# HG changeset patch
# User pimarin
# Date 1677145824 0
# Node ID 4cacc5b8001b548bc51bb7cf33c142a34e99a686

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools

diff -r 000000000000 -r 4cacc5b8001b coverageBed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverageBed.xml	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,159 @@
+<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>of features in file B on the features in file A (bedtools coverage)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools" />
+    <expand macro="requirements">
+        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
+    </expand>
+    <expand macro="stdio" />
+    <command><![CDATA[
+bedtools coverage
+$d
+$hist
+$split
+$strandedness
+$mean
+#if str($overlap_a):
+    -f $overlap_a
+#end if
+#if str($overlap_b):
+    -F $overlap_b
+#end if
+$reciprocal_overlap
+$a_or_b
+-a '$inputA'
+#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
+    -b '$reduce_or_iterate.inputB'
+#else:
+    -b
+    #for $file in $reduce_or_iterate.inputB
+        '$file'
+    #end for
+#end if
+@SORTED@
+#if $inputA.is_of_type('gff'):
+    | sort -k1,1 -k4,2n
+#else:
+    | sort -k1,1 -k2,2n
+#end if
+> '$output'
+    ]]></command>
+    <inputs>
+        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
+        <conditional name="reduce_or_iterate">
+            <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files">
+                <option value="iterate" selected="true">One output file per 'input B' file</option>
+                <option value="reduce">Single output containing results for all 'input B' files</option>
+            </param>
+            <when value="iterate">
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
+                       label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
+            </when>
+            <when value="reduce">
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
+                       label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
+            </when>
+        </conditional>
+        <expand macro="split" />
+        <param name="strandedness" argument="-s" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
+            help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
+        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
+            label="Report the depth at each position in each A feature"
+            help="Positions reported are one based. Each position and depth follow the complete B feature" />
+        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
+            label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
+            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
+        <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"
+            help="Report the mean depth of all positions in each A feature."/>
+        <expand macro="overlap" name="overlap_a" />
+        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
+        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
+            label="Require that the fraction overlap be reciprocal for A AND B."
+            help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />
+        <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
+            label="Require that the minimum fraction be satisfied for A OR B."
+            help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied" />
+        <!-- -sorted -g  -->
+        <expand macro="sorted" />
+    </inputs>
+    <outputs>
+        <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
+            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
+            <output name="output" file="coverageBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="multiCov1.bed" ftype="bed" />
+            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="sorted" value="true"/>
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="multiCov1.bed" ftype="bed" />
+            <param name="reduce_or_iterate_selector" value="reduce" />
+            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="sorted" value="true"/>
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
+            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
+            <param name="overlap_b" value="1"  />
+            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
+            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
+            <param name="overlap_a" value="1E-5"  />
+            <param name="reciprocal_overlap" value="true"  />
+            <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="multiCov1.bed" ftype="bed" />
+            <param name="reduce_or_iterate_selector" value="reduce" />
+            <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
+            <param name="sorted" value="true"/>
+            <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
+            <param name="inputB" value="coverageBed.bam" ftype="bam" />
+            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
+            <param name="inputB" value="coverageBed.bam" ftype="bam" />
+            <param name="mean" value="true"/>
+            <output name="output" file="mean_coverage.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
+file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
+(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
+One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
+overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
+Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
+
+.. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
+
+.. class:: infomark
+
+The lines in the output will be comprised of each interval in A, followed by:
+
+1. The number of features in B that overlapped (by at least one base pair) the A interval.
+2. The number of bases in A that had non-zero coverage from features in B.
+3. The length of the entry in A.
+4. The fraction of bases in A that had non-zero coverage from features in B.
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 4cacc5b8001b macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,266 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">bedtools</xref>
+        </xrefs>
+    </xml>
+    <token name="@TOOL_VERSION@">2.30.0</token>
+    <token name="@SAMTOOLS_VERSION@">1.9</token>
+    <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
+    <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
+    <token name="@PROFILE@">20.05</token>
+    <xml name="stdio">
+        <stdio>
+            <!-- Anything other than zero is an error -->
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <!-- In case the return code has not been set propery check stderr too -->
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
+        <version_command>bedtools --version</version_command>
+    </xml>
+    <xml name="reciprocal">
+        <param name="reciprocal" argument="-r" type="select" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.">
+            <option value="" selected="true">No</option>
+            <option value="-r">Yes</option>
+        </param>
+    </xml>
+    <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" >
+        <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" />
+    </xml>
+    <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A">
+        <expand macro="fraction" name="@NAME@" argument="@ARGUMENT@" label="Minimum overlap required as a fraction of @FRACOF@" help="Default is 1E-9, i.e. 1bp."/>
+    </xml>
+    <token name="@OVERLAP@"><![CDATA[
+        #if str($overlap):
+            -f $overlap
+        #end if
+    ]]></token>
+    <xml name="strand2">
+        <param name="strand" type="select" label="Calculation based on strandedness?">
+            <option value="" selected="true">Overlaps on either strand</option>
+            <option value="-s">Only overlaps occurring on the **same** strand.</option>
+            <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
+        </param>
+    </xml>
+    <xml name="seed">
+        <conditional name="seed">
+            <param name="seed_choose" type="select" label="Choose Seed?">
+                <option value="False" selected="true">Random Shuffling</option>
+                <option value="True">Choose fixed seed</option>
+            </param>
+            <when value="True">
+                <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
+            </when>
+            <when value="False" />
+        </conditional>
+    </xml>
+    <xml name="split">
+        <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
