile(void) { +} + + +void GenomeFile::loadGenomeFileIntoMap() { + + string genomeLine; + int lineNum = 0; + vector<string> genomeFields; // vector for a GENOME entry + + // open the GENOME file for reading + ifstream genome(_genomeFile.c_str(), ios::in); + if ( !genome ) { + cerr << "Error: The requested genome file (" << _genomeFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + + while (getline(genome, genomeLine)) { + + Tokenize(genomeLine,genomeFields); // load the fields into the vector + lineNum++; + + // ignore a blank line + if (genomeFields.size() > 0) { + if (genomeFields[0].find("#") == string::npos) { + + // we need at least 2 columns + if (genomeFields.size() >= 2) { + char *p2End; + long c2; + // make sure the second column is numeric. + c2 = strtol(genomeFields[1].c_str(), &p2End, 10); + + // strtol will set p2End to the start of the string if non-integral, base 10 + if (p2End != genomeFields[1].c_str()) { + string chrom = genomeFields[0]; + int size = atoi(genomeFields[1].c_str()); + _chromSizes[chrom] = size; + _chromList.push_back(chrom); + } + } + else { + cerr << "Less than the req'd two fields were encountered in the genome file (" << _genomeFile << ")"; + cerr << " at line " << lineNum << ". Exiting." << endl; + exit (1); + } + } + } + genomeFields.clear(); + } +} + + +int GenomeFile::getChromSize(const string &chrom) { + chromToSizes::const_iterator chromIt = _chromSizes.find(chrom); + if (chromIt != _chromSizes.end()) + return _chromSizes[chrom]; + else + return -1; // chrom not found. +} + +vector<string> GenomeFile::getChromList() { + return _chromList; +} + +int GenomeFile::getNumberOfChroms() { + return _chromList.size(); +} + +string GenomeFile::getGenomeFileName() { + return _genomeFile; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/genomeFile/genomeFile.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,62 @@ +/***************************************************************************** + genomeFile.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef GENOMEFILE_H +#define GENOMEFILE_H + +#include <map> +#include <string> +#include <iostream> +#include <sstream> +#include <fstream> +#include <cstring> +#include <cstdio> +#include "api/BamReader.h" +#include "api/BamAux.h" +using namespace BamTools; + +using namespace std; + + +// typedef for mapping b/w chrom name and it's size in b.p. +typedef map<string, int, std::less<string> > chromToSizes; + + +class GenomeFile { + +public: + + // Constructor using a file + GenomeFile(const string &genomeFile); + + // Constructor using a vector of BamTools RefVector + GenomeFile(const RefVector &genome); + + // Destructor + ~GenomeFile(void); + + // load a GENOME file into a map keyed by chrom. value is size of chrom. + void loadGenomeFileIntoMap(); + + int getChromSize(const string &chrom); // return the size of a chromosome + vector<string> getChromList(); // return a list of chrom names + int getNumberOfChroms(); // return the number of chroms + string getGenomeFileName(); // return the name of the genome file + + + +private: + string _genomeFile; + chromToSizes _chromSizes; + vector<string> _chromList; +}; + +#endif /* GENOMEFILE_H */
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/gzstream/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,49 @@ +# ============================================================================ +# gzstream, C++ iostream classes wrapping the zlib compression library. +# Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner +# +# This library is free software; you can redistribute it and/or +# modify it under the terms of the GNU Lesser General Public +# License as published by the Free Software Foundation; either +# version 2.1 of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this library; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# ============================================================================ +# +# File : Makefile +# Revision : $Revision: 1.3 $ +# Revision_date : $Date: 2001/10/04 15:09:28 $ +# Author(s) : Deepak Bandyopadhyay, Lutz Kettner +# +# ============================================================================ + +# ---------------------------------------------------------------------------- +# adapt these settings to your need: +# add '-DGZSTREAM_NAMESPACE=name' to CPPFLAGS to place the classes +# in its own namespace. Note, this macro needs to be set while creating +# the library as well while compiling applications based on it. +# As an alternative, gzstream.C and gzstream.h can be edited. +# ---------------------------------------------------------------------------- + +INCLUDES = -I. +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ + +${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h + ${CXX} ${CXXFLAGS} -c -o ${OBJ_DIR}/gzstream.o gzstream.C $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/gzstream/README Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,6 @@ + + gzstream + C++ iostream classes wrapping the zlib compression library. +=========================================================================== + + See index.html for documentation and installation instructions.