# HG changeset patch
# User iuc
# Date 1494343022 14400
# Node ID 45c568e7f1f9b585828abbfa9b223081d056a346
# Parent b02596e3d7a334b1d4240bf419601465c04f0ce0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
diff -r b02596e3d7a3 -r 45c568e7f1f9 macros.xml
--- a/macros.xml Fri Dec 18 19:47:08 2015 -0500
+++ b/macros.xml Tue May 09 11:17:02 2017 -0400
@@ -1,16 +1,17 @@
- samtools
+ samtools
+ 1.3.1
@misc{SAM_def,
title={Definition of SAM/BAM format},
- url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+ url = {https://samtools.github.io/hts-specs/},}
10.1093/bioinformatics/btp352
10.1093/bioinformatics/btr076
@@ -41,7 +42,7 @@
- echo $(samtools --version | head -n 1)", "$(samtools --version | grep -o -E "htslib.*?")
+ &1 | grep Version]]>
@@ -64,7 +65,5 @@
5. Click **Save**
The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
-
-
diff -r b02596e3d7a3 -r 45c568e7f1f9 samtools_stats.xml
--- a/samtools_stats.xml Fri Dec 18 19:47:08 2015 -0500
+++ b/samtools_stats.xml Tue May 09 11:17:02 2017 -0400
@@ -1,144 +1,171 @@
-
+
generate statistics for BAM dataset
- macros.xml
-
-
-
-
+ macros.xml
+
+
+
+
"${output}"
+
+ --most-inserts ${most_inserts}
+ --trim-quality ${trim_quality}
+
+ #if $use_reference.use_ref_selector == "yes":
+ #if $use_reference.reference_source.reference_source_selector != "history":
+ --ref-seq '${use_reference.reference_source.ref_file.fields.path}'
+ #else:
+ --ref-seq '${use_reference.reference_source.ref_file}'
+ #end if
+ #end if
+ > '${output}'
+
#if $split_output.split_output_selector == "yes":
#set outputs_to_split = str($split_output.generate_tables).split(',')
- && mkdir split && echo ${split_output.generate_tables} &&
+ && mkdir split &&
+ echo ${split_output.generate_tables}
#if 'sn' in $outputs_to_split:
- echo "# Summary Numbers\n" > "split/Summary numbers.tab" &&
- grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- >> "split/Summary numbers.tab" ; fi &&
+ && echo "# Summary Numbers" > 'split/Summary numbers.tab' &&
+ echo "" >> 'split/Summary numbers.tab' &&
+ if grep -q ^SN '${output}'; then
+ grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab';
+ fi
#end if
#if 'ffq' in $outputs_to_split:
- echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" &&
- grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi &&
+ && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' &&
+ if grep -q ^FFQ '${output}'; then
+ grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab';
+ fi
#end if
#if 'lfq' in $outputs_to_split:
- echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" &&
- grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi &&
+ && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' &&
+ if grep -q ^LFQ '${output}'; then
+ grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab';
+ fi
#end if
#if 'mpc' in $outputs_to_split:
- echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" &&
- grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi &&
+ && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' &&
+ if grep -q ^MPC '${output}'; then
+ grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab';
+ fi
#end if
#if 'gcf' in $outputs_to_split:
- echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" &&
- grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi &&
+ && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' &&
+ if grep -q ^GCF '${output}'; then
+ grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab';
+ fi
#end if
#if 'gcl' in $outputs_to_split:
- echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" &&
- grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi &&
+ && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' &&
+ if grep -q ^GCL '${output}'; then
+ grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab';
+ fi
#end if
#if 'gcc' in $outputs_to_split:
- echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" &&
- grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi &&
+ && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' &&
+ if grep -q ^GCC '${output}'; then
+ grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab';
+ fi
#end if
#if 'is' in $outputs_to_split:
- echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" &&
- grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- >> "split/Insert sizes.tab" ; fi &&
+ && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' &&
+ if grep -q ^IS '${output}'; then
+ grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab';
+ fi
#end if
#if 'rl' in $outputs_to_split:
- echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" &&
- grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- >> "split/Read lengths.tab" ; fi &&
+ && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' &&
+ if grep -q ^RL '${output}'; then
+ grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab';
+ fi
#end if
#if 'id' in $outputs_to_split:
- echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" &&
- grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- >> "split/Indel distribution.tab" ; fi &&
+ && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' &&
+ if grep -q ^ID '${output}'; then
+ grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab';
+ fi
#end if
#if 'ic' in $outputs_to_split:
- echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > "split/Indels per cycle.tab" &&
- grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- >> "split/Indels per cycle.tab" ; fi &&
+ && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' &&
+ if grep -q ^IC '${output}'; then
+ grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab';
+ fi
#end if
#if 'cov' in $outputs_to_split:
- echo "# Coverage distribution" > "split/Coverage distribution.tab" &&
- grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi &&
+ && echo "# Coverage distribution" > 'split/Coverage distribution.tab' &&
+ if grep -q ^COV '${output}'; then
+ grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab';
+ fi
#end if
#if 'gcd' in $outputs_to_split:
- echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" &&
- grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi &&
+ && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' &&
+ if grep -q ^GCD '${output}'; then
+ grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab';
+ fi
#end if
-
- ## Unix true command below
-
- true
-
#end if
]]>
-
-
-
-
+
+
+
+
-
-
-
+
+
+
-
+
@@ -156,12 +183,12 @@
-
+
-
+
@@ -174,7 +201,7 @@
-
+
@@ -191,19 +218,18 @@
-
-
+
+
+
-
-
-
-
+
+
+
+
-
+
@@ -228,8 +254,9 @@
-
-
+
+
+
@@ -243,7 +270,7 @@
-
+
@@ -263,34 +290,17 @@
,, Coverage distribution min,max,step [1,1000,1]
- -d, --remove-dups Exclude from statistics reads marked as duplicates
- -f, --required-flag Required flag, 0 for unset. See also `samtools flags` [0]
- -F, --filtering-flag Filtering flag, 0 for unset. See also `samtools flags` [0]
- --GC-depth the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
- -h, --help This help message
- -i, --insert-size Maximum insert size [8000]
- -I, --id Include only listed read group or sample name
- -l, --read-length Include in the statistics only reads with the given read length []
- -m, --most-inserts Report only the main part of inserts [0.99]
- -q, --trim-quality The BWA trimming parameter [0]
- -r, --ref-seq Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy
- will provide options for selecting a reference cached as this Galaxy instance or choosing
- one from history.
-
-