+            label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
+            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
+    </xml>
+    <xml name="input_conditional_genome_file" token_optional="false" token_help="">
+        <conditional name="genome_file_opts">
+            <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
+                <option value="loc" selected="true">Locally installed Genome file</option>
+                <option value="hist">Genome file from your history</option>
+            </param>
+            <when value="loc">
+                <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
+                    <options from_data_table="__dbkeys__" />
+                </param>
+            </when>
+            <when value="hist">
+                <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
+            </when>
+        </conditional>
+    </xml>
+    <token name="@GENOME_FILE@">
+#if $genome_file_opts.genome
+    -g 
+    #if $genome_file_opts.genome_file_opts_selector == "loc":
+        '$genome_file_opts.genome.fields.len_path'
+    #elif $genome_file_opts.genome_file_opts_selector == "hist":
+        '$genome_file_opts.genome'
+    #end if
+#end if
+    </token>
+    <token name="@GENOME_FILE_MAKEWINDOWS@">
+#if $type.type_select == "genome":
+    #if $type.genome_file_opts.genome_file_opts_selector == "loc":
+        -g '$type.genome_file_opts.genome.fields.len_path'
+    #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
+        -g '$type.genome_file_opts.genome'
+    #end if
+#end if
+    </token>
+    <token name="@GENOME_FILE_UNION@">
+#if $empty.empty_selector == "-empty":
+    #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
+        -g '$empty.genome_file_opts.genome.fields.len_path'
+    #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
+        -g '$empty.genome_file_opts.genome'
+    #end if
+#end if
+    </token>
+    <token name="@GENOME_FILE_COVERAGE@">
+#if $input_type.input_type_select == "bam":
+    -ibam '$input_type.input'
+#else:
+    -i '$input_type.input'
+    #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
+        -g '$input_type.genome_file_opts.genome.fields.len_path'
+    #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
+        -g '$input_type.genome_file_opts.genome'
+    #end if
+#end if
+    </token>
+    <xml name="closest_D_option">
+        <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false"
+            label="Ignore features in B that are upstream of features in A"
+            help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
+
+        <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false"
+            label="Ignore features in B that are downstream of features in A"
+            help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
+
+        <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false"
+            label="Choose first from features in B that are upstream of features in A"
+            help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
+
+        <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false"
+            label="Choose first from features in B that are downstream of features in A"
+            help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
+    </xml>
+    <xml name="addition">
+        <conditional name="addition">
+            <param name="addition_select" type="select" label="Choose what you want to do">
+                <option value="b" selected="true">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option>
+                <option value="lr">Increase by Start Coordinate and End Coordinate</option>
+            </param>
+            <when value="b">
+                <param name="b" value="1" label="Number of base pairs" type="integer" />
+            </when>
+            <when value="lr">
+                <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
+                <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="print_header">
+        <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false"
+            label="Print the header from the A file prior to results" />
+    </xml>
+    <!-- TODO this is currently not used, but we should make use of it -->
+    <xml name="genome_validator">
+        <validator type="unspecified_build" />
+        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+    </xml>
+
+    <!-- ToDo column_picker -->
+    <xml name="choose_columns">
+        <param name="cols" argument="-c" type="text" value=""
+            label="Specify the column(s) that should be summarized"
+            help="Comma separated">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits"><add value=","/></valid>
+            </sanitizer>
+        </param>
+    </xml>
+
+    <token name="@C_AND_O_ARGUMENT@">
+        #set $col = list()
+        #set $op = list()
+        #for $item in $c_and_o_argument_repeat:
+            #silent $col.append( str($item.col) )
+            #silent $op.append( str($item.operation) )
+        #end for
+        #if $col:
+            -c #echo ','.join($col)#
+            -o #echo ','.join($op)#
+        #end if
+    </token>
+
+    <xml name="c_and_o_argument">
+        <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
+            <yield />
+            <expand macro="choose_operations">
+                <expand macro="math_options" />
+                <expand macro="additional_math_options" />
+            </expand>
+        </repeat>
+    </xml>
+
+    <xml name="choose_operations">
+        <param name="operation" type="select" label="Specify the operation">
+            <yield />
+        </param>
+    </xml>
+
+    <xml name="math_options">
+        <option value="sum" selected="true">Sum - numeric only</option>
+        <option value="min">Min - numeric only</option>
+        <option value="max">Max - numeric only</option>
+        <option value="absmin">AbsMin - numeric only</option>
+        <option value="absmax">AbsMax - numeric only</option>
+        <option value="mean">Mean - numeric only</option>
+        <option value="median">Median - numeric only</option>
+        <option value="mode">Mode - numeric only</option>
+        <option value="antimode">Antimode - numeric only</option>
+        <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
+    </xml>
+    <xml name="additional_math_options">
+        <option value="count">Count - numeric or text</option>
+        <option value="count_disctinct">Count Distinct - numeric or text</option>
+        <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
+        <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
+    </xml>
+    <xml name="sorted">
+        <!-- -sorted -g  -->
+        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
+            label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
+    </xml>
+    <token name="@SORTED@">
+<![CDATA[
+$sorted
+#if str($sorted) != '':
+    #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
+        -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
+    #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
+        -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
+    #end if
+#end if
+]]>
+    </token>
+    <token name="@REFERENCES@">
+<![CDATA[
+------
+
+This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
+
+.. _bedtools package: https://github.com/arq5x/bedtools2
+.. _Quinlan laboratory: http://quinlanlab.org
+
+
+**Citation**
+
+If you use this tool in Galaxy, please cite:
+
+Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
+]]>
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btq033</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
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diff -r 000000000000 -r 4cacc5b8001b test-data/a.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	100	200
+chr1	180	250
+chr1	250	500
+chr1	501	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/all_gff.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_gff.loc	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,15 @@
+#This file lists the locations and dbkeys of all the GFF files
+#This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_gff.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/annotation/apiMel3/apiMel3.gff
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/annotation/hg19/hg19canon.gff
+#hg19full	hg19	Human (Homo sapiens): hg19 Representative transcripts	/path/to/annotation/hg19/hg19_representative_tx.gff
+#
+#Your all_gff.loc file should contain an entry for each different annotation.
+#So there can be multiple gff files for each build, such as with hg19 above.