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/gzstream/gzstream.C Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,165 @@ +// ============================================================================ +// gzstream, C++ iostream classes wrapping the zlib compression library. +// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner +// +// This library is free software; you can redistribute it and/or +// modify it under the terms of the GNU Lesser General Public +// License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// Lesser General Public License for more details. +// +// You should have received a copy of the GNU Lesser General Public +// License along with this library; if not, write to the Free Software +// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +// ============================================================================ +// +// File : gzstream.C +// Revision : $Revision: 1.7 $ +// Revision_date : $Date: 2003/01/08 14:41:27 $ +// Author(s) : Deepak Bandyopadhyay, Lutz Kettner +// +// Standard streambuf implementation following Nicolai Josuttis, "The +// Standard C++ Library". +// ============================================================================ + +#include <gzstream.h> +#include <iostream> +#include <string.h> // for memcpy + +#ifdef GZSTREAM_NAMESPACE +namespace GZSTREAM_NAMESPACE { +#endif + +// ---------------------------------------------------------------------------- +// Internal classes to implement gzstream. See header file for user classes. +// ---------------------------------------------------------------------------- + +// -------------------------------------- +// class gzstreambuf: +// -------------------------------------- + +gzstreambuf* gzstreambuf::open( const char* name, int open_mode) { + if ( is_open()) + return (gzstreambuf*)0; + mode = open_mode; + // no append nor read/write mode + if ((mode & std::ios::ate) || (mode & std::ios::app) + || ((mode & std::ios::in) && (mode & std::ios::out))) + return (gzstreambuf*)0; + char fmode[10]; + char* fmodeptr = fmode; + if ( mode & std::ios::in) + *fmodeptr++ = 'r'; + else if ( mode & std::ios::out) + *fmodeptr++ = 'w'; + *fmodeptr++ = 'b'; + *fmodeptr = '\0'; + file = gzopen( name, fmode); + if (file == 0) + return (gzstreambuf*)0; + opened = 1; + return this; +} + +gzstreambuf * gzstreambuf::close() { + if ( is_open()) { + sync(); + opened = 0; + if ( gzclose( file) == Z_OK) + return this; + } + return (gzstreambuf*)0; +} + +int gzstreambuf::underflow() { // used for input buffer only + if ( gptr() && ( gptr() < egptr())) + return * reinterpret_cast<unsigned char *>( gptr()); + + if ( ! (mode & std::ios::in) || ! opened) + return EOF; + // Josuttis' implementation of inbuf + int n_putback = gptr() - eback(); + if ( n_putback > 4) + n_putback = 4; + memcpy( buffer + (4 - n_putback), gptr() - n_putback, n_putback); + + int num = gzread( file, buffer+4, bufferSize-4); + if (num <= 0) // ERROR or EOF + return EOF; + + // reset buffer pointers + setg( buffer + (4 - n_putback), // beginning of putback area + buffer + 4, // read position + buffer + 4 + num); // end of buffer + + // return next character + return * reinterpret_cast<unsigned char *>( gptr()); +} + +int gzstreambuf::flush_buffer() { + // Separate the writing of the buffer from overflow() and + // sync() operation. + int w = pptr() - pbase(); + if ( gzwrite( file, pbase(), w) != w) + return EOF; + pbump( -w); + return w; +} + +int gzstreambuf::overflow( int c) { // used for output buffer only + if ( ! ( mode & std::ios::out) || ! opened) + return EOF; + if (c != EOF) { + *pptr() = c; + pbump(1); + } + if ( flush_buffer() == EOF) + return EOF; + return c; +} + +int gzstreambuf::sync() { + // Changed to use flush_buffer() instead of overflow( EOF) + // which caused improper behavior with std::endl and flush(), + // bug reported by Vincent Ricard. + if ( pptr() && pptr() > pbase()) { + if ( flush_buffer() == EOF) + return -1; + } + return 0; +} + +// -------------------------------------- +// class gzstreambase: +// -------------------------------------- + +gzstreambase::gzstreambase( const char* name, int mode) { + init( &buf); + open( name, mode); +} + +gzstreambase::~gzstreambase() { + buf.close(); +} + +void gzstreambase::open( const char* name, int open_mode) { + if ( ! buf.open( name, open_mode)) + clear( rdstate() | std::ios::badbit); +} + +void gzstreambase::close() { + if ( buf.is_open()) + if ( ! buf.close()) + clear( rdstate() | std::ios::badbit); +} + +#ifdef GZSTREAM_NAMESPACE +} // namespace GZSTREAM_NAMESPACE +#endif + +// ============================================================================ +// EOF //