+This tool runs the ``samtools stats`` command.
]]>
-
+
diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out1.tab
--- a/test-data/samtools_stats_out1.tab Fri Dec 18 19:47:08 2015 -0500
+++ b/test-data/samtools_stats_out1.tab Tue May 09 11:17:02 2017 -0400
@@ -1,5 +1,6 @@
-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats
-# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat
+# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_2.dat /tmp/tmpO1aTrb/files/000/dataset_1.dat
# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK 1bd20fd8 58ad2167 29883386
@@ -836,258 +837,258 @@
GCL 52.01 1
GCL 52.51 0
GCL 53.02 1
-# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%]
-GCC 1 21.50 29.50 33.50 15.50
-GCC 2 30.00 16.00 11.00 43.00
-GCC 3 33.00 25.00 9.00 33.00
-GCC 4 17.00 29.00 13.00 41.00
-GCC 5 37.00 22.00 12.00 29.00
-GCC 6 36.00 26.00 17.00 21.00
-GCC 7 29.50 13.50 31.50 25.50
-GCC 8 50.50 14.50 19.50 15.50
-GCC 9 17.00 33.00 18.00 32.00
-GCC 10 37.00 14.00 21.00 28.00
-GCC 11 20.50 14.50 29.50 35.50
-GCC 12 30.00 24.00 22.00 24.00
-GCC 13 27.00 15.00 21.00 37.00
-GCC 14 24.00 22.00 26.00 28.00
-GCC 15 25.50 20.50 24.50 29.50
-GCC 16 31.00 15.00 20.00 34.00
-GCC 17 28.00 25.00 14.00 33.00
-GCC 18 30.50 28.50 19.50 21.50
-GCC 19 29.00 26.00 21.00 24.00
-GCC 20 22.50 23.50 17.50 36.50
-GCC 21 35.50 17.50 19.50 27.50
-GCC 22 37.50 28.50 15.50 18.50
-GCC 23 31.00 19.00 13.00 37.00
-GCC 24 37.00 12.00 22.00 29.00
-GCC 25 35.50 22.50 17.50 24.50
-GCC 26 33.50 18.50 15.50 32.50
-GCC 27 34.50 14.50 25.50 25.50
-GCC 28 31.00 14.00 24.00 31.00
-GCC 29 30.00 27.00 24.00 19.00
-GCC 30 31.00 20.00 14.00 35.00
-GCC 31 33.50 29.50 13.50 23.50
-GCC 32 42.50 20.50 19.50 17.50
-GCC 33 25.50 23.50 14.50 36.50
-GCC 34 39.50 16.50 20.50 23.50
-GCC 35 32.50 23.50 21.50 22.50
-GCC 36 42.00 25.00 16.00 17.00
-GCC 37 38.00 17.00 19.00 26.00
-GCC 38 24.00 26.00 25.00 25.00
-GCC 39 22.50 41.50 18.50 17.50
-GCC 40 32.00 16.00 21.00 31.00
-GCC 41 33.00 28.00 19.00 20.00
-GCC 42 30.50 25.50 19.50 24.50
-GCC 43 35.00 29.00 15.00 21.00
-GCC 44 20.00 27.00 22.00 31.00
-GCC 45 40.50 21.50 21.50 16.50
-GCC 46 26.50 20.50 22.50 30.50
-GCC 47 38.50 29.50 16.50 15.50
-GCC 48 27.50 24.50 17.50 30.50
-GCC 49 28.50 32.50 10.50 28.50
-GCC 50 46.50 20.50 9.50 23.50
-GCC 51 34.50 28.50 13.50 23.50
-GCC 52 41.50 23.50 20.50 14.50
-GCC 53 20.00 28.00 26.00 26.00
-GCC 54 31.50 18.50 24.50 25.50
-GCC 55 30.50 22.50 16.50 30.50
-GCC 56 33.50 22.50 13.50 30.50
-GCC 57 23.00 24.00 23.00 30.00
-GCC 58 25.00 37.00 19.00 19.00
-GCC 59 34.00 23.00 24.00 19.00
-GCC 60 29.00 28.00 17.00 26.00
-GCC 61 25.50 23.50 24.50 26.50
-GCC 62 31.50 22.50 16.50 29.50
-GCC 63 27.50 28.50 25.50 18.50
-GCC 64 33.50 21.50 25.50 19.50
-GCC 65 35.50 19.50 18.50 26.50
-GCC 66 34.00 25.00 15.00 26.00
-GCC 67 37.00 23.00 19.00 21.00
-GCC 68 36.50 29.50 13.50 20.50
-GCC 69 38.50 19.50 20.50 21.50
-GCC 70 38.50 16.50 18.50 26.50
-GCC 71 25.50 38.50 21.50 14.50
-GCC 72 29.00 29.00 25.00 17.00
-GCC 73 32.50 20.50 21.50 25.50
-GCC 74 28.50 32.50 12.50 26.50
-GCC 75 41.50 12.50 18.50 27.50
-GCC 76 24.50 29.50 23.50 22.50
-GCC 77 36.00 21.00 18.00 25.00
-GCC 78 27.00 34.00 22.00 17.00
-GCC 79 21.50 26.50 25.50 26.50
-GCC 80 34.00 19.00 28.00 19.00
-GCC 81 17.00 26.00 26.00 31.00
-GCC 82 31.00 30.00 23.00 16.00
-GCC 83 31.50 26.50 12.50 29.50
-GCC 84 19.00 41.00 21.00 19.00
-GCC 85 37.50 24.50 16.50 21.50
-GCC 86 15.00 48.00 15.00 22.00
-GCC 87 41.00 16.00 18.00 25.00
-GCC 88 23.50 27.50 27.50 21.50
-GCC 89 26.50 27.50 26.50 19.50
-GCC 90 18.50 23.50 24.50 33.50
-GCC 91 27.00 32.00 22.00 19.00
-GCC 92 23.50 17.50 27.50 31.50
-GCC 93 25.50 37.50 15.50 21.50
-GCC 94 27.00 17.00 24.00 32.00
-GCC 95 26.50 37.50 14.50 21.50
-GCC 96 29.50 25.50 16.50 28.50
-GCC 97 29.00 31.00 21.00 19.00
-GCC 98 18.00 33.00 22.00 27.00
-GCC 99 24.50 33.50 24.50 17.50
-GCC 100 24.50 16.50 24.50 34.50
-GCC 101 25.00 40.00 19.00 16.00
-GCC 102 17.50 17.50 32.50 32.50
-GCC 103 31.00 26.00 16.00 27.00
-GCC 104 26.50 29.50 20.50 23.50
-GCC 105 34.00 33.00 21.00 12.00
-GCC 106 23.00 31.00 26.00 20.00
-GCC 107 17.50 35.50 23.50 23.50
-GCC 108 24.50 30.50 23.50 21.50
-GCC 109 17.00 31.00 22.00 30.00
-GCC 110 16.00 35.00 24.00 25.00
-GCC 111 24.00 32.00 23.00 21.00
-GCC 112 37.00 28.00 16.00 19.00
-GCC 113 19.50 22.50 32.50 25.50
-GCC 114 17.00 31.00 35.00 17.00
-GCC 115 29.50 24.50 23.50 22.50
-GCC 116 22.00 30.00 34.00 14.00
-GCC 117 27.00 23.00 19.00 31.00
-GCC 118 25.50 14.50 34.50 25.50
-GCC 119 22.50 34.50 20.50 22.50
-GCC 120 17.50 24.50 26.50 31.50
-GCC 121 27.50 33.50 22.50 16.50
-GCC 122 17.00 23.00 25.00 35.00
-GCC 123 23.50 46.50 11.50 18.50
-GCC 124 9.00 32.00 34.00 25.00
-GCC 125 24.00 27.00 19.00 30.00
-GCC 126 26.00 17.00 28.00 29.00
-GCC 127 26.50 16.50 21.50 35.50
-GCC 128 18.00 34.00 31.00 17.00
-GCC 129 25.50 25.50 27.50 21.50
-GCC 130 25.00 20.00 22.00 33.00
-GCC 131 17.50 39.50 24.50 18.50
-GCC 132 21.00 28.00 23.00 28.00
-GCC 133 13.50 31.50 35.50 19.50
-GCC 134 24.50 19.50 30.50 25.50
-GCC 135 16.50 23.50 30.50 29.50
-GCC 136 28.00 32.00 15.00 25.00
-GCC 137 22.50 21.50 30.50 25.50
-GCC 138 14.50 34.50 24.50 26.50
-GCC 139 20.50 29.50 24.50 25.50
-GCC 140 17.00 23.00 30.00 30.00
-GCC 141 20.50 23.50 25.50 30.50
-GCC 142 18.00 29.00 38.00 15.00
-GCC 143 22.00 24.00 27.00 27.00
-GCC 144 21.50 30.50 26.50 21.50
-GCC 145 22.00 21.00 29.00 28.00
-GCC 146 25.00 16.00 39.00 20.00
-GCC 147 26.50 22.50 30.50 20.50
-GCC 148 12.50 28.50 36.50 22.50
-GCC 149 26.50 23.50 23.50 26.50
-GCC 150 14.00 29.00 24.00 33.00
-GCC 151 19.50 30.50 32.50 17.50
-GCC 152 18.50 17.50 29.50 34.50
-GCC 153 22.50 22.50 31.50 23.50
-GCC 154 22.00 21.00 29.00 28.00
-GCC 155 21.00 26.00 19.00 34.00
-GCC 156 14.50 23.50 35.50 26.50
-GCC 157 22.00 31.00 23.00 24.00
-GCC 158 22.50 29.50 24.50 23.50
-GCC 159 17.50 12.50 46.50 23.50
-GCC 160 24.50 26.50 26.50 22.50
-GCC 161 13.00 23.00 45.00 19.00
-GCC 162 31.50 16.50 22.50 29.50
-GCC 163 19.50 21.50 35.50 23.50
-GCC 164 29.00 18.00 21.00 32.00
-GCC 165 14.50 17.50 35.50 32.50
-GCC 166 17.50 37.50 28.50 16.50
-GCC 167 16.50 21.50 31.50 30.50
-GCC 168 14.00 25.00 30.00 31.00
-GCC 169 18.50 20.50 23.50 37.50
-GCC 170 19.00 23.00 28.00 30.00
-GCC 171 20.00 28.00 33.00 19.00
-GCC 172 19.00 20.00 32.00 29.00
-GCC 173 24.50 16.50 33.50 25.50
-GCC 174 17.50 23.50 33.50 25.50
-GCC 175 33.50 17.50 35.50 13.50
-GCC 176 16.50 32.50 28.50 22.50
-GCC 177 19.00 22.00 27.00 32.00
-GCC 178 16.00 26.00 30.00 28.00
-GCC 179 18.00 18.00 22.00 42.00
-GCC 180 21.00 22.00 34.00 23.00
-GCC 181 20.50 19.50 35.50 24.50
-GCC 182 32.50 18.50 22.50 26.50
-GCC 183 24.50 13.50 28.50 33.50
-GCC 184 15.00 29.00 30.00 26.00
-GCC 185 15.00 32.00 33.00 20.00
-GCC 186 22.50 23.50 34.50 19.50
-GCC 187 19.00 14.00 40.00 27.00
-GCC 188 27.50 21.50 27.50 23.50
-GCC 189 17.00 22.00 34.00 27.00
-GCC 190 23.00 30.00 23.00 24.00
-GCC 191 25.00 22.00 28.00 25.00
-GCC 192 34.50 24.50 13.50 27.50
-GCC 193 18.50 25.50 25.50 30.50
-GCC 194 18.50 33.50 24.50 23.50
-GCC 195 16.00 26.00 23.00 35.00
-GCC 196 21.50 25.50 24.50 28.50
-GCC 197 20.00 21.00 23.00 36.00
-GCC 198 17.00 21.00 37.00 25.00
-GCC 199 20.50 18.50 25.50 35.50
-GCC 200 21.00 29.00 21.00 29.00
-GCC 201 27.00 21.00 23.00 29.00
-GCC 202 21.50 24.50 19.50 34.50
-GCC 203 21.50 24.50 26.50 27.50
-GCC 204 27.00 29.00 24.00 20.00
-GCC 205 19.50 21.50 22.50 36.50
-GCC 206 26.50 24.50 21.50 27.50
-GCC 207 22.50 21.50 19.50 36.50
-GCC 208 14.00 35.00 29.00 22.00
-GCC 209 16.00 23.00 12.00 49.00