+testid	testdbkey	testdisplay	${__HERE__}/a.bed
diff -r 000000000000 -r 4cacc5b8001b test-data/annotateBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotateBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	100	200	nasty	1	-
+chr2	500	1000	ugly	2	+
+chr3	1000	5000	big	3	-
+
diff -r 000000000000 -r 4cacc5b8001b test-data/annotateBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotateBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	150	200	geneA	1	+
+chr1	175	250	geneB	2	+
+chr3	0	10000	geneC	3	-
diff -r 000000000000 -r 4cacc5b8001b test-data/annotateBed3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotateBed3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	0	10000	cons1	1	+
+chr2	700	10000	cons2	2	-
+chr3	4000	10000	cons3	3	+
diff -r 000000000000 -r 4cacc5b8001b test-data/annotateBed4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotateBed4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	0	120	known	1	-
+chr1	150	160	known	2	-
+chr2	0	10000	known	3	+
+
diff -r 000000000000 -r 4cacc5b8001b test-data/annotateBed_result.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotateBed_result.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+#						annotateBed2.bed	annotateBed3.bed	annotateBed4.bed
+chr1	100	200	nasty	1	-	0.500000	1.000000	0.300000
+chr2	500	1000	ugly	2	+	0.000000	0.600000	1.000000
+chr3	1000	5000	big	3	-	1.000000	0.250000	0.000000
diff -r 000000000000 -r 4cacc5b8001b test-data/bamToBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamToBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,8 @@
+dummy_chr	1278	1354	GA5:3:2:1710:1301#0	18	+
+dummy_chr	128881	128957	GA5:3:24:462:583#0	37	+
+dummy_chr	5591012	5591088	GA5:3:29:1241:1653#0	37	+
+dummy_chr	11880047	11880123	GA5:3:33:1591:303#0	37	+
+dummy_chr	11880930	11881006	GA5:3:31:677:1537#0	37	-
+dummy_chr	11913867	11913943	GA5:3:49:1480:1116#0	37	-
+dummy_chr	13030395	13030471	GA5:3:61:213:1812#0	37	-
+dummy_chr	15055983	15056059	GA5:3:116:1581:552#0	37	-
diff -r 000000000000 -r 4cacc5b8001b test-data/bamToBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamToBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,8 @@
+dummy_chr	1278	1354	GA5:3:2:1710:1301#0	0	+
+dummy_chr	128881	128957	GA5:3:24:462:583#0	3	+
+dummy_chr	5591012	5591088	GA5:3:29:1241:1653#0	1	+
+dummy_chr	11880047	11880123	GA5:3:33:1591:303#0	0	+
+dummy_chr	11880930	11881006	GA5:3:31:677:1537#0	0	-
+dummy_chr	11913867	11913943	GA5:3:49:1480:1116#0	1	-
+dummy_chr	13030395	13030471	GA5:3:61:213:1812#0	1	-
+dummy_chr	15055983	15056059	GA5:3:116:1581:552#0	0	-
diff -r 000000000000 -r 4cacc5b8001b test-data/bamToBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamToBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	200	chr5	5000	5100	bedpe_example1	255	+	-
+chr9	1000	5000	chr9	3000	3800	bedpe_example2	255	+	-
diff -r 000000000000 -r 4cacc5b8001b test-data/bed12.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed12.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	14756	15038	JUNC00000001	294	-	14756	15038	255,0,0	2	73,69	0,213
+chr1	14969	15836	JUNC00000002	144	-	14969	15836	255,0,0	2	69,41	0,826
+chr1	15905	16677	JUNC00000003	12	-	15905	16677	255,0,0	2	42,71	0,701
diff -r 000000000000 -r 4cacc5b8001b test-data/bed12ToBed6_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed12ToBed6_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+chr1	14756	14829	JUNC00000001	294	-
+chr1	14969	15038	JUNC00000001	294	-
+chr1	14969	15038	JUNC00000002	144	-
+chr1	15795	15836	JUNC00000002	144	-
+chr1	15905	15947	JUNC00000003	12	-
+chr1	16606	16677	JUNC00000003	12	-
diff -r 000000000000 -r 4cacc5b8001b test-data/bedToBam1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedToBam1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,5 @@
+chr1	100	200	foo
+chr1	180	250	bar
+chr1	250	500	world
+chr1	501	1000	peace
+
diff -r 000000000000 -r 4cacc5b8001b test-data/bedToBam_result.bam
Binary file test-data/bedToBam_result.bam has changed
diff -r 000000000000 -r 4cacc5b8001b test-data/bedpeToBamBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedpeToBamBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	200	chr5	5000	5100	bedpe_example1	30	+	-
+chr9	1000	5000	chr9	3000	3800	bedpe_example2	100	+	-
diff -r 000000000000 -r 4cacc5b8001b test-data/bedpeToBam_result1.bam
Binary file test-data/bedpeToBam_result1.bam has changed
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBedA.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBedA.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	200
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBedB.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBedB.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	500	1000
+chr1	1300	2000
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_a.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_a.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20	a1	1	-
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_b1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_b1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	5	6	b1.1	1	-
+chr1	30	40	b1.2	2	+
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_b2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_b2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	0	1	b2.1	1	-
+chr1	21	22	b2.2	2	+
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_c.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_c.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20	a1	1	+
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_d.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_d.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	7	8	b1	1	+
+chr1	22	23	b2	2	-
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	200	chr1	500	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	a1	1	-	1	chr1	5	6	b1.1	1	-	5
+chr1	10	20	a1	1	-	2	chr1	21	22	b2.2	2	+	2
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20	a1	1	-	2	chr1	21	22	b2.2	2	+	2
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_result4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	a1	1	+	chr1	7	8	b1	1	+	-3
+chr1	10	20	a1	1	+	chr1	22	23	b2	2	-	3
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_result5.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result5.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	a1	1	+	chr1	7	8	b1	1	+	-3
+chr1	10	20	a1	1	+	chr1	22	23	b2	2	-	3
diff -r 000000000000 -r 4cacc5b8001b test-data/closestBed_result6.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result6.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	100	200	chr1	100	200
+chr1	100	200	chr1	180	250
+chr1	100	200	chr1	250	500
diff -r 000000000000 -r 4cacc5b8001b test-data/clusterBed_result.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clusterBed_result.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	100	200	1
+chr1	180	250	1
+chr1	250	500	1
+chr1	501	1000	2
diff -r 000000000000 -r 4cacc5b8001b test-data/complementBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/complementBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	0	100
+chr1	500	501
+chr1	1000	197195432
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBed.bam
Binary file test-data/coverageBed.bam has changed
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBedA.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBedA.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	10	20
+chr1	20	30
+chr1	30	40
+chr1	100	200
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBedA2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBedA2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1	100
+dummy_chr	1000	1000000
+super_dummy_chr	1	100
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBedB.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBedB.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	0	100
+chr1	100	200
+chr2	0	100
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	10	20	1	10	10	1.0000000
+chr1	20	30	1	10	10	1.0000000
+chr1	30	40	1	10	10	1.0000000
+chr1	100	200	1	100	100	1.0000000
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBed_result2_F1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBed_result2_F1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	10	20	0	0	10	0.0000000
+chr1	20	30	0	0	10	0.0000000
+chr1	30	40	0	0	10	0.0000000
+chr1	100	200	1	100	100	1.0000000
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBed_result3_f1r.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBed_result3_f1r.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	10	20	1	10	10	1.0000000
+chr1	20	30	1	10	10	1.0000000
+chr1	30	40	1	10	10	1.0000000
+chr1	100	200	1	100	100	1.0000000
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBed_result4_2bam.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBed_result4_2bam.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	4	152	999000	0.0001522
diff -r 000000000000 -r 4cacc5b8001b test-data/coverageBed_result5_unsorted.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBed_result5_unsorted.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	2	152	999000	0.0001522
+super_dummy_chr	1	100	0	0	99	0.0000000
diff -r 000000000000 -r 4cacc5b8001b test-data/dbkeys.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbkeys.loc	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,14 @@
+#This file lists the locations and dbkeys of all the genome files
+#See here for details: http://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format
+#You can add elements to this data table using the data_manager_fetch_genome_dbkeys_all_fasta data manager.