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/gzstream/gzstream.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,121 @@ +// ============================================================================ +// gzstream, C++ iostream classes wrapping the zlib compression library. +// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner +// +// This library is free software; you can redistribute it and/or +// modify it under the terms of the GNU Lesser General Public +// License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// Lesser General Public License for more details. +// +// You should have received a copy of the GNU Lesser General Public +// License along with this library; if not, write to the Free Software +// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +// ============================================================================ +// +// File : gzstream.h +// Revision : $Revision: 1.5 $ +// Revision_date : $Date: 2002/04/26 23:30:15 $ +// Author(s) : Deepak Bandyopadhyay, Lutz Kettner +// +// Standard streambuf implementation following Nicolai Josuttis, "The +// Standard C++ Library". +// ============================================================================ + +#ifndef GZSTREAM_H +#define GZSTREAM_H 1 + +// standard C++ with new header file names and std:: namespace +#include <iostream> +#include <fstream> +#include <zlib.h> + +#ifdef GZSTREAM_NAMESPACE +namespace GZSTREAM_NAMESPACE { +#endif + +// ---------------------------------------------------------------------------- +// Internal classes to implement gzstream. See below for user classes. +// ---------------------------------------------------------------------------- + +class gzstreambuf : public std::streambuf { +private: + static const int bufferSize = 47+256; // size of data buff + // totals 512 bytes under g++ for igzstream at the end. + + gzFile file; // file handle for compressed file + char buffer[bufferSize]; // data buffer + char opened; // open/close state of stream + int mode; // I/O mode + + int flush_buffer(); +public: + gzstreambuf() : opened(0) { + setp( buffer, buffer + (bufferSize-1)); + setg( buffer + 4, // beginning of putback area + buffer + 4, // read position + buffer + 4); // end position + // ASSERT: both input & output capabilities will not be used together + } + int is_open() { return opened; } + gzstreambuf* open( const char* name, int open_mode); + gzstreambuf* close(); + ~gzstreambuf() { close(); } + + virtual int overflow( int c = EOF); + virtual int underflow(); + virtual int sync(); +}; + +class gzstreambase : virtual public std::ios { +protected: + gzstreambuf buf; +public: + gzstreambase() { init(&buf); } + gzstreambase( const char* name, int open_mode); + ~gzstreambase(); + void open( const char* name, int open_mode); + void close(); + gzstreambuf* rdbuf() { return &buf; } +}; + +// ---------------------------------------------------------------------------- +// User classes. Use igzstream and ogzstream analogously to ifstream and +// ofstream respectively. They read and write files based on the gz* +// function interface of the zlib. Files are compatible with gzip compression. +// ---------------------------------------------------------------------------- + +class igzstream : public gzstreambase, public std::istream { +public: + igzstream() : std::istream( &buf) {} + igzstream( const char* name, int open_mode = std::ios::in) + : gzstreambase( name, open_mode), std::istream( &buf) {} + gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); } + void open( const char* name, int open_mode = std::ios::in) { + gzstreambase::open( name, open_mode); + } +}; + +class ogzstream : public gzstreambase, public std::ostream { +public: + ogzstream() : std::ostream( &buf) {} + ogzstream( const char* name, int mode = std::ios::out) + : gzstreambase( name, mode), std::ostream( &buf) {} + gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); } + void open( const char* name, int open_mode = std::ios::out) { + gzstreambase::open( name, open_mode); + } +}; + +#ifdef GZSTREAM_NAMESPACE +} // namespace GZSTREAM_NAMESPACE +#endif + +#endif // GZSTREAM_H +// ============================================================================ +// EOF // +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/gzstream/version Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,1 @@ +1.5 (08 Jan 2003)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/lineFileUtilities/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,29 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= lineFileUtilities.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS= +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/lineFileUtilities/lineFileUtilities.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,15 @@ +// +// lineFileUtilities.cpp +// BEDTools +// +// Created by Aaron Quinlan Spring 2009. +// Copyright 2009 Aaron Quinlan. All rights reserved. +// +// Summary: Contains common functions for processing text files. +// +#include <sstream> +#include <iostream> +#include "lineFileUtilities.h" + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/lineFileUtilities/lineFileUtilities.