-GCC 210 18.50 19.50 40.50 21.50
-GCC 211 26.00 20.00 22.00 32.00
-GCC 212 21.00 31.00 18.00 30.00
-GCC 213 24.00 15.00 31.00 30.00
-GCC 214 17.50 24.50 25.50 32.50
-GCC 215 26.00 24.00 23.00 27.00
-GCC 216 21.50 17.50 25.50 35.50
-GCC 217 26.00 29.00 17.00 28.00
-GCC 218 20.00 27.00 21.00 32.00
-GCC 219 17.00 21.00 21.00 41.00
-GCC 220 25.50 23.50 23.50 27.50
-GCC 221 21.50 23.50 20.50 34.50
-GCC 222 21.50 21.50 18.50 38.50
-GCC 223 20.00 27.00 28.00 25.00
-GCC 224 22.50 22.50 24.50 30.50
-GCC 225 14.50 35.50 30.50 19.50
-GCC 226 20.00 23.00 26.00 31.00
-GCC 227 20.50 24.50 23.50 31.50
-GCC 228 33.00 19.00 26.00 22.00
-GCC 229 22.50 24.50 18.50 34.50
-GCC 230 21.00 32.00 16.00 31.00
-GCC 231 23.00 28.00 30.00 19.00
-GCC 232 23.50 21.50 12.50 42.50
-GCC 233 21.00 27.00 25.00 27.00
-GCC 234 16.50 27.50 22.50 33.50
-GCC 235 20.00 15.00 28.00 37.00
-GCC 236 28.00 23.00 21.00 28.00
-GCC 237 20.50 19.50 22.50 37.50
-GCC 238 21.50 29.50 24.50 24.50
-GCC 239 20.00 8.00 17.00 55.00
-GCC 240 28.00 24.00 16.00 32.00
-GCC 241 22.50 22.50 16.50 38.50
-GCC 242 29.00 25.00 13.00 33.00
-GCC 243 22.50 15.50 23.50 38.50
-GCC 244 20.50 23.50 16.50 39.50
-GCC 245 28.00 23.00 19.00 30.00
-GCC 246 21.00 29.00 25.00 25.00
-GCC 247 32.00 14.00 13.00 41.00
-GCC 248 18.00 18.00 25.00 39.00
-GCC 249 25.00 23.00 21.00 31.00
-GCC 250 27.50 22.50 17.50 32.50
-GCC 251 13.50 20.50 36.50 29.50
+# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
+GCC 1 21.94 30.10 34.18 13.78 2.04 0.00
+GCC 2 30.00 16.00 11.00 43.00 0.00 0.00
+GCC 3 33.00 25.00 9.00 33.00 0.00 0.00
+GCC 4 17.00 29.00 13.00 41.00 0.00 0.00
+GCC 5 37.00 22.00 12.00 29.00 0.00 0.00
+GCC 6 36.00 26.00 17.00 21.00 0.00 0.00
+GCC 7 29.50 13.50 31.50 25.50 0.00 0.00
+GCC 8 50.50 14.50 19.50 15.50 0.00 0.00
+GCC 9 17.00 33.00 18.00 32.00 0.00 0.00
+GCC 10 37.00 14.00 21.00 28.00 0.00 0.00
+GCC 11 20.50 14.50 29.50 35.50 0.00 0.00
+GCC 12 30.00 24.00 22.00 24.00 0.00 0.00
+GCC 13 27.00 15.00 21.00 37.00 0.00 0.00
+GCC 14 24.24 22.22 26.26 27.27 1.01 0.00
+GCC 15 25.50 20.50 24.50 29.50 0.00 0.00
+GCC 16 31.00 15.00 20.00 34.00 0.00 0.00
+GCC 17 28.00 25.00 14.00 33.00 0.00 0.00
+GCC 18 30.50 28.50 19.50 21.50 0.00 0.00
+GCC 19 29.00 26.00 21.00 24.00 0.00 0.00
+GCC 20 22.50 23.50 17.50 36.50 0.00 0.00
+GCC 21 35.50 17.50 19.50 27.50 0.00 0.00
+GCC 22 37.50 28.50 15.50 18.50 0.00 0.00
+GCC 23 31.31 19.19 13.13 36.36 1.01 0.00
+GCC 24 37.00 12.00 22.00 29.00 0.00 0.00
+GCC 25 35.50 22.50 17.50 24.50 0.00 0.00
+GCC 26 33.50 18.50 15.50 32.50 0.00 0.00
+GCC 27 34.50 14.50 25.50 25.50 0.00 0.00
+GCC 28 31.00 14.00 24.00 31.00 0.00 0.00
+GCC 29 30.00 27.00 24.00 19.00 0.00 0.00
+GCC 30 31.00 20.00 14.00 35.00 0.00 0.00
+GCC 31 33.50 29.50 13.50 23.50 0.00 0.00
+GCC 32 42.50 20.50 19.50 17.50 0.00 0.00
+GCC 33 25.50 23.50 14.50 36.50 0.00 0.00
+GCC 34 39.50 16.50 20.50 23.50 0.00 0.00
+GCC 35 32.50 23.50 21.50 22.50 0.00 0.00
+GCC 36 42.00 25.00 16.00 17.00 0.00 0.00
+GCC 37 38.00 17.00 19.00 26.00 0.00 0.00
+GCC 38 24.00 26.00 25.00 25.00 0.00 0.00
+GCC 39 22.50 41.50 18.50 17.50 0.00 0.00
+GCC 40 32.00 16.00 21.00 31.00 0.00 0.00
+GCC 41 33.00 28.00 19.00 20.00 0.00 0.00
+GCC 42 30.50 25.50 19.50 24.50 0.00 0.00
+GCC 43 35.00 29.00 15.00 21.00 0.00 0.00
+GCC 44 20.00 27.00 22.00 31.00 0.00 0.00
+GCC 45 40.50 21.50 21.50 16.50 0.00 0.00
+GCC 46 26.50 20.50 22.50 30.50 0.00 0.00
+GCC 47 38.50 29.50 16.50 15.50 0.00 0.00
+GCC 48 27.50 24.50 17.50 30.50 0.00 0.00
+GCC 49 28.50 32.50 10.50 28.50 0.00 0.00
+GCC 50 46.50 20.50 9.50 23.50 0.00 0.00
+GCC 51 34.50 28.50 13.50 23.50 0.00 0.00
+GCC 52 41.50 23.50 20.50 14.50 0.00 0.00
+GCC 53 20.00 28.00 26.00 26.00 0.00 0.00
+GCC 54 31.50 18.50 24.50 25.50 0.00 0.00
+GCC 55 30.50 22.50 16.50 30.50 0.00 0.00
+GCC 56 33.50 22.50 13.50 30.50 0.00 0.00
+GCC 57 23.00 24.00 23.00 30.00 0.00 0.00
+GCC 58 25.00 37.00 19.00 19.00 0.00 0.00
+GCC 59 34.00 23.00 24.00 19.00 0.00 0.00
+GCC 60 29.00 28.00 17.00 26.00 0.00 0.00
+GCC 61 25.50 23.50 24.50 26.50 0.00 0.00
+GCC 62 31.50 22.50 16.50 29.50 0.00 0.00
+GCC 63 27.50 28.50 25.50 18.50 0.00 0.00
+GCC 64 33.50 21.50 25.50 19.50 0.00 0.00
+GCC 65 35.50 19.50 18.50 26.50 0.00 0.00
+GCC 66 34.00 25.00 15.00 26.00 0.00 0.00
+GCC 67 37.00 23.00 19.00 21.00 0.00 0.00
+GCC 68 36.50 29.50 13.50 20.50 0.00 0.00
+GCC 69 38.50 19.50 20.50 21.50 0.00 0.00
+GCC 70 38.50 16.50 18.50 26.50 0.00 0.00
+GCC 71 25.50 38.50 21.50 14.50 0.00 0.00
+GCC 72 29.00 29.00 25.00 17.00 0.00 0.00
+GCC 73 32.50 20.50 21.50 25.50 0.00 0.00
+GCC 74 28.50 32.50 12.50 26.50 0.00 0.00
+GCC 75 41.50 12.50 18.50 27.50 0.00 0.00
+GCC 76 24.50 29.50 23.50 22.50 0.00 0.00
+GCC 77 36.00 21.00 18.00 25.00 0.00 0.00
+GCC 78 27.00 34.00 22.00 17.00 0.00 0.00
+GCC 79 21.50 26.50 25.50 26.50 0.00 0.00
+GCC 80 34.00 19.00 28.00 19.00 0.00 0.00
+GCC 81 17.00 26.00 26.00 31.00 0.00 0.00
+GCC 82 31.00 30.00 23.00 16.00 0.00 0.00
+GCC 83 31.50 26.50 12.50 29.50 0.00 0.00
+GCC 84 19.00 41.00 21.00 19.00 0.00 0.00
+GCC 85 37.50 24.50 16.50 21.50 0.00 0.00
+GCC 86 15.00 48.00 15.00 22.00 0.00 0.00
+GCC 87 41.00 16.00 18.00 25.00 0.00 0.00
+GCC 88 23.50 27.50 27.50 21.50 0.00 0.00
+GCC 89 26.50 27.50 26.50 19.50 0.00 0.00
+GCC 90 18.50 23.50 24.50 33.50 0.00 0.00
+GCC 91 27.00 32.00 22.00 19.00 0.00 0.00
+GCC 92 23.50 17.50 27.50 31.50 0.00 0.00
+GCC 93 25.50 37.50 15.50 21.50 0.00 0.00
+GCC 94 27.00 17.00 24.00 32.00 0.00 0.00
+GCC 95 26.77 37.88 14.65 20.71 1.01 0.00
+GCC 96 29.50 25.50 16.50 28.50 0.00 0.00
+GCC 97 29.00 31.00 21.00 19.00 0.00 0.00
+GCC 98 18.18 33.33 22.22 26.26 1.01 0.00
+GCC 99 24.50 33.50 24.50 17.50 0.00 0.00
+GCC 100 24.50 16.50 24.50 34.50 0.00 0.00
+GCC 101 25.00 40.00 19.00 16.00 0.00 0.00
+GCC 102 17.50 17.50 32.50 32.50 0.00 0.00
+GCC 103 31.00 26.00 16.00 27.00 0.00 0.00
+GCC 104 26.50 29.50 20.50 23.50 0.00 0.00
+GCC 105 34.00 33.00 21.00 12.00 0.00 0.00
+GCC 106 23.00 31.00 26.00 20.00 0.00 0.00
+GCC 107 17.68 35.86 23.74 22.73 1.01 0.00
+GCC 108 24.75 30.81 23.74 20.71 1.01 0.00
+GCC 109 17.00 31.00 22.00 30.00 0.00 0.00
+GCC 110 16.16 35.35 24.24 24.24 1.01 0.00
+GCC 111 24.24 32.32 23.23 20.20 1.01 0.00
+GCC 112 37.37 28.28 16.16 18.18 1.01 0.00
+GCC 113 19.70 22.73 32.83 24.75 1.01 0.00
+GCC 114 17.00 31.00 35.00 17.00 0.00 0.00
+GCC 115 29.50 24.50 23.50 22.50 0.00 0.00
+GCC 116 22.00 30.00 34.00 14.00 0.00 0.00
+GCC 117 27.00 23.00 19.00 31.00 0.00 0.00
+GCC 118 25.50 14.50 34.50 25.50 0.00 0.00
+GCC 119 22.50 34.50 20.50 22.50 0.00 0.00
+GCC 120 17.50 24.50 26.50 31.50 0.00 0.00
+GCC 121 27.78 33.84 22.73 15.66 1.01 0.00
+GCC 122 17.00 23.00 25.00 35.00 0.00 0.00
+GCC 123 23.50 46.50 11.50 18.50 0.00 0.00
+GCC 124 9.00 32.00 34.00 25.00 0.00 0.00
+GCC 125 24.00 27.00 19.00 30.00 0.00 0.00
+GCC 126 26.00 17.00 28.00 29.00 0.00 0.00
+GCC 127 26.50 16.50 21.50 35.50 0.00 0.00
+GCC 128 18.00 34.00 31.00 17.00 0.00 0.00
+GCC 129 25.50 25.50 27.50 21.50 0.00 0.00
+GCC 130 25.00 20.00 22.00 33.00 0.00 0.00
+GCC 131 17.50 39.50 24.50 18.50 0.00 0.00
+GCC 132 21.00 28.00 23.00 28.00 0.00 0.00
+GCC 133 13.50 31.50 35.50 19.50 0.00 0.00
+GCC 134 24.50 19.50 30.50 25.50 0.00 0.00
+GCC 135 16.50 23.50 30.50 29.50 0.00 0.00
+GCC 136 28.00 32.00 15.00 25.00 0.00 0.00
+GCC 137 22.50 21.50 30.50 25.50 0.00 0.00
+GCC 138 14.50 34.50 24.50 26.50 0.00 0.00
+GCC 139 20.50 29.50 24.50 25.50 0.00 0.00
+GCC 140 17.00 23.00 30.00 30.00 0.00 0.00
+GCC 141 20.50 23.50 25.50 30.50 0.00 0.00
+GCC 142 18.00 29.00 38.00 15.00 0.00 0.00