+#Alternatively, index files created using samtools faidx (http://www.htslib.org/doc/faidx.html) contain 3 extra columns, but work fine.
+#This file has the format (white space characters are TAB characters):
+#
+#<dbkey>	<display_name>	<file_path>
+#
+#So, dbkeys.loc could look something like this:
+#
+#apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.len
+#hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.len
+#
+mm9	Mus Musculus	${__HERE__}/mm9.len
\ No newline at end of file
diff -r 000000000000 -r 4cacc5b8001b test-data/expandBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expandBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	1,2,3	10,20,30
+chr1	40	50	4,5,6	40,50,60
diff -r 000000000000 -r 4cacc5b8001b test-data/expandBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expandBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+chr1	10	20	1,2,3	10
+chr1	10	20	1,2,3	20
+chr1	10	20	1,2,3	30
+chr1	40	50	4,5,6	40
+chr1	40	50	4,5,6	50
+chr1	40	50	4,5,6	60
diff -r 000000000000 -r 4cacc5b8001b test-data/expandBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expandBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+chr1	10	20	1	10
+chr1	10	20	2	20
+chr1	10	20	3	30
+chr1	40	50	4	40
+chr1	40	50	5	50
+chr1	40	50	6	60
diff -r 000000000000 -r 4cacc5b8001b test-data/expandInput.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expandInput.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	1,2,3	10,20,30
+chr1	40	50	4,5,6	40,50,60
diff -r 000000000000 -r 4cacc5b8001b test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>     <dbkey> <display_name>  <file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon      hg18    Human (Homo sapiens): hg18 Canonical    /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full       hg18    Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full       hg19    Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
+testid	testdbkey	testdisplay	${__HERE__}/nucBed1.fasta
\ No newline at end of file
diff -r 000000000000 -r 4cacc5b8001b test-data/fisherBed.len
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fisherBed.len	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	500
diff -r 000000000000 -r 4cacc5b8001b test-data/fisherBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fisherBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20
+chr1	30	40
+chr1	51	52
diff -r 000000000000 -r 4cacc5b8001b test-data/fisherBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fisherBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	15	25
+chr1	51	52
diff -r 000000000000 -r 4cacc5b8001b test-data/fisherBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fisherBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,14 @@
+# Number of query intervals: 3
+# Number of db intervals: 2
+# Number of overlaps: 2
+# Number of possible intervals (estimated): 34
+# phyper(2 - 1, 3, 34 - 3, 2, lower.tail=F)
+# Contingency Table Of Counts
+#_________________________________________
+#           |  in -b       | not in -b    |
+#     in -a | 2            | 1            |
+# not in -a | 0            | 31           |
+#_________________________________________
+# p-values for fisher's exact test
+left	right	two-tail	ratio
+1	0.0053476	0.0053476	inf
diff -r 000000000000 -r 4cacc5b8001b test-data/flankBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flankBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,8 @@
+chr1	95	100
+chr1	200	205
+chr1	175	180
+chr1	250	255
+chr1	245	250
+chr1	500	505
+chr1	496	501
+chr1	1000	1005
diff -r 000000000000 -r 4cacc5b8001b test-data/flankBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flankBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,8 @@
+chr1	98	100
+chr1	200	203
+chr1	178	180
+chr1	250	253
+chr1	248	250
+chr1	500	503
+chr1	499	501
+chr1	1000	1003
diff -r 000000000000 -r 4cacc5b8001b test-data/genomeCoverageBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genomeCoverageBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20
+chr1	20	30
+chr2	0	500
diff -r 000000000000 -r 4cacc5b8001b test-data/genomeCoverageBed1.len
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genomeCoverageBed1.len	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	1000
+chr2	500
diff -r 000000000000 -r 4cacc5b8001b test-data/genomeCoverageBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genomeCoverageBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	0	1000	1000	1
+chr2	0	500	500	1
+genome	0	1500	1500	1
diff -r 000000000000 -r 4cacc5b8001b test-data/getfastaBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/getfastaBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+>chr1:10-100
+TTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTA
diff -r 000000000000 -r 4cacc5b8001b test-data/getfastaBed_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/getfastaBed_result2.tabular	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1:10-100	TTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTA
diff -r 000000000000 -r 4cacc5b8001b test-data/getfastaBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/getfastaBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+>::chr1:10-100
+TTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTA
diff -r 000000000000 -r 4cacc5b8001b test-data/getfastaBed_result4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/getfastaBed_result4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+>chr1
+TTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTA
diff -r 000000000000 -r 4cacc5b8001b test-data/groupbyBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/groupbyBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,14 @@
+chr21	9719758	9729320	variant1	chr21	9719768	9721892	ALR/Alpha	1004	+
+chr21	9719758	9729320	variant1	chr21	9721905	9725582	ALR/Alpha	1010	+
+chr21	9719758	9729320	variant1	chr21	9725582	9725977	L1PA3	3288	+
+chr21	9719758	9729320	variant1	chr21	9726021	9729309	ALR/Alpha	1051	+
+chr21	9729310	9757478	variant2	chr21	9729320	9729809	L1PA3	3897	-
+chr21	9729310	9757478	variant2	chr21	9729809	9730866	L1P1	8367	+
+chr21	9729310	9757478	variant2	chr21	9730866	9734026	ALR/Alpha	1036	-
+chr21	9729310	9757478	variant2	chr21	9734037	9757471	ALR/Alpha	1182	-
+chr21	9795588	9796685	variant3	chr21	9795589	9795713	(GAATG)n	308	+
+chr21	9795588	9796685	variant3	chr21	9795736	9795894	(GAATG)n	683	+
+chr21	9795588	9796685	variant3	chr21	9795911	9796007	(GAATG)n	345	+
+chr21	9795588	9796685	variant3	chr21	9796028	9796187	(GAATG)n	756	+
+chr21	9795588	9796685	variant3	chr21	9796202	9796615	(GAATG)n	891	+
+chr21	9795588	9796685	variant3	chr21	9796637	9796824	(GAATG)n	621	+
diff -r 000000000000 -r 4cacc5b8001b test-data/groupbyBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/groupbyBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr21	9719758	9729320	6353
+chr21	9729310	9757478	14482
+chr21	9795588	9796685	3604
diff -r 000000000000 -r 4cacc5b8001b test-data/groupbyBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/groupbyBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr21	9719758	9729320	1004
+chr21	9729310	9757478	1036
+chr21	9795588	9796685	308
diff -r 000000000000 -r 4cacc5b8001b test-data/groupbyBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/groupbyBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr21	9719758	9729320	variant1	1030.5
+chr21	9729310	9757478	variant2	2539.5
+chr21	9795588	9796685	variant3	652
diff -r 000000000000 -r 4cacc5b8001b test-data/igv_bed_script.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/igv_bed_script.txt	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,7 @@
+snapshotDirectory ./
+goto chr1:14756-15038
+snapshot chr1_14756_15038.png
+goto chr1:14969-15836
+snapshot chr1_14969_15836.png
+goto chr1:15905-16677
+snapshot chr1_15905_16677.png
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-A.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-A.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20
+chr1	30	40
+
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-A2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-A2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	1	140
+chr1	100	200