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,52 @@ +#ifndef LINEFILEUTILITIES_H +#define LINEFILEUTILITIES_H + +#include <vector> +#include <string> +#include <cstring> +#include <cstdlib> +#include <sstream> + +using namespace std; + +// templated function to convert objects to strings +template <typename T> +inline +std::string ToString(const T & value) { + std::stringstream ss; + ss << value; + return ss.str(); +} + +// tokenize into a list of strings. +inline +void Tokenize(const string &str, vector<string> &elems, const string &delimiter = "\t") +{ + char* tok; + char cchars [str.size()+1]; + char* cstr = &cchars[0]; + strcpy(cstr, str.c_str()); + tok = strtok(cstr, delimiter.c_str()); + while (tok != NULL) { + elems.push_back(tok); + tok = strtok(NULL, delimiter.c_str()); + } +} + +// tokenize into a list of integers +inline +void Tokenize(const string &str, vector<int> &elems, const string &delimiter = "\t") +{ + char* tok; + char cchars [str.size()+1]; + char* cstr = &cchars[0]; + strcpy(cstr, str.c_str()); + tok = strtok(cstr, delimiter.c_str()); + while (tok != NULL) { + elems.push_back(atoi(tok)); + tok = strtok(NULL, delimiter.c_str()); + } +} + +#endif /* LINEFILEUTILITIES_H */ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/sequenceUtilities/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,29 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= sequenceUtils.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS = +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/sequenceUtilities/sequenceUtils.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,126 @@ +// +// sequenceUtils.cpp +// BEDTools +// +// Created by Aaron Quinlan Spring 2009. +// Copyright 2009 Aaron Quinlan. All rights reserved. +// +// Summary: Contains common functions for manipulating DNA sequences. +// +// Acknowledgment: I am grateful to Michael Stromberg for the code below to +// reverse complement a sequence. + +#include "sequenceUtils.h" + +// Performs an in-place sequence reversal +void reverseSequence(string &seq) { + std::reverse(seq.begin(), seq.end()); +} + +// Performs an in-place reverse complement conversion +void reverseComplement(string &seq) { + + // reverse the sequence + reverseSequence(seq); + + // swap the bases + for(unsigned int i = 0; i < seq.length(); i++) { + switch(seq[i]) { + case 'A': + seq[i] = 'T'; + break; + case 'C': + seq[i] = 'G'; + break; + case 'G': + seq[i] = 'C'; + break; + case 'T': + seq[i] = 'A'; + break; + case 'a': + seq[i] = 't'; + break; + case 'c': + seq[i] = 'g'; + break; + case 'g': + seq[i] = 'c'; + break; + case 't': + seq[i] = 'a'; + break; + default: + break; + } + } +} + + +void toLowerCase(std::string &seq) +{ + const int length = seq.length(); + for(int i=0; i < length; ++i) + { + seq[i] = std::tolower(seq[i]); + } +} + + +void toUpperCase(std::string &seq) +{ + const int length = seq.length(); + for(int i=0; i < length; ++i) + { + seq[i] = std::toupper(seq[i]); + } +} + + +void getDnaContent(const string &seq, int &a, int &c, int &g, int &t, int &n, int &other) +{ + // swap the bases + for(unsigned int i = 0; i < seq.length(); i++) { + switch(seq[i]) { + case 'A': + case 'a': + a++; + break; + case 'C': + case 'c': + c++; + break; + case 'G': + case 'g': + g++; + break; + case 'T': + case 't': + t++; + break; + case 'N': + case 'n': + n++; + break; + default: + other++; + break; + } + } +} + + +int countPattern(const string &seq, const string &pattern) +{ + // swap the bases + int patternLength = pattern.size(); + int patternCount = 0; + for(unsigned int i = 0; i < seq.length(); i++) { + if (seq.substr(i,patternLength) == pattern) { + patternCount++; + } + } + return patternCount; +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/sequenceUtilities/sequenceUtils.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,27 @@ +#ifndef SEQUENCEUTILS_H +#define SEQUENCEUTILS_H + +#include <string> +#include <algorithm> +#include <cctype> + +using namespace std; + +// Performs an in-place sequence reversal +void reverseSequence(string &seq); + +// Performs an in-place reverse complement conversion +void reverseComplement(string &seq); + +// Converts every character in a string to lowercase +void toLowerCase(string &seq); + +// Converts every character in a string to uppercase +void toUpperCase(string &seq); + +// Calculates the number of a, c, g, t, n, and other bases found in a sequence +void getDnaContent(const string &seq, int &a, int &c, int &g, int &t, int &n, int &other); + +int countPattern(const string &seq, const string &pattern); + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/stringUtilities/stringUtilities.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,18 @@ +#ifndef STRINGUTILITIES_H +#define STRINGUTILITIES_H + +#include <cctype> +#include <string> + +/**************************************************** +// isInteger(s): Tests if string s is a valid integer +*****************************************************/ +inline bool isInteger(const std::string& s) { + int len = s.length(); + for (int i = 0; i < len; i++) { + if (!std::isdigit(s[i])) return false; + return true; +} + +#endif /* STRINGUTILITIES_H */ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/tabFile/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,29 @@ +OBJ_DIR = ../../../obj/ +BIN_DIR = ../../../bin/ +UTILITIES_DIR = ../../utils/ +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/ + +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= tabFile.