+GCC 143 22.00 24.00 27.00 27.00 0.00 0.00
+GCC 144 21.50 30.50 26.50 21.50 0.00 0.00
+GCC 145 22.00 21.00 29.00 28.00 0.00 0.00
+GCC 146 25.00 16.00 39.00 20.00 0.00 0.00
+GCC 147 26.50 22.50 30.50 20.50 0.00 0.00
+GCC 148 12.50 28.50 36.50 22.50 0.00 0.00
+GCC 149 26.50 23.50 23.50 26.50 0.00 0.00
+GCC 150 14.00 29.00 24.00 33.00 0.00 0.00
+GCC 151 19.50 30.50 32.50 17.50 0.00 0.00
+GCC 152 18.50 17.50 29.50 34.50 0.00 0.00
+GCC 153 22.50 22.50 31.50 23.50 0.00 0.00
+GCC 154 22.00 21.00 29.00 28.00 0.00 0.00
+GCC 155 21.00 26.00 19.00 34.00 0.00 0.00
+GCC 156 14.50 23.50 35.50 26.50 0.00 0.00
+GCC 157 22.00 31.00 23.00 24.00 0.00 0.00
+GCC 158 22.50 29.50 24.50 23.50 0.00 0.00
+GCC 159 17.50 12.50 46.50 23.50 0.00 0.00
+GCC 160 24.50 26.50 26.50 22.50 0.00 0.00
+GCC 161 13.00 23.00 45.00 19.00 0.00 0.00
+GCC 162 31.50 16.50 22.50 29.50 0.00 0.00
+GCC 163 19.50 21.50 35.50 23.50 0.00 0.00
+GCC 164 29.00 18.00 21.00 32.00 0.00 0.00
+GCC 165 14.50 17.50 35.50 32.50 0.00 0.00
+GCC 166 17.50 37.50 28.50 16.50 0.00 0.00
+GCC 167 16.50 21.50 31.50 30.50 0.00 0.00
+GCC 168 14.00 25.00 30.00 31.00 0.00 0.00
+GCC 169 18.50 20.50 23.50 37.50 0.00 0.00
+GCC 170 19.00 23.00 28.00 30.00 0.00 0.00
+GCC 171 20.00 28.00 33.00 19.00 0.00 0.00
+GCC 172 19.00 20.00 32.00 29.00 0.00 0.00
+GCC 173 24.50 16.50 33.50 25.50 0.00 0.00
+GCC 174 17.50 23.50 33.50 25.50 0.00 0.00
+GCC 175 33.50 17.50 35.50 13.50 0.00 0.00
+GCC 176 16.50 32.50 28.50 22.50 0.00 0.00
+GCC 177 19.00 22.00 27.00 32.00 0.00 0.00
+GCC 178 16.00 26.00 30.00 28.00 0.00 0.00
+GCC 179 18.00 18.00 22.00 42.00 0.00 0.00
+GCC 180 21.00 22.00 34.00 23.00 0.00 0.00
+GCC 181 20.50 19.50 35.50 24.50 0.00 0.00
+GCC 182 32.50 18.50 22.50 26.50 0.00 0.00
+GCC 183 24.50 13.50 28.50 33.50 0.00 0.00
+GCC 184 15.00 29.00 30.00 26.00 0.00 0.00
+GCC 185 15.00 32.00 33.00 20.00 0.00 0.00
+GCC 186 22.50 23.50 34.50 19.50 0.00 0.00
+GCC 187 19.00 14.00 40.00 27.00 0.00 0.00
+GCC 188 27.50 21.50 27.50 23.50 0.00 0.00
+GCC 189 17.00 22.00 34.00 27.00 0.00 0.00
+GCC 190 23.00 30.00 23.00 24.00 0.00 0.00
+GCC 191 25.00 22.00 28.00 25.00 0.00 0.00
+GCC 192 34.50 24.50 13.50 27.50 0.00 0.00
+GCC 193 18.50 25.50 25.50 30.50 0.00 0.00
+GCC 194 18.50 33.50 24.50 23.50 0.00 0.00
+GCC 195 16.00 26.00 23.00 35.00 0.00 0.00
+GCC 196 21.50 25.50 24.50 28.50 0.00 0.00
+GCC 197 20.00 21.00 23.00 36.00 0.00 0.00
+GCC 198 17.00 21.00 37.00 25.00 0.00 0.00
+GCC 199 20.50 18.50 25.50 35.50 0.00 0.00
+GCC 200 21.00 29.00 21.00 29.00 0.00 0.00
+GCC 201 27.00 21.00 23.00 29.00 0.00 0.00
+GCC 202 21.50 24.50 19.50 34.50 0.00 0.00
+GCC 203 21.50 24.50 26.50 27.50 0.00 0.00
+GCC 204 27.00 29.00 24.00 20.00 0.00 0.00
+GCC 205 19.50 21.50 22.50 36.50 0.00 0.00
+GCC 206 26.50 24.50 21.50 27.50 0.00 0.00
+GCC 207 22.50 21.50 19.50 36.50 0.00 0.00
+GCC 208 14.00 35.00 29.00 22.00 0.00 0.00
+GCC 209 16.00 23.00 12.00 49.00 0.00 0.00
+GCC 210 18.50 19.50 40.50 21.50 0.00 0.00
+GCC 211 26.00 20.00 22.00 32.00 0.00 0.00
+GCC 212 21.00 31.00 18.00 30.00 0.00 0.00
+GCC 213 24.00 15.00 31.00 30.00 0.00 0.00
+GCC 214 17.50 24.50 25.50 32.50 0.00 0.00
+GCC 215 26.00 24.00 23.00 27.00 0.00 0.00
+GCC 216 21.50 17.50 25.50 35.50 0.00 0.00
+GCC 217 26.00 29.00 17.00 28.00 0.00 0.00
+GCC 218 20.00 27.00 21.00 32.00 0.00 0.00
+GCC 219 17.00 21.00 21.00 41.00 0.00 0.00
+GCC 220 25.50 23.50 23.50 27.50 0.00 0.00
+GCC 221 21.50 23.50 20.50 34.50 0.00 0.00
+GCC 222 21.50 21.50 18.50 38.50 0.00 0.00
+GCC 223 20.00 27.00 28.00 25.00 0.00 0.00
+GCC 224 22.50 22.50 24.50 30.50 0.00 0.00
+GCC 225 14.50 35.50 30.50 19.50 0.00 0.00
+GCC 226 20.00 23.00 26.00 31.00 0.00 0.00
+GCC 227 20.50 24.50 23.50 31.50 0.00 0.00
+GCC 228 33.00 19.00 26.00 22.00 0.00 0.00
+GCC 229 22.50 24.50 18.50 34.50 0.00 0.00
+GCC 230 21.00 32.00 16.00 31.00 0.00 0.00
+GCC 231 23.00 28.00 30.00 19.00 0.00 0.00
+GCC 232 23.50 21.50 12.50 42.50 0.00 0.00
+GCC 233 21.00 27.00 25.00 27.00 0.00 0.00
+GCC 234 16.50 27.50 22.50 33.50 0.00 0.00
+GCC 235 20.00 15.00 28.00 37.00 0.00 0.00
+GCC 236 28.00 23.00 21.00 28.00 0.00 0.00
+GCC 237 20.50 19.50 22.50 37.50 0.00 0.00
+GCC 238 21.50 29.50 24.50 24.50 0.00 0.00
+GCC 239 20.00 8.00 17.00 55.00 0.00 0.00
+GCC 240 28.00 24.00 16.00 32.00 0.00 0.00
+GCC 241 22.50 22.50 16.50 38.50 0.00 0.00
+GCC 242 29.00 25.00 13.00 33.00 0.00 0.00
+GCC 243 22.50 15.50 23.50 38.50 0.00 0.00
+GCC 244 20.50 23.50 16.50 39.50 0.00 0.00
+GCC 245 28.00 23.00 19.00 30.00 0.00 0.00
+GCC 246 21.00 29.00 25.00 25.00 0.00 0.00
+GCC 247 32.00 14.00 13.00 41.00 0.00 0.00
+GCC 248 18.00 18.00 25.00 39.00 0.00 0.00
+GCC 249 25.00 23.00 21.00 31.00 0.00 0.00
+GCC 250 27.50 22.50 17.50 32.50 0.00 0.00
+GCC 251 13.50 20.50 36.50 29.50 0.00 0.00
# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
RL 251 200
diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out2.tab
--- a/test-data/samtools_stats_out2.tab Fri Dec 18 19:47:08 2015 -0500
+++ b/test-data/samtools_stats_out2.tab Tue May 09 11:17:02 2017 -0400
@@ -1,5 +1,6 @@
-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats
-# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat
+# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_5.dat /tmp/tmpO1aTrb/files/000/dataset_4.dat
# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK 1bd20fd8 58ad2167 29883386
@@ -836,258 +837,258 @@
GCL 52.01 1
GCL 52.51 0
GCL 53.02 1
-# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%]
-GCC 1 21.50 29.50 33.50 15.50
-GCC 2 30.00 16.00 11.00 43.00
-GCC 3 33.00 25.00 9.00 33.00
-GCC 4 17.00 29.00 13.00 41.00
-GCC 5 37.00 22.00 12.00 29.00
-GCC 6 36.00 26.00 17.00 21.00
-GCC 7 29.50 13.50 31.50 25.50
-GCC 8 50.50 14.50 19.50 15.50
-GCC 9 17.00 33.00 18.00 32.00
-GCC 10 37.00 14.00 21.00 28.00
-GCC 11 20.50 14.50 29.50 35.50
-GCC 12 30.00 24.00 22.00 24.00
-GCC 13 27.00 15.00 21.00 37.00
-GCC 14 24.00 22.00 26.00 28.00
-GCC 15 25.50 20.50 24.50 29.50
-GCC 16 31.00 15.00 20.00 34.00
-GCC 17 28.00 25.00 14.00 33.00
-GCC 18 30.50 28.50 19.50 21.50
-GCC 19 29.00 26.00 21.00 24.00
-GCC 20 22.50 23.50 17.50 36.50
-GCC 21 35.50 17.50 19.50 27.50
-GCC 22 37.50 28.50 15.50 18.50
-GCC 23 31.00 19.00 13.00 37.00
-GCC 24 37.00 12.00 22.00 29.00
-GCC 25 35.50 22.50 17.50 24.50
-GCC 26 33.50 18.50 15.50 32.50
-GCC 27 34.50 14.50 25.50 25.50
-GCC 28 31.00 14.00 24.00 31.00
-GCC 29 30.00 27.00 24.00 19.00
-GCC 30 31.00 20.00 14.00 35.00
-GCC 31 33.50 29.50 13.50 23.50
-GCC 32 42.50 20.50 19.50 17.50
-GCC 33 25.50 23.50 14.50 36.50
-GCC 34 39.50 16.50 20.50 23.50
-GCC 35 32.50 23.50 21.50 22.50
-GCC 36 42.00 25.00 16.00 17.00
-GCC 37 38.00 17.00 19.00 26.00
-GCC 38 24.00 26.00 25.00 25.00
-GCC 39 22.50 41.50 18.50 17.50
-GCC 40 32.00 16.00 21.00 31.00
-GCC 41 33.00 28.00 19.00 20.00
-GCC 42 30.50 25.50 19.50 24.50
-GCC 43 35.00 29.00 15.00 21.00
-GCC 44 20.00 27.00 22.00 31.00
-GCC 45 40.50 21.50 21.50 16.50
-GCC 46 26.50 20.50 22.50 30.50
-GCC 47 38.50 29.50 16.50 15.50
-GCC 48 27.50 24.50 17.50 30.50
-GCC 49 28.50 32.50 10.50 28.50
-GCC 50 46.50 20.50 9.50 23.50
-GCC 51 34.50 28.50 13.50 23.50
-GCC 52 41.50 23.50 20.50 14.50
-GCC 53 20.00 28.00 26.00 26.00
-GCC 54 31.50 18.50 24.50 25.50
-GCC 55 30.50 22.50 16.50 30.50
-GCC 56 33.50 22.50 13.50 30.50
-GCC 57 23.00 24.00 23.00 30.00
-GCC 58 25.00 37.00 19.00 19.00
-GCC 59 34.00 23.00 24.00 19.00
-GCC 60 29.00 28.00 17.00 26.00
-GCC 61 25.50 23.50 24.50 26.50
-GCC 62 31.50 22.50 16.50 29.50
-GCC 63 27.50 28.50 25.50 18.50
-GCC 64 33.50 21.50 25.50 19.50
-GCC 65 35.50 19.50 18.50 26.50