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-B.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-B.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	15	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-B2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-B2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	130	201
+chr1	130	200000
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-count.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-count.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	1
+chr1	30	40	0
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-d1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-d1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,10 @@
+chr1	5	25
+chr1	65	75
+chr1	95	100
+chr2	5	25
+chr2	65	75
+chr2	95	100
+chr3	5	25
+chr3	65	75
+chr3	95	100
+
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-d2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-d2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+chr1	40	50
+chr1	110	125
+chr2	40	50
+chr2	110	125
+chr3	40	50
+chr3	110	125
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-d3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-d3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	85	115
+chr2	85	115
+chr3	85	115
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-default.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-default.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	15	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-fracA-rec.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-fracA-rec.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	200	chr1	130	201
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-fracA.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-fracA.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	200	chr1	130	201
+chr1	100	200	chr1	130	200000
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-invert.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-invert.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	30	40
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-loj.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-loj.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	chr1	15	20
+chr1	30	40	.	-1	-1
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-multiple-fracA.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-multiple-fracA.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	40	45	2	chr1	40	50
+chr2	40	45	2	chr2	40	50
+chr3	40	45	2	chr3	40	50
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-multiple-invert.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-multiple-invert.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr3	150	200
+chr4	10	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-multiple-wa-wb-wnames.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-multiple-wa-wb-wnames.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,18 @@
+chr1	1	20	intersect-d1_bed	chr1	5	25
+chr1	40	45	intersect-d2_bed	chr1	40	50
+chr1	70	90	intersect-d1_bed	chr1	65	75
+chr1	70	90	intersect-d3_bed	chr1	85	115
+chr1	105	120	intersect-d2_bed	chr1	110	125
+chr1	105	120	intersect-d3_bed	chr1	85	115
+chr2	1	20	intersect-d1_bed	chr2	5	25
+chr2	40	45	intersect-d2_bed	chr2	40	50
+chr2	70	90	intersect-d1_bed	chr2	65	75
+chr2	70	90	intersect-d3_bed	chr2	85	115
+chr2	105	120	intersect-d2_bed	chr2	110	125
+chr2	105	120	intersect-d3_bed	chr2	85	115
+chr3	1	20	intersect-d1_bed	chr3	5	25
+chr3	40	45	intersect-d2_bed	chr3	40	50
+chr3	70	90	intersect-d1_bed	chr3	65	75
+chr3	70	90	intersect-d3_bed	chr3	85	115
+chr3	105	120	intersect-d2_bed	chr3	110	125
+chr3	105	120	intersect-d3_bed	chr3	85	115
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-multiple-wa-wb.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-multiple-wa-wb.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,18 @@
+chr1	1	20	1	chr1	5	25
+chr1	40	45	2	chr1	40	50
+chr1	70	90	1	chr1	65	75
+chr1	70	90	3	chr1	85	115
+chr1	105	120	2	chr1	110	125
+chr1	105	120	3	chr1	85	115
+chr2	1	20	1	chr2	5	25
+chr2	40	45	2	chr2	40	50
+chr2	70	90	1	chr2	65	75
+chr2	70	90	3	chr2	85	115
+chr2	105	120	2	chr2	110	125
+chr2	105	120	3	chr2	85	115
+chr3	1	20	1	chr3	5	25
+chr3	40	45	2	chr3	40	50
+chr3	70	90	1	chr3	65	75
+chr3	70	90	3	chr3	85	115
+chr3	105	120	2	chr3	110	125
+chr3	105	120	3	chr3	85	115
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-multiple.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-multiple.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,18 @@
+chr1	5	20
+chr1	40	45
+chr1	70	75
+chr1	85	90
+chr1	110	120
+chr1	105	115
+chr2	5	20
+chr2	40	45
+chr2	70	75
+chr2	85	90
+chr2	110	120
+chr2	105	115
+chr3	5	20
+chr3	40	45
+chr3	70	75
+chr3	85	90
+chr3	110	120
+chr3	105	115
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-query.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-query.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,14 @@
+chr1	1	20
+chr1	40	45
+chr1	70	90
+chr1	105	120
+chr2	1	20
+chr2	40	45
+chr2	70	90
+chr2	105	120
+chr3	1	20
+chr3	40	45
+chr3	70	90
+chr3	105	120
+chr3	150	200
+chr4	10	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-unique.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-unique.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-uniue.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-uniue.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-wa-wb.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-wa-wb.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20	chr1	15	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-wa.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-wa.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-wao.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-wao.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20	chr1	15	20	5
+chr1	30	40	.	-1	-1	0
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-wb.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-wb.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	15	20	chr1	15	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersect-wo.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersect-wo.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20	chr1	15	20	5
diff -r 000000000000 -r 4cacc5b8001b test-data/intersectBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersectBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20
+chr1	30	40
diff -r 000000000000 -r 4cacc5b8001b test-data/intersectBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersectBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	15	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersectBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersectBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersectBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersectBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	20	chr1	15	20
diff -r 000000000000 -r 4cacc5b8001b test-data/intersectBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intersectBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	30	40
diff -r 000000000000 -r 4cacc5b8001b test-data/jaccardBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jaccardBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	10	20
+chr1	30	40
diff -r 000000000000 -r 4cacc5b8001b test-data/jaccardBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jaccardBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	15	20
diff -r 000000000000 -r 4cacc5b8001b test-data/jaccardBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jaccardBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+intersection	union	jaccard	n_intersections
+5	20	0.25	1
diff -r 000000000000 -r 4cacc5b8001b test-data/jaccardBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jaccardBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+intersection	union	jaccard	n_intersections
+5	20	0.25	1
diff -r 000000000000 -r 4cacc5b8001b test-data/linksBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/linksBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr21	9928613	10012791	uc002yip.1 0	-
+chr21	9928613	10012791	uc002yiq.1 0	-
diff -r 000000000000 -r 4cacc5b8001b test-data/linksBed_result1.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/linksBed_result1.html	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,33 @@
+<html>
+	<body>
+<title>/tmp/tmp5hihJcfiles/000/dataset_1.dat</title>
+<br>Firefox users: Press and hold the "apple" or "alt" key and click link to open in new tab.