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/tabFile/tabFile.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,99 @@ +/***************************************************************************** + tabFile.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "tabFile.h" + +/******************************************* +Class methods +*******************************************/ + +// Constructor +TabFile::TabFile(const string &tabFile) +: _tabFile(tabFile) +{} + +// Destructor +TabFile::~TabFile(void) { +} + + +void TabFile::Open(void) { + if (_tabFile == "stdin") { + _tabStream = &cin; + } + else { + size_t foundPos; + foundPos = _tabFile.find_last_of(".gz"); + // is this a GZIPPED TAB file? + if (foundPos == _tabFile.size() - 1) { + igzstream tabs(_tabFile.c_str(), ios::in); + if ( !tabs ) { + cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + else { + // if so, close it (this was just a test) + tabs.close(); + // now set a pointer to the stream so that we + // can read the file later on. + _tabStream = new igzstream(_tabFile.c_str(), ios::in); + } + } + // not GZIPPED. + else { + + ifstream tabs(_tabFile.c_str(), ios::in); + // can we open the file? + if ( !tabs ) { + cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl; + exit (1); + } + else { + // if so, close it (this was just a test) + tabs.close(); + // now set a pointer to the stream so that we + // can read the file later on. + _tabStream = new ifstream(_tabFile.c_str(), ios::in); + } + } + } +} + + +// Close the TAB file +void TabFile::Close(void) { + if (_tabFile != "stdin") delete _tabStream; +} + + +TabLineStatus TabFile::GetNextTabLine(TAB_FIELDS &tabFields, int &lineNum) { + + // make sure there are still lines to process. + // if so, tokenize, return the TAB_FIELDS. + if (_tabStream->good() == true) { + string tabLine; + tabFields.reserve(20); + + // parse the tabStream pointer + getline(*_tabStream, tabLine); + lineNum++; + + // split into a string vector. + Tokenize(tabLine, tabFields); + + // parse the line and validate it + return parseTabLine(tabFields, lineNum); + } + + // default if file is closed or EOF + return TAB_INVALID; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/tabFile/tabFile.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,80 @@ +/***************************************************************************** + tabFile.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licensed under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef TABFILE_H +#define TABFILE_H + +#include "gzstream.h" +#include <vector> +#include <string> +#include <iostream> + +using namespace std; + +// enum to flag the state of a given line in a TAB file. +enum TabLineStatus +{ + TAB_INVALID = -1, + TAB_HEADER = 0, + TAB_BLANK = 1, + TAB_VALID = 2 +}; + +typedef vector<string> TAB_FIELDS; + +//************************************************ +// TabFile Class methods and elements +//************************************************ +class TabFile { + +public: + + // Constructor + TabFile(const string &tabFile); + + // Destructor + ~TabFile(void); + + // Open a TAB file for reading (creates an istream pointer) + void Open(void); + + // Close an opened TAB file. + void Close(void); + + // Get the next TAB entry in an opened TAB file. + TabLineStatus GetNextTabLine (TAB_FIELDS &tab, int &lineNum); + +private: + + // data + istream *_tabStream; + string _tabFile; + + // methods + inline TabLineStatus parseTabLine (const vector<string> &lineVector, int &lineNum) { + // bail out if we have a blank line + if (lineVector.size() == 0) + return TAB_BLANK; + // real line with data + if (lineVector[0][0] != '#') { + return TAB_VALID; + } + // comment or header line + else { + lineNum--; + return TAB_HEADER; + } + // default + return TAB_INVALID; + } +}; + +#endif /* TABFILE_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/utils/version/version.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,8 @@ +#ifndef VERSION_H +#define VERSION_H + +// define the version. All tools in the +// suite carry the same version number. +#define VERSION "2.14.2" + +#endif /* VERSION_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/windowBed/Makefile Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,51 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \ + -I$(UTILITIES_DIR)/version/ \ + -I$(UTILITIES_DIR)/gzstream/ \ + -I$(UTILITIES_DIR)/genomeFile/ \ + -I$(UTILITIES_DIR)/lineFileUtilities/ \ + -I$(UTILITIES_DIR)/fileType/ \ + -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/BamTools-Ancillary +# ---------------------------------- +# define our source and object files +# ---------------------------------- +SOURCES= windowMain.cpp windowBed.cpp +OBJECTS= $(SOURCES:.cpp=.o) +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o +EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) +BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) +PROGRAM= windowBed + + +all: $(PROGRAM) + +.PHONY: all + +$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" + @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS) + +$(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp + @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) + +$(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ + +clean: + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +.PHONY: clean