-GCC 66 34.00 25.00 15.00 26.00
-GCC 67 37.00 23.00 19.00 21.00
-GCC 68 36.50 29.50 13.50 20.50
-GCC 69 38.50 19.50 20.50 21.50
-GCC 70 38.50 16.50 18.50 26.50
-GCC 71 25.50 38.50 21.50 14.50
-GCC 72 29.00 29.00 25.00 17.00
-GCC 73 32.50 20.50 21.50 25.50
-GCC 74 28.50 32.50 12.50 26.50
-GCC 75 41.50 12.50 18.50 27.50
-GCC 76 24.50 29.50 23.50 22.50
-GCC 77 36.00 21.00 18.00 25.00
-GCC 78 27.00 34.00 22.00 17.00
-GCC 79 21.50 26.50 25.50 26.50
-GCC 80 34.00 19.00 28.00 19.00
-GCC 81 17.00 26.00 26.00 31.00
-GCC 82 31.00 30.00 23.00 16.00
-GCC 83 31.50 26.50 12.50 29.50
-GCC 84 19.00 41.00 21.00 19.00
-GCC 85 37.50 24.50 16.50 21.50
-GCC 86 15.00 48.00 15.00 22.00
-GCC 87 41.00 16.00 18.00 25.00
-GCC 88 23.50 27.50 27.50 21.50
-GCC 89 26.50 27.50 26.50 19.50
-GCC 90 18.50 23.50 24.50 33.50
-GCC 91 27.00 32.00 22.00 19.00
-GCC 92 23.50 17.50 27.50 31.50
-GCC 93 25.50 37.50 15.50 21.50
-GCC 94 27.00 17.00 24.00 32.00
-GCC 95 26.50 37.50 14.50 21.50
-GCC 96 29.50 25.50 16.50 28.50
-GCC 97 29.00 31.00 21.00 19.00
-GCC 98 18.00 33.00 22.00 27.00
-GCC 99 24.50 33.50 24.50 17.50
-GCC 100 24.50 16.50 24.50 34.50
-GCC 101 25.00 40.00 19.00 16.00
-GCC 102 17.50 17.50 32.50 32.50
-GCC 103 31.00 26.00 16.00 27.00
-GCC 104 26.50 29.50 20.50 23.50
-GCC 105 34.00 33.00 21.00 12.00
-GCC 106 23.00 31.00 26.00 20.00
-GCC 107 17.50 35.50 23.50 23.50
-GCC 108 24.50 30.50 23.50 21.50
-GCC 109 17.00 31.00 22.00 30.00
-GCC 110 16.00 35.00 24.00 25.00
-GCC 111 24.00 32.00 23.00 21.00
-GCC 112 37.00 28.00 16.00 19.00
-GCC 113 19.50 22.50 32.50 25.50
-GCC 114 17.00 31.00 35.00 17.00
-GCC 115 29.50 24.50 23.50 22.50
-GCC 116 22.00 30.00 34.00 14.00
-GCC 117 27.00 23.00 19.00 31.00
-GCC 118 25.50 14.50 34.50 25.50
-GCC 119 22.50 34.50 20.50 22.50
-GCC 120 17.50 24.50 26.50 31.50
-GCC 121 27.50 33.50 22.50 16.50
-GCC 122 17.00 23.00 25.00 35.00
-GCC 123 23.50 46.50 11.50 18.50
-GCC 124 9.00 32.00 34.00 25.00
-GCC 125 24.00 27.00 19.00 30.00
-GCC 126 26.00 17.00 28.00 29.00
-GCC 127 26.50 16.50 21.50 35.50
-GCC 128 18.00 34.00 31.00 17.00
-GCC 129 25.50 25.50 27.50 21.50
-GCC 130 25.00 20.00 22.00 33.00
-GCC 131 17.50 39.50 24.50 18.50
-GCC 132 21.00 28.00 23.00 28.00
-GCC 133 13.50 31.50 35.50 19.50
-GCC 134 24.50 19.50 30.50 25.50
-GCC 135 16.50 23.50 30.50 29.50
-GCC 136 28.00 32.00 15.00 25.00
-GCC 137 22.50 21.50 30.50 25.50
-GCC 138 14.50 34.50 24.50 26.50
-GCC 139 20.50 29.50 24.50 25.50
-GCC 140 17.00 23.00 30.00 30.00
-GCC 141 20.50 23.50 25.50 30.50
-GCC 142 18.00 29.00 38.00 15.00
-GCC 143 22.00 24.00 27.00 27.00
-GCC 144 21.50 30.50 26.50 21.50
-GCC 145 22.00 21.00 29.00 28.00
-GCC 146 25.00 16.00 39.00 20.00
-GCC 147 26.50 22.50 30.50 20.50
-GCC 148 12.50 28.50 36.50 22.50
-GCC 149 26.50 23.50 23.50 26.50
-GCC 150 14.00 29.00 24.00 33.00
-GCC 151 19.50 30.50 32.50 17.50
-GCC 152 18.50 17.50 29.50 34.50
-GCC 153 22.50 22.50 31.50 23.50
-GCC 154 22.00 21.00 29.00 28.00
-GCC 155 21.00 26.00 19.00 34.00
-GCC 156 14.50 23.50 35.50 26.50
-GCC 157 22.00 31.00 23.00 24.00
-GCC 158 22.50 29.50 24.50 23.50
-GCC 159 17.50 12.50 46.50 23.50
-GCC 160 24.50 26.50 26.50 22.50
-GCC 161 13.00 23.00 45.00 19.00
-GCC 162 31.50 16.50 22.50 29.50
-GCC 163 19.50 21.50 35.50 23.50
-GCC 164 29.00 18.00 21.00 32.00
-GCC 165 14.50 17.50 35.50 32.50
-GCC 166 17.50 37.50 28.50 16.50
-GCC 167 16.50 21.50 31.50 30.50
-GCC 168 14.00 25.00 30.00 31.00
-GCC 169 18.50 20.50 23.50 37.50
-GCC 170 19.00 23.00 28.00 30.00
-GCC 171 20.00 28.00 33.00 19.00
-GCC 172 19.00 20.00 32.00 29.00
-GCC 173 24.50 16.50 33.50 25.50
-GCC 174 17.50 23.50 33.50 25.50
-GCC 175 33.50 17.50 35.50 13.50
-GCC 176 16.50 32.50 28.50 22.50
-GCC 177 19.00 22.00 27.00 32.00
-GCC 178 16.00 26.00 30.00 28.00
-GCC 179 18.00 18.00 22.00 42.00
-GCC 180 21.00 22.00 34.00 23.00
-GCC 181 20.50 19.50 35.50 24.50
-GCC 182 32.50 18.50 22.50 26.50
-GCC 183 24.50 13.50 28.50 33.50
-GCC 184 15.00 29.00 30.00 26.00
-GCC 185 15.00 32.00 33.00 20.00
-GCC 186 22.50 23.50 34.50 19.50
-GCC 187 19.00 14.00 40.00 27.00
-GCC 188 27.50 21.50 27.50 23.50
-GCC 189 17.00 22.00 34.00 27.00
-GCC 190 23.00 30.00 23.00 24.00
-GCC 191 25.00 22.00 28.00 25.00
-GCC 192 34.50 24.50 13.50 27.50
-GCC 193 18.50 25.50 25.50 30.50
-GCC 194 18.50 33.50 24.50 23.50
-GCC 195 16.00 26.00 23.00 35.00
-GCC 196 21.50 25.50 24.50 28.50
-GCC 197 20.00 21.00 23.00 36.00
-GCC 198 17.00 21.00 37.00 25.00
-GCC 199 20.50 18.50 25.50 35.50
-GCC 200 21.00 29.00 21.00 29.00
-GCC 201 27.00 21.00 23.00 29.00
-GCC 202 21.50 24.50 19.50 34.50
-GCC 203 21.50 24.50 26.50 27.50
-GCC 204 27.00 29.00 24.00 20.00
-GCC 205 19.50 21.50 22.50 36.50
-GCC 206 26.50 24.50 21.50 27.50
-GCC 207 22.50 21.50 19.50 36.50
-GCC 208 14.00 35.00 29.00 22.00
-GCC 209 16.00 23.00 12.00 49.00
-GCC 210 18.50 19.50 40.50 21.50
-GCC 211 26.00 20.00 22.00 32.00
-GCC 212 21.00 31.00 18.00 30.00
-GCC 213 24.00 15.00 31.00 30.00
-GCC 214 17.50 24.50 25.50 32.50
-GCC 215 26.00 24.00 23.00 27.00
-GCC 216 21.50 17.50 25.50 35.50
-GCC 217 26.00 29.00 17.00 28.00
-GCC 218 20.00 27.00 21.00 32.00
-GCC 219 17.00 21.00 21.00 41.00
-GCC 220 25.50 23.50 23.50 27.50
-GCC 221 21.50 23.50 20.50 34.50
-GCC 222 21.50 21.50 18.50 38.50
-GCC 223 20.00 27.00 28.00 25.00
-GCC 224 22.50 22.50 24.50 30.50
-GCC 225 14.50 35.50 30.50 19.50
-GCC 226 20.00 23.00 26.00 31.00
-GCC 227 20.50 24.50 23.50 31.50
-GCC 228 33.00 19.00 26.00 22.00
-GCC 229 22.50 24.50 18.50 34.50
-GCC 230 21.00 32.00 16.00 31.00
-GCC 231 23.00 28.00 30.00 19.00
-GCC 232 23.50 21.50 12.50 42.50
-GCC 233 21.00 27.00 25.00 27.00
-GCC 234 16.50 27.50 22.50 33.50
-GCC 235 20.00 15.00 28.00 37.00
-GCC 236 28.00 23.00 21.00 28.00
-GCC 237 20.50 19.50 22.50 37.50
-GCC 238 21.50 29.50 24.50 24.50
-GCC 239 20.00 8.00 17.00 55.00
-GCC 240 28.00 24.00 16.00 32.00
-GCC 241 22.50 22.50 16.50 38.50
-GCC 242 29.00 25.00 13.00 33.00
-GCC 243 22.50 15.50 23.50 38.50
-GCC 244 20.50 23.50 16.50 39.50
-GCC 245 28.00 23.00 19.00 30.00
-GCC 246 21.00 29.00 25.00 25.00
-GCC 247 32.00 14.00 13.00 41.00
-GCC 248 18.00 18.00 25.00 39.00
-GCC 249 25.00 23.00 21.00 31.00
-GCC 250 27.50 22.50 17.50 32.50
-GCC 251 13.50 20.50 36.50 29.50
+# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
+GCC 1 21.94 30.10 34.18 13.78 2.04 0.00
+GCC 2 30.00 16.00 11.00 43.00 0.00 0.00
+GCC 3 33.00 25.00 9.00 33.00 0.00 0.00
+GCC 4 17.00 29.00 13.00 41.00 0.00 0.00
+GCC 5 37.00 22.00 12.00 29.00 0.00 0.00
+GCC 6 36.00 26.00 17.00 21.00 0.00 0.00
+GCC 7 29.50 13.50 31.50 25.50 0.00 0.00
+GCC 8 50.50 14.50 19.50 15.50 0.00 0.00
+GCC 9 17.00 33.00 18.00 32.00 0.00 0.00
+GCC 10 37.00 14.00 21.00 28.00 0.00 0.00
+GCC 11 20.50 14.50 29.50 35.50 0.00 0.00
+GCC 12 30.00 24.00 22.00 24.00 0.00 0.00
+GCC 13 27.00 15.00 21.00 37.00 0.00 0.00
+GCC 14 24.24 22.22 26.26 27.27 1.01 0.00
+GCC 15 25.50 20.50 24.50 29.50 0.00 0.00
+GCC 16 31.00 15.00 20.00 34.00 0.00 0.00
+GCC 17 28.00 25.00 14.00 33.00 0.00 0.00
+GCC 18 30.50 28.50 19.50 21.50 0.00 0.00
+GCC 19 29.00 26.00 21.00 24.00 0.00 0.00
+GCC 20 22.50 23.50 17.50 36.50 0.00 0.00
+GCC 21 35.50 17.50 19.50 27.50 0.00 0.00
+GCC 22 37.50 28.50 15.50 18.50 0.00 0.00
+GCC 23 31.31 19.19 13.13 36.36 1.01 0.00
+GCC 24 37.00 12.00 22.00 29.00 0.00 0.00
+GCC 25 35.50 22.50 17.50 24.50 0.00 0.00
+GCC 26 33.50 18.50 15.50 32.50 0.00 0.00
+GCC 27 34.50 14.50 25.50 25.50 0.00 0.00
+GCC 28 31.00 14.00 24.00 31.00 0.00 0.00
+GCC 29 30.00 27.00 24.00 19.00 0.00 0.00
+GCC 30 31.00 20.00 14.00 35.00 0.00 0.00
+GCC 31 33.50 29.50 13.50 23.50 0.00 0.00