+<p style="font-family:courier">
+<table border="0" align="justify"
+<h3>BED Entries from: stdin </h3>
+<tr>
+	<td>
+		<a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=&db=&position=chr21:9928613-10012791>chr21:9928614-10012791</a>
+	</td>
+	<td>
+uc002yip.1 0
+	</td>
+	<td>
+-
+	</td>
+</tr>
+<tr>
+	<td>
+		<a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=&db=&position=chr21:9928613-10012791>chr21:9928614-10012791</a>
+	</td>
+	<td>
+uc002yiq.1 0
+	</td>
+	<td>
+-
+	</td>
+</tr>
+</table>
+</p>
+	</body>
+</html>
diff -r 000000000000 -r 4cacc5b8001b test-data/linksBed_result2.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/linksBed_result2.html	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,33 @@
+<html>
+	<body>
+<title>/tmp/tmp5hihJcfiles/000/dataset_3.dat</title>
+<br>Firefox users: Press and hold the "apple" or "alt" key and click link to open in new tab.
+<p style="font-family:courier">
+<table border="0" align="justify"
+<h3>BED Entries from: stdin </h3>
+<tr>
+	<td>
+		<a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&db=mm9&position=chr21:9928613-10012791>chr21:9928614-10012791</a>
+	</td>
+	<td>
+uc002yip.1 0
+	</td>
+	<td>
+-
+	</td>
+</tr>
+<tr>
+	<td>
+		<a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&db=mm9&position=chr21:9928613-10012791>chr21:9928614-10012791</a>
+	</td>
+	<td>
+uc002yiq.1 0
+	</td>
+	<td>
+-
+	</td>
+</tr>
+</table>
+</p>
+	</body>
+</html>
diff -r 000000000000 -r 4cacc5b8001b test-data/makeWindowBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeWindowBed1.bed	Thu Feb 23 09:50:24 2023 +0000
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diff -r 000000000000 -r 4cacc5b8001b test-data/makeWindowBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeWindowBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
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diff -r 000000000000 -r 4cacc5b8001b test-data/makeWindowBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeWindowBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3944 @@
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diff -r 000000000000 -r 4cacc5b8001b test-data/makeWindowBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeWindowBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,100 @@
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diff -r 000000000000 -r 4cacc5b8001b test-data/makeWindowBed_result4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeWindowBed_result4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,45 @@
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diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20	a1	1	+
+chr1	50	60	a2	2	-
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diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,5 @@
+chr1	12	14	b1	2	+
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diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+chr1	10	20	a1	1	+
+chr1	50	60	a2	2	-
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+chr9	10	20	a1	1	+
+chr9	50	60	a2	2	-
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diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,10 @@
+chr1	12	14	b1	2	+
+chr1	13	15	b2	5	-
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+chr1	82	85	b4	2	-
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+chr9	12	14	b1	2	+
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diff -r 000000000000 -r 4cacc5b8001b test-data/mapBedA.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBedA.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	10	20	a1	1	+
+chr1	50	60	a2	2	-
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+
diff -r 000000000000 -r 4cacc5b8001b test-data/mapBedB.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBedB.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,5 @@
+chr1	12	14	b1	2	+
+chr1	13	15	b2	5	-
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+chr1	82	85	b4	2	-
+chr1	85	87	b5	3	+
diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20	a1	1	+	4
+chr1	50	60	a2	2	-	.
+chr1	80	90	a3	3	-	2.5
diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20	a1	1	+	2,5,5
+chr1	50	60	a2	2	-	.
+chr1	80	90	a3	3	-	2,3
diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20	a1	1	+	5
+chr1	50	60	a2	2	-	.
+chr1	80	90	a3	3	-	3
diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed_result4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed_result4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20	a1	1	+	2,5
+chr1	50	60	a2	2	-	.
+chr1	80	90	a3	3	-	2
diff -r 000000000000 -r 4cacc5b8001b test-data/mapBed_result5.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapBed_result5.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+chr1	10	20	a1	1	+	2,5
+chr1	50	60	a2	2	-	.
+chr1	80	90	a3	3	-	2
+chr9	10	20	a1	1	+	2,5
+chr9	50	60	a2	2	-	.