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/windowBed/windowBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,253 @@ +/***************************************************************************** + windowBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "windowBed.h" + + +/* + Constructor +*/ +BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop, + bool anyHit, bool noHit, bool writeCount, bool strandWindows, + bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam) { + + _bedAFile = bedAFile; + _bedBFile = bedBFile; + + _leftSlop = leftSlop; + _rightSlop = rightSlop; + + _anyHit = anyHit; + _noHit = noHit; + _writeCount = writeCount; + _strandWindows = strandWindows; + _matchOnSameStrand = matchOnSameStrand; + _matchOnDiffStrand = matchOnDiffStrand; + _bamInput = bamInput; + _bamOutput = bamOutput; + _isUncompressedBam = isUncompressedBam; + + _bedA = new BedFile(bedAFile); + _bedB = new BedFile(bedBFile); + + if (_bamInput == false) + WindowIntersectBed(); + else + WindowIntersectBam(_bedAFile); +} + + + +/* + Destructor +*/ +BedWindow::~BedWindow(void) { +} + + + +void BedWindow::FindWindowOverlaps(const BED &a, vector<BED> &hits) { + + /* + Adjust the start and end of a based on the requested window + */ + + // update the current feature's start and end + // according to the slop requested (slop = 0 by default) + CHRPOS aFudgeStart = 0; + CHRPOS aFudgeEnd; + AddWindow(a, aFudgeStart, aFudgeEnd); + + /* + Now report the hits (if any) based on the window around a. + */ + // get the hits in B for the A feature + _bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, _matchOnSameStrand, _matchOnDiffStrand); + + int numOverlaps = 0; + + // loop through the hits and report those that meet the user's criteria + vector<BED>::const_iterator h = hits.begin(); + vector<BED>::const_iterator hitsEnd = hits.end(); + for (; h != hitsEnd; ++h) { + + int s = max(aFudgeStart, h->start); + int e = min(aFudgeEnd, h->end); + int overlapBases = (e - s); // the number of overlapping bases b/w a and b + int aLength = (a.end - a.start); // the length of a in b.p. + + if (s < e) { + // is there enough overlap (default ~ 1bp) + if ( ((float) overlapBases / (float) aLength) > 0 ) { + numOverlaps++; + if (_anyHit == false && _noHit == false && _writeCount == false) { + _bedA->reportBedTab(a); + _bedB->reportBedNewLine(*h); + } + } + } + } + if (_anyHit == true && (numOverlaps >= 1)) { + _bedA->reportBedNewLine(a); } + else if (_writeCount == true) { + _bedA->reportBedTab(a); printf("\t%d\n", numOverlaps); + } + else if (_noHit == true && (numOverlaps == 0)) { + _bedA->reportBedNewLine(a); + } +} + + +bool BedWindow::FindOneOrMoreWindowOverlaps(const BED &a) { + + // update the current feature's start and end + // according to the slop requested (slop = 0 by default) + CHRPOS aFudgeStart = 0; + CHRPOS aFudgeEnd; + AddWindow(a, aFudgeStart, aFudgeEnd); + + bool overlapsFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _matchOnSameStrand, _matchOnDiffStrand); + return overlapsFound; +} + + +void BedWindow::WindowIntersectBed() { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedFileIntoMap(); + + BED a, nullBed; + int lineNum = 0; // current input line number + BedLineStatus bedStatus; + vector<BED> hits; // vector of potential hits + hits.reserve(100); + + _bedA->Open(); + while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + FindWindowOverlaps(a, hits); + hits.clear(); + a = nullBed; + } + } + _bedA->Close(); +} + + +void BedWindow::WindowIntersectBam(string bamFile) { + + // load the "B" bed file into a map so + // that we can easily compare "A" to it for overlaps + _bedB->loadBedFileIntoMap(); + + // open the BAM file + BamReader reader; + BamWriter writer; + reader.Open(bamFile); + + // get header & reference information + string bamHeader = reader.GetHeaderText(); + RefVector refs = reader.GetReferenceData(); + + // open a BAM output to stdout if we are writing BAM + if (_bamOutput == true) { + // set compression mode + BamWriter::CompressionMode compressionMode = BamWriter::Compressed; + if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed; + writer.SetCompressionMode(compressionMode); + // open our BAM writer + writer.Open("stdout", bamHeader, refs); + } + + vector<BED> hits; // vector of potential hits + // reserve some space + hits.reserve(100); + + _bedA->bedType = 6; + BamAlignment bam; + bool overlapsFound; + // get each set of alignments for each pair. + while (reader.GetNextAlignment(bam)) { + + if (bam.IsMapped()) { + BED a; + a.chrom = refs.at(bam.RefID).RefName; + a.start = bam.Position; + a.end = bam.GetEndPosition(false, false); + + // build the name field from the BAM alignment. + a.name = bam.Name; + if (bam.IsFirstMate()) a.name += "/1"; + if (bam.IsSecondMate()) a.name += "/2"; + + a.score = ToString(bam.MapQuality); + a.strand = "+"; if (bam.IsReverseStrand()) a.strand = "-"; + + if (_bamOutput == true) { + overlapsFound = FindOneOrMoreWindowOverlaps(a); + if (overlapsFound == true) { + if (_noHit == false) + writer.SaveAlignment(bam); + } + else { + if (_noHit == true) + writer.SaveAlignment(bam); + } + } + else { + FindWindowOverlaps(a, hits); + hits.clear(); + } + } + // BAM IsMapped() is false + else if (_noHit == true) { + writer.SaveAlignment(bam); + } + } + + // close the relevant BAM files. + reader.Close(); + if (_bamOutput == true) { + writer.Close(); + } +} + + +void BedWindow::AddWindow(const BED &a, CHRPOS &fudgeStart, CHRPOS &fudgeEnd) { + // Does the user want to treat the windows based on strand? + // If so, + // if "+", then left is left and right is right + // if "-", the left is right and right is left. + if (_strandWindows) { + if (a.strand == "+") { + if ((int) (a.start - _leftSlop) > 0) + fudgeStart = a.start - _leftSlop; + else fudgeStart = 0; + fudgeEnd = a.end + _rightSlop; + } + else { + if ((int) (a.start - _rightSlop) > 0) + fudgeStart = a.start - _rightSlop; + else fudgeStart = 0; + fudgeEnd = a.end + _leftSlop; + } + } + // If not, add the windows irrespective of strand + else { + if ((int) (a.start - _leftSlop) > 0) + fudgeStart = a.start - _leftSlop; + else fudgeStart = 0; + fudgeEnd = a.end + _rightSlop; + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/windowBed/windowBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,69 @@ +/***************************************************************************** + windowBed.h + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#ifndef WINDOWBED_H +#define WINDOWBED_H + +#include "api/BamReader.h" +#include "api/BamWriter.h" +#include "api/BamAux.h" +using namespace BamTools; + +#include "bedFile.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class BedWindow { + +public: + + // constructor + BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop, + bool anyHit, bool noHit, bool writeCount, bool strandWindows, + bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam); + + // destructor + ~BedWindow(void); + +private: + + string _bedAFile; + string _bedBFile; + bool _anyHit; + bool _writeCount; + int _leftSlop; + int _rightSlop; + bool _noHit; + bool _strandWindows; + bool _matchOnSameStrand; + bool _matchOnDiffStrand; + bool _bamInput; + bool _bamOutput; + bool _isUncompressedBam; + + // instance of a bed file class. + BedFile *_bedA, *_bedB; + + // methods + void WindowIntersectBed(); + void WindowIntersectBam(string bamFile); + void FindWindowOverlaps(const BED &a, vector<BED> &hits); + bool FindOneOrMoreWindowOverlaps(const BED &a); + void AddWindow(const BED &a, CHRPOS &fudgeStart, CHRPOS &fudgeEnd); + +}; +#endif /* WINDOWBED_H */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/windowBed/windowMain.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,263 @@ +/***************************************************************************** + windowMain.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "windowBed.h" +#include "version.h" + +using namespace std; + +// define the version +#define PROGRAM_NAME "windowBed" + +// define our parameter checking macro +#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) + +// function declarations +void ShowHelp(void); + + +int main(int argc, char* argv[]) { + + // our configuration variables + bool showHelp = false; + + // input files + string bedAFile; + string bedBFile; + + // input arguments + int leftSlop = 1000; + int rightSlop = 1000; + + bool haveBedA = false; + bool haveBedB = false; + bool noHit = false; + bool anyHit = false; + bool writeCount = false; + bool haveSlop = false; + bool haveLeft = false; + bool haveRight = false; + bool strandWindows = false; + bool matchOnSameStrand = false; + bool matchOnDiffStrand = false; + bool inputIsBam = false; + bool outputIsBam = true; + bool uncompressedBam = false; + + // check to see if we should print out some help + if(argc <= 1) showHelp = true; + + for(int i = 1; i < argc; i++) { + int parameterLength = (int)strlen(argv[i]); + + if((PARAMETER_CHECK("-h", 2, parameterLength)) || + (PARAMETER_CHECK("--help", 5, parameterLength))) { + showHelp = true; + } + } + + if(showHelp) ShowHelp(); + + // do some parsing (all of these parameters require 2 strings) + for(int i = 1; i < argc; i++) { + + int parameterLength = (int)strlen(argv[i]); + + if(PARAMETER_CHECK("-a", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-abam", 5, parameterLength)) { + if ((i+1) < argc) { + haveBedA = true; + inputIsBam = true; + bedAFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-b", 2, parameterLength)) { + if ((i+1) < argc) { + haveBedB = true; + bedBFile = argv[i + 1]; + i++; + } + } + else if(PARAMETER_CHECK("-bed", 4, parameterLength)) { + outputIsBam = false; + } + else if(PARAMETER_CHECK("-u", 2, parameterLength)) { + anyHit = true; + } + else if(PARAMETER_CHECK("-c", 2, parameterLength)) { + writeCount = true; + } + else if (PARAMETER_CHECK("-v", 2, parameterLength)) { + noHit = true; + } + else