+GCC 32 42.50 20.50 19.50 17.50 0.00 0.00
+GCC 33 25.50 23.50 14.50 36.50 0.00 0.00
+GCC 34 39.50 16.50 20.50 23.50 0.00 0.00
+GCC 35 32.50 23.50 21.50 22.50 0.00 0.00
+GCC 36 42.00 25.00 16.00 17.00 0.00 0.00
+GCC 37 38.00 17.00 19.00 26.00 0.00 0.00
+GCC 38 24.00 26.00 25.00 25.00 0.00 0.00
+GCC 39 22.50 41.50 18.50 17.50 0.00 0.00
+GCC 40 32.00 16.00 21.00 31.00 0.00 0.00
+GCC 41 33.00 28.00 19.00 20.00 0.00 0.00
+GCC 42 30.50 25.50 19.50 24.50 0.00 0.00
+GCC 43 35.00 29.00 15.00 21.00 0.00 0.00
+GCC 44 20.00 27.00 22.00 31.00 0.00 0.00
+GCC 45 40.50 21.50 21.50 16.50 0.00 0.00
+GCC 46 26.50 20.50 22.50 30.50 0.00 0.00
+GCC 47 38.50 29.50 16.50 15.50 0.00 0.00
+GCC 48 27.50 24.50 17.50 30.50 0.00 0.00
+GCC 49 28.50 32.50 10.50 28.50 0.00 0.00
+GCC 50 46.50 20.50 9.50 23.50 0.00 0.00
+GCC 51 34.50 28.50 13.50 23.50 0.00 0.00
+GCC 52 41.50 23.50 20.50 14.50 0.00 0.00
+GCC 53 20.00 28.00 26.00 26.00 0.00 0.00
+GCC 54 31.50 18.50 24.50 25.50 0.00 0.00
+GCC 55 30.50 22.50 16.50 30.50 0.00 0.00
+GCC 56 33.50 22.50 13.50 30.50 0.00 0.00
+GCC 57 23.00 24.00 23.00 30.00 0.00 0.00
+GCC 58 25.00 37.00 19.00 19.00 0.00 0.00
+GCC 59 34.00 23.00 24.00 19.00 0.00 0.00
+GCC 60 29.00 28.00 17.00 26.00 0.00 0.00
+GCC 61 25.50 23.50 24.50 26.50 0.00 0.00
+GCC 62 31.50 22.50 16.50 29.50 0.00 0.00
+GCC 63 27.50 28.50 25.50 18.50 0.00 0.00
+GCC 64 33.50 21.50 25.50 19.50 0.00 0.00
+GCC 65 35.50 19.50 18.50 26.50 0.00 0.00
+GCC 66 34.00 25.00 15.00 26.00 0.00 0.00
+GCC 67 37.00 23.00 19.00 21.00 0.00 0.00
+GCC 68 36.50 29.50 13.50 20.50 0.00 0.00
+GCC 69 38.50 19.50 20.50 21.50 0.00 0.00
+GCC 70 38.50 16.50 18.50 26.50 0.00 0.00
+GCC 71 25.50 38.50 21.50 14.50 0.00 0.00
+GCC 72 29.00 29.00 25.00 17.00 0.00 0.00
+GCC 73 32.50 20.50 21.50 25.50 0.00 0.00
+GCC 74 28.50 32.50 12.50 26.50 0.00 0.00
+GCC 75 41.50 12.50 18.50 27.50 0.00 0.00
+GCC 76 24.50 29.50 23.50 22.50 0.00 0.00
+GCC 77 36.00 21.00 18.00 25.00 0.00 0.00
+GCC 78 27.00 34.00 22.00 17.00 0.00 0.00
+GCC 79 21.50 26.50 25.50 26.50 0.00 0.00
+GCC 80 34.00 19.00 28.00 19.00 0.00 0.00
+GCC 81 17.00 26.00 26.00 31.00 0.00 0.00
+GCC 82 31.00 30.00 23.00 16.00 0.00 0.00
+GCC 83 31.50 26.50 12.50 29.50 0.00 0.00
+GCC 84 19.00 41.00 21.00 19.00 0.00 0.00
+GCC 85 37.50 24.50 16.50 21.50 0.00 0.00
+GCC 86 15.00 48.00 15.00 22.00 0.00 0.00
+GCC 87 41.00 16.00 18.00 25.00 0.00 0.00
+GCC 88 23.50 27.50 27.50 21.50 0.00 0.00
+GCC 89 26.50 27.50 26.50 19.50 0.00 0.00
+GCC 90 18.50 23.50 24.50 33.50 0.00 0.00
+GCC 91 27.00 32.00 22.00 19.00 0.00 0.00
+GCC 92 23.50 17.50 27.50 31.50 0.00 0.00
+GCC 93 25.50 37.50 15.50 21.50 0.00 0.00
+GCC 94 27.00 17.00 24.00 32.00 0.00 0.00
+GCC 95 26.77 37.88 14.65 20.71 1.01 0.00
+GCC 96 29.50 25.50 16.50 28.50 0.00 0.00
+GCC 97 29.00 31.00 21.00 19.00 0.00 0.00
+GCC 98 18.18 33.33 22.22 26.26 1.01 0.00
+GCC 99 24.50 33.50 24.50 17.50 0.00 0.00
+GCC 100 24.50 16.50 24.50 34.50 0.00 0.00
+GCC 101 25.00 40.00 19.00 16.00 0.00 0.00
+GCC 102 17.50 17.50 32.50 32.50 0.00 0.00
+GCC 103 31.00 26.00 16.00 27.00 0.00 0.00
+GCC 104 26.50 29.50 20.50 23.50 0.00 0.00
+GCC 105 34.00 33.00 21.00 12.00 0.00 0.00
+GCC 106 23.00 31.00 26.00 20.00 0.00 0.00
+GCC 107 17.68 35.86 23.74 22.73 1.01 0.00
+GCC 108 24.75 30.81 23.74 20.71 1.01 0.00
+GCC 109 17.00 31.00 22.00 30.00 0.00 0.00
+GCC 110 16.16 35.35 24.24 24.24 1.01 0.00
+GCC 111 24.24 32.32 23.23 20.20 1.01 0.00
+GCC 112 37.37 28.28 16.16 18.18 1.01 0.00
+GCC 113 19.70 22.73 32.83 24.75 1.01 0.00
+GCC 114 17.00 31.00 35.00 17.00 0.00 0.00
+GCC 115 29.50 24.50 23.50 22.50 0.00 0.00
+GCC 116 22.00 30.00 34.00 14.00 0.00 0.00
+GCC 117 27.00 23.00 19.00 31.00 0.00 0.00
+GCC 118 25.50 14.50 34.50 25.50 0.00 0.00
+GCC 119 22.50 34.50 20.50 22.50 0.00 0.00
+GCC 120 17.50 24.50 26.50 31.50 0.00 0.00
+GCC 121 27.78 33.84 22.73 15.66 1.01 0.00
+GCC 122 17.00 23.00 25.00 35.00 0.00 0.00
+GCC 123 23.50 46.50 11.50 18.50 0.00 0.00
+GCC 124 9.00 32.00 34.00 25.00 0.00 0.00
+GCC 125 24.00 27.00 19.00 30.00 0.00 0.00
+GCC 126 26.00 17.00 28.00 29.00 0.00 0.00
+GCC 127 26.50 16.50 21.50 35.50 0.00 0.00
+GCC 128 18.00 34.00 31.00 17.00 0.00 0.00
+GCC 129 25.50 25.50 27.50 21.50 0.00 0.00
+GCC 130 25.00 20.00 22.00 33.00 0.00 0.00
+GCC 131 17.50 39.50 24.50 18.50 0.00 0.00
+GCC 132 21.00 28.00 23.00 28.00 0.00 0.00
+GCC 133 13.50 31.50 35.50 19.50 0.00 0.00
+GCC 134 24.50 19.50 30.50 25.50 0.00 0.00
+GCC 135 16.50 23.50 30.50 29.50 0.00 0.00
+GCC 136 28.00 32.00 15.00 25.00 0.00 0.00
+GCC 137 22.50 21.50 30.50 25.50 0.00 0.00
+GCC 138 14.50 34.50 24.50 26.50 0.00 0.00
+GCC 139 20.50 29.50 24.50 25.50 0.00 0.00
+GCC 140 17.00 23.00 30.00 30.00 0.00 0.00
+GCC 141 20.50 23.50 25.50 30.50 0.00 0.00
+GCC 142 18.00 29.00 38.00 15.00 0.00 0.00
+GCC 143 22.00 24.00 27.00 27.00 0.00 0.00
+GCC 144 21.50 30.50 26.50 21.50 0.00 0.00
+GCC 145 22.00 21.00 29.00 28.00 0.00 0.00
+GCC 146 25.00 16.00 39.00 20.00 0.00 0.00
+GCC 147 26.50 22.50 30.50 20.50 0.00 0.00
+GCC 148 12.50 28.50 36.50 22.50 0.00 0.00
+GCC 149 26.50 23.50 23.50 26.50 0.00 0.00
+GCC 150 14.00 29.00 24.00 33.00 0.00 0.00
+GCC 151 19.50 30.50 32.50 17.50 0.00 0.00
+GCC 152 18.50 17.50 29.50 34.50 0.00 0.00
+GCC 153 22.50 22.50 31.50 23.50 0.00 0.00
+GCC 154 22.00 21.00 29.00 28.00 0.00 0.00
+GCC 155 21.00 26.00 19.00 34.00 0.00 0.00
+GCC 156 14.50 23.50 35.50 26.50 0.00 0.00
+GCC 157 22.00 31.00 23.00 24.00 0.00 0.00
+GCC 158 22.50 29.50 24.50 23.50 0.00 0.00
+GCC 159 17.50 12.50 46.50 23.50 0.00 0.00
+GCC 160 24.50 26.50 26.50 22.50 0.00 0.00
+GCC 161 13.00 23.00 45.00 19.00 0.00 0.00
+GCC 162 31.50 16.50 22.50 29.50 0.00 0.00
+GCC 163 19.50 21.50 35.50 23.50 0.00 0.00
+GCC 164 29.00 18.00 21.00 32.00 0.00 0.00
+GCC 165 14.50 17.50 35.50 32.50 0.00 0.00
+GCC 166 17.50 37.50 28.50 16.50 0.00 0.00
+GCC 167 16.50 21.50 31.50 30.50 0.00 0.00
+GCC 168 14.00 25.00 30.00 31.00 0.00 0.00
+GCC 169 18.50 20.50 23.50 37.50 0.00 0.00
+GCC 170 19.00 23.00 28.00 30.00 0.00 0.00
+GCC 171 20.00 28.00 33.00 19.00 0.00 0.00
+GCC 172 19.00 20.00 32.00 29.00 0.00 0.00
+GCC 173 24.50 16.50 33.50 25.50 0.00 0.00
+GCC 174 17.50 23.50 33.50 25.50 0.00 0.00
+GCC 175 33.50 17.50 35.50 13.50 0.00 0.00
+GCC 176 16.50 32.50 28.50 22.50 0.00 0.00
+GCC 177 19.00 22.00 27.00 32.00 0.00 0.00
+GCC 178 16.00 26.00 30.00 28.00 0.00 0.00
+GCC 179 18.00 18.00 22.00 42.00 0.00 0.00
+GCC 180 21.00 22.00 34.00 23.00 0.00 0.00
+GCC 181 20.50 19.50 35.50 24.50 0.00 0.00
+GCC 182 32.50 18.50 22.50 26.50 0.00 0.00
+GCC 183 24.50 13.50 28.50 33.50 0.00 0.00
+GCC 184 15.00 29.00 30.00 26.00 0.00 0.00
+GCC 185 15.00 32.00 33.00 20.00 0.00 0.00
+GCC 186 22.50 23.50 34.50 19.50 0.00 0.00
+GCC 187 19.00 14.00 40.00 27.00 0.00 0.00
+GCC 188 27.50 21.50 27.50 23.50 0.00 0.00
+GCC 189 17.00 22.00 34.00 27.00 0.00 0.00
+GCC 190 23.00 30.00 23.00 24.00 0.00 0.00
+GCC 191 25.00 22.00 28.00 25.00 0.00 0.00
+GCC 192 34.50 24.50 13.50 27.50 0.00 0.00
+GCC 193 18.50 25.50 25.50 30.50 0.00 0.00
+GCC 194 18.50 33.50 24.50 23.50 0.00 0.00
+GCC 195 16.00 26.00 23.00 35.00 0.00 0.00
+GCC 196 21.50 25.50 24.50 28.50 0.00 0.00
+GCC 197 20.00 21.00 23.00 36.00 0.00 0.00
+GCC 198 17.00 21.00 37.00 25.00 0.00 0.00
+GCC 199 20.50 18.50 25.50 35.50 0.00 0.00
+GCC 200 21.00 29.00 21.00 29.00 0.00 0.00
+GCC 201 27.00 21.00 23.00 29.00 0.00 0.00
+GCC 202 21.50 24.50 19.50 34.50 0.00 0.00
+GCC 203 21.50 24.50 26.50 27.50 0.00 0.00
+GCC 204 27.00 29.00 24.00 20.00 0.00 0.00
+GCC 205 19.50 21.50 22.50 36.50 0.00 0.00
+GCC 206 26.50 24.50 21.50 27.50 0.00 0.00