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diff -r 000000000000 -r 4cacc5b8001b test-data/maskFastaBed_result1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result1.fasta	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+>chr1
+GACTCATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 000000000000 -r 4cacc5b8001b test-data/maskFastaBed_result2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result2.fasta	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+>chr1
+GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
+tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 000000000000 -r 4cacc5b8001b test-data/maskFastaBed_result3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result3.fasta	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+>chr1 description
+GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
+tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 000000000000 -r 4cacc5b8001b test-data/mean_coverage.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean_coverage.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1	100	0.0000000
+dummy_chr	1000	1000000	0.0001522
+super_dummy_chr	1	100	0.0000000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	100	200
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diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	100	200	a1	1	+
+chr1	180	250	a2	2	+
+chr1	250	500	a3	3	-
+chr1	501	1000	a4	4	+
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	100	200
+chr1	180	250
+chr1	250	500
+chr1	501	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	200
+chr1	501	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed_result.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed_result.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	500
+chr1	501	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	100	250
+chr1	250	500
+chr1	501	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	500
+chr1	501	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed_result4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed_result4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/mergedBed_result5.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mergedBed_result5.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	1000	2
diff -r 000000000000 -r 4cacc5b8001b test-data/mm9.len
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9.len	Thu Feb 23 09:50:24 2023 +0000
@@ -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
+
diff -r 000000000000 -r 4cacc5b8001b test-data/mm9_chr1.len
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_chr1.len	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	197195432
diff -r 000000000000 -r 4cacc5b8001b test-data/multiCov1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiCov1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+dummy_chr	1	100
+dummy_chr	1000	1000000
diff -r 000000000000 -r 4cacc5b8001b test-data/multiCovBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiCovBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+dummy_chr	1	100	0	0
+dummy_chr	1000	1000000	2	2
diff -r 000000000000 -r 4cacc5b8001b test-data/multiIntersectBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiIntersectBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	6	12
+chr1	10	20
+chr1	22	27
+chr1	24	30
diff -r 000000000000 -r 4cacc5b8001b test-data/multiIntersectBed1.len
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiIntersectBed1.len	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	5000
diff -r 000000000000 -r 4cacc5b8001b test-data/multiIntersectBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiIntersectBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	12	32
+chr1	14	30
diff -r 000000000000 -r 4cacc5b8001b test-data/multiIntersectBed3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiIntersectBed3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	8	15
+chr1	10	14
+chr1	32	34
diff -r 000000000000 -r 4cacc5b8001b test-data/multiIntersectBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiIntersectBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,8 @@
+chr1	6	8	1	1	1	0	0
+chr1	8	12	2	1,3	1	0	1
+chr1	12	15	3	1,2,3	1	1	1
+chr1	15	20	2	1,2	1	1	0
+chr1	20	22	1	2	0	1	0
+chr1	22	30	2	1,2	1	1	0
+chr1	30	32	1	2	0	1	0
+chr1	32	34	1	3	0	0	1
diff -r 000000000000 -r 4cacc5b8001b test-data/multiIntersectBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiIntersectBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,9 @@
+chrom	start	end	num	list	/tmp/tmpTVZ0hffiles/000/dataset_5.dat	/tmp/tmpTVZ0hffiles/000/dataset_6.dat	/tmp/tmpTVZ0hffiles/000/dataset_7.dat
+chr1	6	8	1	1	1	0	0
+chr1	8	12	2	1,3	1	0	1
+chr1	12	15	3	1,2,3	1	1	1
+chr1	15	20	2	1,2	1	1	0
+chr1	20	22	1	2	0	1	0
+chr1	22	30	2	1,2	1	1	0
+chr1	30	32	1	2	0	1	0
+chr1	32	34	1	3	0	0	1
diff -r 000000000000 -r 4cacc5b8001b test-data/multiIntersectBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiIntersectBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,10 @@
+chr1	0	6	0	none	0	0	0
+chr1	6	8	1	1	1	0	0
+chr1	8	12	2	1,3	1	0	1
+chr1	12	15	3	1,2,3	1	1	1
+chr1	15	20	2	1,2	1	1	0
+chr1	20	22	1	2	0	1	0
+chr1	22	30	2	1,2	1	1	0
+chr1	30	32	1	2	0	1	0
+chr1	32	34	1	3	0	0	1
+chr1	34	5000	0	none	0	0	0
diff -r 000000000000 -r 4cacc5b8001b test-data/multicov1_by_srma_in3.cov.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multicov1_by_srma_in3.cov.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	2	152	999000	0.0001522
diff -r 000000000000 -r 4cacc5b8001b test-data/nucBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	100
diff -r 000000000000 -r 4cacc5b8001b test-data/nucBed1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed1.fasta	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+>chr1 description
+GACTCATGATTTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGA
+TAGAACTTCATGTGCCTGTAAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 000000000000 -r 4cacc5b8001b test-data/nucBed1.fasta.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed1.fasta.fai	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	359	18	80	81
diff -r 000000000000 -r 4cacc5b8001b test-data/nucBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	10	100	chr1
diff -r 000000000000 -r 4cacc5b8001b test-data/nucBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+#1_usercol	2_usercol	3_usercol	4_pct_at	5_pct_gc	6_num_A	7_num_C	8_num_G	9_num_T	10_num_N	11_num_oth	12_seq_len
+chr1	10	100	0.588889	0.411111	19	16	21	34	0	0	90
diff -r 000000000000 -r 4cacc5b8001b test-data/nucBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+#1_usercol	2_usercol	3_usercol	4_pct_at	5_pct_gc	6_num_A	7_num_C	8_num_G	9_num_T	10_num_N	11_num_oth	12_seq_len	13_seq
+chr1	10	100	0.588889	0.411111	19	16	21	34	0	0	90	TTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTA
diff -r 000000000000 -r 4cacc5b8001b test-data/nucBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+#1_usercol	2_usercol	3_usercol	4_pct_at	5_pct_gc	6_num_A	7_num_C	8_num_G	9_num_T	10_num_N	11_num_oth	12_seq_len	13_seq	14_user_patt_count
+chr1	10	100	0.588889	0.411111	19	16	21	34	0	0	90	TTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTA	1
diff -r 000000000000 -r 4cacc5b8001b test-data/overlapBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/overlapBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	200	chr1	500	1000	-300
diff -r 000000000000 -r 4cacc5b8001b test-data/reldistBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reldistBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+reldist	count	total	fraction
+0.00	4	4	1.000
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBed.len
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBed.len	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	10000
+chr2	8000
+chr3	5000
+chr4	2000
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	0	100	a1	1	+
+chr1	0	1000	a2	2	-
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	0	10000
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBedA.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBedA.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	0	100	a1	1	+
+chr1	0	1000	a2	2	-
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBedGenome.genome
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBedGenome.genome	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,5 @@
+chr1	10000
+chr2	8000
+chr3	5000
+chr4	2000
+
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr2	1528	1628	a1	1	+
+chr1	7462	8462	a2	2	-
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	1528	1628	a1	1	+
+chr1	2462	3462	a2	2	-
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr2	1528	1628	a1	1	+
+chr2	5665	6665	a2	2	-
diff -r 000000000000 -r 4cacc5b8001b test-data/shuffleBed_result4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shuffleBed_result4.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	6467	6567	a1	1	+
+chr2	7167	8000	a2	2	-
diff -r 000000000000 -r 4cacc5b8001b test-data/slopBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slopBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	95	205
+chr1	175	255
+chr1	245	505
+chr1	496	1005
diff -r 000000000000 -r 4cacc5b8001b test-data/slopBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slopBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	98	203
+chr1	178	253
+chr1	248	503
+chr1	499	1003
diff -r 000000000000 -r 4cacc5b8001b test-data/sortBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	800	1000
+chr1	80	180
+chr1	1	10
+chr1	750	10000
diff -r 000000000000 -r 4cacc5b8001b test-data/sortBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	800	1000
+chr10	80	180
+chr2	1	10
diff -r 000000000000 -r 4cacc5b8001b test-data/sortBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	1	10
+chr1	80	180
+chr1	750	10000
+chr1	800	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/sortBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	800	1000
+chr10	80	180
+chr2	1	10
diff -r 000000000000 -r 4cacc5b8001b test-data/sortBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	800	1000
+chr2	1	10
+chr10	80	180
diff -r 000000000000 -r 4cacc5b8001b test-data/spacingBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spacingBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,4 @@
+chr1	100	200	.