if (PARAMETER_CHECK("-sw", 3, parameterLength)) { + strandWindows = true; + } + else if (PARAMETER_CHECK("-sm", 3, parameterLength)) { + matchOnSameStrand = true; + } + else if (PARAMETER_CHECK("-Sm", 3, parameterLength)) { + matchOnDiffStrand = true; + } + else if (PARAMETER_CHECK("-w", 2, parameterLength)) { + if ((i+1) < argc) { + haveSlop = true; + leftSlop = atoi(argv[i + 1]); + rightSlop = leftSlop; + i++; + } + } + else if (PARAMETER_CHECK("-l", 2, parameterLength)) { + if ((i+1) < argc) { + haveLeft = true; + leftSlop = atoi(argv[i + 1]); + i++; + } + } + else if (PARAMETER_CHECK("-r", 2, parameterLength)) { + if ((i+1) < argc) { + haveRight = true; + rightSlop = atoi(argv[i + 1]); + i++; + } + } + else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) { + uncompressedBam = true; + } + else { + cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; + showHelp = true; + } + } + + // make sure we have both input files + if (!haveBedA || !haveBedB) { + cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && noHit) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (anyHit && writeCount) { + cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (haveLeft && (leftSlop < 0)) { + cerr << endl << "*****" << endl << "*****ERROR: Upstream window (-l) must be positive." << endl << "*****" << endl; + showHelp = true; + } + + if (haveRight && (rightSlop < 0)) { + cerr << endl << "*****" << endl << "*****ERROR: Downstream window (-r) must be positive." << endl << "*****" << endl; + showHelp = true; + } + + if (haveSlop && (haveLeft || haveRight)) { + cerr << endl << "*****" << endl << "*****ERROR: Cannot choose -w with -l or -r. Either specify -l and -r or specify solely -w" << endl << "*****" << endl; + showHelp = true; + } + + if ((haveLeft && !haveRight) || (haveRight && !haveLeft)) { + cerr << endl << "*****" << endl << "*****ERROR: Please specify both -l and -r." << endl << "*****" << endl; + showHelp = true; + } + + if (matchOnSameStrand && matchOnDiffStrand) { + cerr << endl << "*****" << endl << "*****ERROR: Use either -sm or -Sm, not both." << endl << "*****" << endl; + showHelp = true; + } + + if (!showHelp) { + BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit, + noHit, writeCount, strandWindows, matchOnSameStrand, matchOnDiffStrand, + inputIsBam, outputIsBam, uncompressedBam); + delete bi; + return 0; + } + else { + ShowHelp(); + } +} + + +void ShowHelp(void) { + + cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; + + cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; + + cerr << "Summary: Examines a \"window\" around each feature in A and" << endl; + cerr << "\t reports all features in B that overlap the window. For each" << endl; + cerr << "\t overlap the entire entry in A and B are reported." << endl << endl; + + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl; + + cerr << "Options: " << endl; + + cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl; + + cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl; + + cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl; + cerr << "\t\tis to write output in BAM when using -abam." << endl << endl; + + cerr << "\t-w\t" << "Base pairs added upstream and downstream of each entry" << endl; + cerr << "\t\tin A when searching for overlaps in B." << endl; + cerr << "\t\t- Creates symterical \"windows\" around A." << endl; + cerr << "\t\t- Default is 1000 bp." << endl; + cerr << "\t\t- (INTEGER)" << endl << endl; + + cerr << "\t-l\t" << "Base pairs added upstream (left of) of each entry" << endl; + cerr << "\t\tin A when searching for overlaps in B." << endl; + cerr << "\t\t- Allows one to define assymterical \"windows\"." << endl; + cerr << "\t\t- Default is 1000 bp." << endl; + cerr << "\t\t- (INTEGER)" << endl << endl; + + cerr << "\t-r\t" << "Base pairs added downstream (right of) of each entry" << endl; + cerr << "\t\tin A when searching for overlaps in B." << endl; + cerr << "\t\t- Allows one to define assymterical \"windows\"." << endl; + cerr << "\t\t- Default is 1000 bp." << endl; + cerr << "\t\t- (INTEGER)" << endl << endl; + + cerr << "\t-sw\t" << "Define -l and -r based on strand. For example if used, -l 500" << endl; + cerr << "\t\tfor a negative-stranded feature will add 500 bp downstream." << endl; + cerr << "\t\t- Default = disabled." << endl << endl; + + cerr << "\t-sm\t" << "Only report hits in B that overlap A on the _same_ strand." << endl; + cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + + cerr << "\t-Sm\t" << "Only report hits in B that overlap A on the _opposite_ strand." << endl; + cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + + cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl; + cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl << endl; + + cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl; + cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl; + cerr << "\t\t- Overlaps restricted by -f." << endl << endl; + + cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl; + cerr << "\t\t- Similar to \"grep -v.\"" << endl << endl; + + // end the program here + exit(1); +}