+GCC 207 22.50 21.50 19.50 36.50 0.00 0.00
+GCC 208 14.00 35.00 29.00 22.00 0.00 0.00
+GCC 209 16.00 23.00 12.00 49.00 0.00 0.00
+GCC 210 18.50 19.50 40.50 21.50 0.00 0.00
+GCC 211 26.00 20.00 22.00 32.00 0.00 0.00
+GCC 212 21.00 31.00 18.00 30.00 0.00 0.00
+GCC 213 24.00 15.00 31.00 30.00 0.00 0.00
+GCC 214 17.50 24.50 25.50 32.50 0.00 0.00
+GCC 215 26.00 24.00 23.00 27.00 0.00 0.00
+GCC 216 21.50 17.50 25.50 35.50 0.00 0.00
+GCC 217 26.00 29.00 17.00 28.00 0.00 0.00
+GCC 218 20.00 27.00 21.00 32.00 0.00 0.00
+GCC 219 17.00 21.00 21.00 41.00 0.00 0.00
+GCC 220 25.50 23.50 23.50 27.50 0.00 0.00
+GCC 221 21.50 23.50 20.50 34.50 0.00 0.00
+GCC 222 21.50 21.50 18.50 38.50 0.00 0.00
+GCC 223 20.00 27.00 28.00 25.00 0.00 0.00
+GCC 224 22.50 22.50 24.50 30.50 0.00 0.00
+GCC 225 14.50 35.50 30.50 19.50 0.00 0.00
+GCC 226 20.00 23.00 26.00 31.00 0.00 0.00
+GCC 227 20.50 24.50 23.50 31.50 0.00 0.00
+GCC 228 33.00 19.00 26.00 22.00 0.00 0.00
+GCC 229 22.50 24.50 18.50 34.50 0.00 0.00
+GCC 230 21.00 32.00 16.00 31.00 0.00 0.00
+GCC 231 23.00 28.00 30.00 19.00 0.00 0.00
+GCC 232 23.50 21.50 12.50 42.50 0.00 0.00
+GCC 233 21.00 27.00 25.00 27.00 0.00 0.00
+GCC 234 16.50 27.50 22.50 33.50 0.00 0.00
+GCC 235 20.00 15.00 28.00 37.00 0.00 0.00
+GCC 236 28.00 23.00 21.00 28.00 0.00 0.00
+GCC 237 20.50 19.50 22.50 37.50 0.00 0.00
+GCC 238 21.50 29.50 24.50 24.50 0.00 0.00
+GCC 239 20.00 8.00 17.00 55.00 0.00 0.00
+GCC 240 28.00 24.00 16.00 32.00 0.00 0.00
+GCC 241 22.50 22.50 16.50 38.50 0.00 0.00
+GCC 242 29.00 25.00 13.00 33.00 0.00 0.00
+GCC 243 22.50 15.50 23.50 38.50 0.00 0.00
+GCC 244 20.50 23.50 16.50 39.50 0.00 0.00
+GCC 245 28.00 23.00 19.00 30.00 0.00 0.00
+GCC 246 21.00 29.00 25.00 25.00 0.00 0.00
+GCC 247 32.00 14.00 13.00 41.00 0.00 0.00
+GCC 248 18.00 18.00 25.00 39.00 0.00 0.00
+GCC 249 25.00 23.00 21.00 31.00 0.00 0.00
+GCC 250 27.50 22.50 17.50 32.50 0.00 0.00
+GCC 251 13.50 20.50 36.50 29.50 0.00 0.00
# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
RL 251 200
diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out2/gcc.tab
--- a/test-data/samtools_stats_out2/gcc.tab Fri Dec 18 19:47:08 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,252 +0,0 @@
-# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)
-1 21.50 29.50 33.50 15.50
-2 30.00 16.00 11.00 43.00
-3 33.00 25.00 9.00 33.00
-4 17.00 29.00 13.00 41.00
-5 37.00 22.00 12.00 29.00
-6 36.00 26.00 17.00 21.00
-7 29.50 13.50 31.50 25.50
-8 50.50 14.50 19.50 15.50
-9 17.00 33.00 18.00 32.00
-10 37.00 14.00 21.00 28.00
-11 20.50 14.50 29.50 35.50
-12 30.00 24.00 22.00 24.00
-13 27.00 15.00 21.00 37.00
-14 24.00 22.00 26.00 28.00
-15 25.50 20.50 24.50 29.50
-16 31.00 15.00 20.00 34.00
-17 28.00 25.00 14.00 33.00
-18 30.50 28.50 19.50 21.50
-19 29.00 26.00 21.00 24.00
-20 22.50 23.50 17.50 36.50
-21 35.50 17.50 19.50 27.50
-22 37.50 28.50 15.50 18.50
-23 31.00 19.00 13.00 37.00
-24 37.00 12.00 22.00 29.00
-25 35.50 22.50 17.50 24.50
-26 33.50 18.50 15.50 32.50
-27 34.50 14.50 25.50 25.50
-28 31.00 14.00 24.00 31.00
-29 30.00 27.00 24.00 19.00
-30 31.00 20.00 14.00 35.00
-31 33.50 29.50 13.50 23.50
-32 42.50 20.50 19.50 17.50
-33 25.50 23.50 14.50 36.50
-34 39.50 16.50 20.50 23.50
-35 32.50 23.50 21.50 22.50
-36 42.00 25.00 16.00 17.00
-37 38.00 17.00 19.00 26.00
-38 24.00 26.00 25.00 25.00
-39 22.50 41.50 18.50 17.50
-40 32.00 16.00 21.00 31.00
-41 33.00 28.00 19.00 20.00
-42 30.50 25.50 19.50 24.50
-43 35.00 29.00 15.00 21.00
-44 20.00 27.00 22.00 31.00
-45 40.50 21.50 21.50 16.50
-46 26.50 20.50 22.50 30.50
-47 38.50 29.50 16.50 15.50
-48 27.50 24.50 17.50 30.50
-49 28.50 32.50 10.50 28.50
-50 46.50 20.50 9.50 23.50
-51 34.50 28.50 13.50 23.50
-52 41.50 23.50 20.50 14.50
-53 20.00 28.00 26.00 26.00
-54 31.50 18.50 24.50 25.50
-55 30.50 22.50 16.50 30.50
-56 33.50 22.50 13.50 30.50
-57 23.00 24.00 23.00 30.00
-58 25.00 37.00 19.00 19.00
-59 34.00 23.00 24.00 19.00
-60 29.00 28.00 17.00 26.00
-61 25.50 23.50 24.50 26.50
-62 31.50 22.50 16.50 29.50
-63 27.50 28.50 25.50 18.50
-64 33.50 21.50 25.50 19.50
-65 35.50 19.50 18.50 26.50
-66 34.00 25.00 15.00 26.00
-67 37.00 23.00 19.00 21.00
-68 36.50 29.50 13.50 20.50
-69 38.50 19.50 20.50 21.50
-70 38.50 16.50 18.50 26.50
-71 25.50 38.50 21.50 14.50
-72 29.00 29.00 25.00 17.00
-73 32.50 20.50 21.50 25.50
-74 28.50 32.50 12.50 26.50
-75 41.50 12.50 18.50 27.50
-76 24.50 29.50 23.50 22.50
-77 36.00 21.00 18.00 25.00
-78 27.00 34.00 22.00 17.00
-79 21.50 26.50 25.50 26.50
-80 34.00 19.00 28.00 19.00
-81 17.00 26.00 26.00 31.00
-82 31.00 30.00 23.00 16.00
-83 31.50 26.50 12.50 29.50
-84 19.00 41.00 21.00 19.00
-85 37.50 24.50 16.50 21.50
-86 15.00 48.00 15.00 22.00
-87 41.00 16.00 18.00 25.00
-88 23.50 27.50 27.50 21.50
-89 26.50 27.50 26.50 19.50
-90 18.50 23.50 24.50 33.50
-91 27.00 32.00 22.00 19.00
-92 23.50 17.50 27.50 31.50
-93 25.50 37.50 15.50 21.50
-94 27.00 17.00 24.00 32.00
-95 26.50 37.50 14.50 21.50
-96 29.50 25.50 16.50 28.50
-97 29.00 31.00 21.00 19.00
-98 18.00 33.00 22.00 27.00
-99 24.50 33.50 24.50 17.50
-100 24.50 16.50 24.50 34.50
-101 25.00 40.00 19.00 16.00
-102 17.50 17.50 32.50 32.50
-103 31.00 26.00 16.00 27.00
-104 26.50 29.50 20.50 23.50
-105 34.00 33.00 21.00 12.00
-106 23.00 31.00 26.00 20.00
-107 17.50 35.50 23.50 23.50
-108 24.50 30.50 23.50 21.50
-109 17.00 31.00 22.00 30.00
-110 16.00 35.00 24.00 25.00
-111 24.00 32.00 23.00 21.00
-112 37.00 28.00 16.00 19.00
-113 19.50 22.50 32.50 25.50
-114 17.00 31.00 35.00 17.00
-115 29.50 24.50 23.50 22.50
-116 22.00 30.00 34.00 14.00
-117 27.00 23.00 19.00 31.00
-118 25.50 14.50 34.50 25.50
-119 22.50 34.50 20.50 22.50
-120 17.50 24.50 26.50 31.50
-121 27.50 33.50 22.50 16.50
-122 17.00 23.00 25.00 35.00
-123 23.50 46.50 11.50 18.50
-124 9.00 32.00 34.00 25.00
-125 24.00 27.00 19.00 30.00
-126 26.00 17.00 28.00 29.00
-127 26.50 16.50 21.50 35.50
-128 18.00 34.00 31.00 17.00
-129 25.50 25.50 27.50 21.50
-130 25.00 20.00 22.00 33.00
-131 17.50 39.50 24.50 18.50
-132 21.00 28.00 23.00 28.00
-133 13.50 31.50 35.50 19.50
-134 24.50 19.50 30.50 25.50
-135 16.50 23.50 30.50 29.50
-136 28.00 32.00 15.00 25.00
-137 22.50 21.50 30.50 25.50
-138 14.50 34.50 24.50 26.50
-139 20.50 29.50 24.50 25.50
-140 17.00 23.00 30.00 30.00
-141 20.50 23.50 25.50 30.50
-142 18.00 29.00 38.00 15.00
-143 22.00 24.00 27.00 27.00
-144 21.50 30.50 26.50 21.50
-145 22.00 21.00 29.00 28.00
-146 25.00 16.00 39.00 20.00
-147 26.50 22.50 30.50 20.50
-148 12.50 28.50 36.50 22.50
-149 26.50 23.50 23.50 26.50
-150 14.00 29.00 24.00 33.00
-151 19.50 30.50 32.50 17.50
-152 18.50 17.50 29.50 34.50
-153 22.50 22.50 31.50 23.50
-154 22.00 21.00 29.00 28.00
-155 21.00 26.00 19.00 34.00
-156 14.50 23.50 35.50 26.50
-157 22.00 31.00 23.00 24.00
-158 22.50 29.50 24.50 23.50
-159 17.50 12.50 46.50 23.50
-160 24.50 26.50 26.50 22.50
-161 13.00 23.00 45.00 19.00
-162 31.50 16.50 22.50 29.50
-163 19.50 21.50 35.50 23.50
-164 29.00 18.00 21.00 32.00
-165 14.50 17.50 35.50 32.50
-166 17.50 37.50 28.50 16.50
-167 16.50 21.50 31.50 30.50
-168 14.00 25.00 30.00 31.00
-169 18.50 20.50 23.50 37.50
-170 19.00 23.00 28.00 30.00
-171 20.00 28.00 33.00 19.00
-172 19.00 20.00 32.00 29.00
-173 24.50 16.50 33.50 25.50
-174 17.50 23.50 33.50 25.50
-175 33.50 17.50 35.50 13.50
-176 16.50 32.50 28.50 22.50
-177 19.00 22.00 27.00 32.00
-178 16.00 26.00 30.00 28.00
-179 18.00 18.00 22.00 42.00
-180 21.00 22.00 34.00 23.00
-181 20.50 19.50 35.50 24.50
-182 32.50 18.50 22.50 26.50
-183 24.50 13.50 28.50 33.50