+chr1	180	250	-1
+chr1	250	500	0
+chr1	501	1000	1
diff -r 000000000000 -r 4cacc5b8001b test-data/srma_in3.bam
Binary file test-data/srma_in3.bam has changed
diff -r 000000000000 -r 4cacc5b8001b test-data/subtractBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subtractBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+chr1	10	20
+chr1	100	200
+chr1	301	400
diff -r 000000000000 -r 4cacc5b8001b test-data/subtractBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subtractBed2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	0	30
+chr1	180	300
diff -r 000000000000 -r 4cacc5b8001b test-data/subtractBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subtractBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	180
+chr1	301	400
diff -r 000000000000 -r 4cacc5b8001b test-data/subtractBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subtractBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	200
+chr1	301	400
diff -r 000000000000 -r 4cacc5b8001b test-data/subtractBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subtractBed_result3.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	301	400
diff -r 000000000000 -r 4cacc5b8001b test-data/tagBed1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tagBed1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1100	1479	foo
+dummy_chr	120882	127882	bar
+dummy_chr	5590013	5596013	42
diff -r 000000000000 -r 4cacc5b8001b test-data/tagBed_result1.bam
Binary file test-data/tagBed_result1.bam has changed
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs1.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs1.bg	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	1000	1500	10
+chr1	2000	2100	20
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs1.len
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs1.len	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	5000
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs2.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs2.bg	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	900 1600	60
+chr1	1700	2050	50
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs3.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs3.bg	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	1980	2070	80
+chr1	2090	2100	20
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs_result1.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs_result1.bg	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,5 @@
+chr1	1000	1500	10	N/A	N/A
+chr1	1980	2000	N/A	N/A	80
+chr1	2000	2070	20	N/A	80
+chr1	2070	2090	20	N/A	N/A
+chr1	2090	2100	20	N/A	20
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs_result2.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs_result2.bg	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,6 @@
+chrom	start	end
+chr1	1000	1500	10	N/A	N/A
+chr1	1980	2000	N/A	N/A	80
+chr1	2000	2070	20	N/A	80
+chr1	2070	2090	20	N/A	N/A
+chr1	2090	2100	20	N/A	20
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs_result3.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs_result3.bg	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,8 @@
+chr1	0	1000	N/A	N/A	N/A
+chr1	1000	1500	10	N/A	N/A
+chr1	1500	1980	N/A	N/A	N/A
+chr1	1980	2000	N/A	N/A	80
+chr1	2000	2070	20	N/A	80
+chr1	2070	2090	20	N/A	N/A
+chr1	2090	2100	20	N/A	20
+chr1	2100	5000	N/A	N/A	N/A
diff -r 000000000000 -r 4cacc5b8001b test-data/unionBedGraphs_result4.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unionBedGraphs_result4.bg	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,8 @@
+chr1	0	1000	N/A	N/A	N/A
+chr1	1000	1500	10	N/A	N/A
+chr1	1500	1980	N/A	N/A	N/A
+chr1	1980	2000	N/A	N/A	80
+chr1	2000	2070	20	N/A	80
+chr1	2070	2090	20	N/A	N/A
+chr1	2090	2100	20	N/A	20
+chr1	2100	5000	N/A	N/A	N/A
diff -r 000000000000 -r 4cacc5b8001b test-data/windowBedA.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/windowBedA.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	200
diff -r 000000000000 -r 4cacc5b8001b test-data/windowBedB.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/windowBedB.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	500	1000
+chr1	1300	2000
diff -r 000000000000 -r 4cacc5b8001b test-data/windowBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/windowBed_result1.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,1 @@
+chr1	100	200	chr1	500	1000
diff -r 000000000000 -r 4cacc5b8001b test-data/windowBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/windowBed_result2.bed	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,2 @@
+chr1	100	200	chr1	500	1000
+chr1	100	200	chr1	1300	2000
diff -r 000000000000 -r 4cacc5b8001b tool-data/all_gff.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_gff.loc.sample	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,14 @@
+#This file lists the locations and dbkeys of all the GFF files
+#This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_gff.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/annotation/apiMel3/apiMel3.gff
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/annotation/hg19/hg19canon.gff
+#hg19full	hg19	Human (Homo sapiens): hg19 Representative transcripts	/path/to/annotation/hg19/hg19_representative_tx.gff
+#
+#Your all_gff.loc file should contain an entry for each different annotation.
+#So there can be multiple gff files for each build, such as with hg19 above.
diff -r 000000000000 -r 4cacc5b8001b tool-data/dbkeys.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dbkeys.loc.sample	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,13 @@
+#This file lists the locations and dbkeys of all the genome files
+#See here for details: http://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format
+#You can add elements to this data table using the data_manager_fetch_genome_dbkeys_all_fasta data manager.
+#Alternatively, index files created using samtools faidx (http://www.htslib.org/doc/faidx.html) contain 3 extra columns, but work fine.
+#This file has the format (white space characters are TAB characters):
+#
+#<dbkey>	<display_name>	<file_path>
+#
+#So, dbkeys.loc could look something like this:
+#
+#apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.len
+#hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.len
+#
diff -r 000000000000 -r 4cacc5b8001b tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>     <dbkey> <display_name>  <file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon      hg18    Human (Homo sapiens): hg18 Canonical    /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full       hg18    Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full       hg19    Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 4cacc5b8001b tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,17 @@
+<tables>
+    <!-- Locations of all sam indexes under genome directory -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+    <!-- Locations of all gff files with annotations of genome builds -->
+    <table name="all_gff" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_gff.loc" />
+    </table>
+    <!-- Locations of dbkeys and len files under genome directory -->
+    <table name="__dbkeys__" comment_char="#">
+        <columns>value, name, len_path</columns>
+        <file path="tool-data/dbkeys.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 4cacc5b8001b tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Feb 23 09:50:24 2023 +0000
@@ -0,0 +1,17 @@
+<tables>
+    <!-- Locations of all sam indexes under genome directory -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+    <!-- Locations of all gff files with annotations of genome builds -->
+    <table name="all_gff" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_gff.loc" />
+    </table>
+    <!-- Locations of dbkeys and len files under genome directory -->
+    <table name="__dbkeys__" comment_char="#">
+        <columns>value, name, len_path</columns>
+        <file path="${__HERE__}/test-data/dbkeys.loc" />
+    </table>
+</tables>