-184 15.00 29.00 30.00 26.00
-185 15.00 32.00 33.00 20.00
-186 22.50 23.50 34.50 19.50
-187 19.00 14.00 40.00 27.00
-188 27.50 21.50 27.50 23.50
-189 17.00 22.00 34.00 27.00
-190 23.00 30.00 23.00 24.00
-191 25.00 22.00 28.00 25.00
-192 34.50 24.50 13.50 27.50
-193 18.50 25.50 25.50 30.50
-194 18.50 33.50 24.50 23.50
-195 16.00 26.00 23.00 35.00
-196 21.50 25.50 24.50 28.50
-197 20.00 21.00 23.00 36.00
-198 17.00 21.00 37.00 25.00
-199 20.50 18.50 25.50 35.50
-200 21.00 29.00 21.00 29.00
-201 27.00 21.00 23.00 29.00
-202 21.50 24.50 19.50 34.50
-203 21.50 24.50 26.50 27.50
-204 27.00 29.00 24.00 20.00
-205 19.50 21.50 22.50 36.50
-206 26.50 24.50 21.50 27.50
-207 22.50 21.50 19.50 36.50
-208 14.00 35.00 29.00 22.00
-209 16.00 23.00 12.00 49.00
-210 18.50 19.50 40.50 21.50
-211 26.00 20.00 22.00 32.00
-212 21.00 31.00 18.00 30.00
-213 24.00 15.00 31.00 30.00
-214 17.50 24.50 25.50 32.50
-215 26.00 24.00 23.00 27.00
-216 21.50 17.50 25.50 35.50
-217 26.00 29.00 17.00 28.00
-218 20.00 27.00 21.00 32.00
-219 17.00 21.00 21.00 41.00
-220 25.50 23.50 23.50 27.50
-221 21.50 23.50 20.50 34.50
-222 21.50 21.50 18.50 38.50
-223 20.00 27.00 28.00 25.00
-224 22.50 22.50 24.50 30.50
-225 14.50 35.50 30.50 19.50
-226 20.00 23.00 26.00 31.00
-227 20.50 24.50 23.50 31.50
-228 33.00 19.00 26.00 22.00
-229 22.50 24.50 18.50 34.50
-230 21.00 32.00 16.00 31.00
-231 23.00 28.00 30.00 19.00
-232 23.50 21.50 12.50 42.50
-233 21.00 27.00 25.00 27.00
-234 16.50 27.50 22.50 33.50
-235 20.00 15.00 28.00 37.00
-236 28.00 23.00 21.00 28.00
-237 20.50 19.50 22.50 37.50
-238 21.50 29.50 24.50 24.50
-239 20.00 8.00 17.00 55.00
-240 28.00 24.00 16.00 32.00
-241 22.50 22.50 16.50 38.50
-242 29.00 25.00 13.00 33.00
-243 22.50 15.50 23.50 38.50
-244 20.50 23.50 16.50 39.50
-245 28.00 23.00 19.00 30.00
-246 21.00 29.00 25.00 25.00
-247 32.00 14.00 13.00 41.00
-248 18.00 18.00 25.00 39.00
-249 25.00 23.00 21.00 31.00
-250 27.50 22.50 17.50 32.50
-251 13.50 20.50 36.50 29.50
diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out2/mpc.tab
--- a/test-data/samtools_stats_out2/mpc.tab Fri Dec 18 19:47:08 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,253 +0,0 @@
-# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0
-2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0
-3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0
-4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0
-5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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-244 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-245 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-246 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-247 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0
-248 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 2 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0
-249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0
-250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0
-251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0
-252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out2/sn.tab
--- a/test-data/samtools_stats_out2/sn.tab Fri Dec 18 19:47:08 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-# Summary Numbers
-
-raw total sequences: 200
-filtered sequences: 0
-sequences: 200
-is sorted: 1
-1st fragments: 100
-last fragments: 100
-reads mapped: 25
-reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
-reads unmapped: 175
-reads properly paired: 0 # proper-pair bit set
-reads paired: 200 # paired-end technology bit set
-reads duplicated: 0 # PCR or optical duplicate bit set
-reads MQ0: 6 # mapped and MQ=0
-reads QC failed: 0
-non-primary alignments: 0
-total length: 50200 # ignores clipping
-bases mapped: 6275 # ignores clipping
-bases mapped (cigar): 6275 # more accurate
-bases trimmed: 0
-bases duplicated: 0
-mismatches: 591 # from NM fields
-error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
-average length: 251
-maximum length: 251
-average quality: 34.7
-insert size average: 0.0
-insert size standard deviation: 0.0
-inward oriented pairs: 0
-outward oriented pairs: 0
-pairs with other orientation: 0
-pairs on different chromosomes: 0
diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out2__gcc.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2__gcc.tab Tue May 09 11:17:02 2017 -0400
@@ -0,0 +1,252 @@
+# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)
+1 21.94 30.10 34.18 13.78 2.04 0.00
+2 30.00 16.00 11.00 43.00 0.00 0.00
+3 33.00 25.00 9.00 33.00 0.00 0.00
+4 17.00 29.00 13.00 41.00 0.00 0.00
+5 37.00 22.00 12.00 29.00 0.00 0.00
+6 36.00 26.00 17.00 21.00 0.00 0.00
+7 29.50 13.50 31.50 25.50 0.00 0.00
+8 50.50 14.50 19.50 15.50 0.00 0.00
+9 17.00 33.00 18.00 32.00 0.00 0.00
+10 37.00 14.00 21.00 28.00 0.00 0.00
+11 20.50 14.50 29.50 35.50 0.00 0.00
+12 30.00 24.00 22.00 24.00 0.00 0.00
+13 27.00 15.00 21.00 37.00 0.00 0.00
+14 24.24 22.22 26.26 27.27 1.01 0.00
+15 25.50 20.50 24.50 29.50 0.00 0.00
+16 31.00 15.00 20.00 34.00 0.00 0.00
+17 28.00 25.00 14.00 33.00 0.00 0.00
+18 30.50 28.50 19.50 21.50 0.00 0.00
+19 29.00 26.00 21.00 24.00 0.00 0.00
+20 22.50 23.50 17.50 36.50 0.00 0.00
+21 35.50 17.50 19.50 27.50 0.00 0.00
+22 37.50 28.50 15.50 18.50 0.00 0.00
+23 31.31 19.19 13.13 36.36 1.01 0.00
+24 37.00 12.00 22.00 29.00 0.00 0.00
+25 35.50 22.50 17.50 24.50 0.00 0.00
+26 33.50 18.50 15.50 32.50 0.00 0.00
+27 34.50 14.50 25.50 25.50 0.00 0.00
+28 31.00 14.00 24.00 31.00 0.00 0.00
+29 30.00 27.00 24.00 19.00 0.00 0.00
+30 31.00 20.00 14.00 35.00 0.00 0.00
+31 33.50 29.50 13.50 23.50 0.00 0.00
+32 42.50 20.50 19.50 17.50 0.00 0.00
+33 25.50 23.50 14.50 36.50 0.00 0.00
+34 39.50 16.50 20.50 23.50 0.00 0.00
+35 32.50 23.50 21.50 22.50 0.00 0.00
+36 42.00 25.00 16.00 17.00 0.00 0.00
+37 38.00 17.00 19.00 26.00 0.00 0.00
+38 24.00 26.00 25.00 25.00 0.00 0.00
+39 22.50 41.50 18.50 17.50 0.00 0.00
+40 32.00 16.00 21.00 31.00 0.00 0.00
+41 33.00 28.00 19.00 20.00 0.00 0.00
+42 30.50 25.50 19.50 24.50 0.00 0.00
+43 35.00 29.00 15.00 21.00 0.00 0.00
+44 20.00 27.00 22.00 31.00 0.00 0.00
+45 40.50 21.50 21.50 16.50 0.00 0.00
+46 26.50 20.50 22.50 30.50 0.00 0.00
+47 38.50 29.50 16.50 15.50 0.00 0.00
+48 27.50 24.50 17.50 30.50 0.00 0.00
+49 28.50 32.50 10.50 28.50 0.00 0.00
+50 46.50 20.50 9.50 23.50 0.00 0.00
+51 34.50 28.50 13.50 23.50 0.00 0.00
+52 41.50 23.50 20.50 14.50 0.00 0.00
+53 20.00 28.00 26.00 26.00 0.00 0.00
+54 31.50 18.50 24.50 25.50 0.00 0.00
+55 30.50 22.50 16.50 30.50 0.00 0.00
+56 33.50 22.50 13.50 30.50 0.00 0.00
+57 23.00 24.00 23.00 30.00 0.00 0.00
+58 25.00 37.00 19.00 19.00 0.00 0.00
+59 34.00 23.00 24.00 19.00 0.00 0.00
+60 29.00 28.00 17.00 26.00 0.00 0.00
+61 25.50 23.50 24.50 26.50 0.00 0.00
+62 31.50 22.50 16.50 29.50 0.00 0.00
+63 27.50 28.50 25.50 18.50 0.00 0.00
+64 33.50 21.50 25.50 19.50 0.00 0.00
+65 35.50 19.50 18.50 26.50 0.00 0.00
+66 34.00 25.00 15.00 26.00 0.00 0.00
+67 37.00 23.00 19.00 21.00 0.00 0.00
+68 36.50 29.50 13.50 20.50 0.00 0.00
+69 38.50 19.50 20.50 21.50 0.00 0.00
+70 38.50 16.50 18.50 26.50 0.00 0.00
+71 25.50 38.50 21.50 14.50 0.00 0.00
+72 29.00 29.00 25.00 17.00 0.00 0.00
+73 32.50 20.50 21.50 25.50 0.00 0.00
+74 28.50 32.50 12.50 26.50 0.00 0.00
+75 41.50 12.50 18.50 27.50 0.00 0.00
+76 24.50 29.50 23.50 22.50 0.00 0.00
+77 36.00 21.00 18.00 25.00 0.00 0.00
+78 27.00 34.00 22.00 17.00 0.00 0.00
+79 21.50 26.50 25.50 26.50 0.00 0.00
+80 34.00 19.00 28.00 19.00 0.00 0.00
+81 17.00 26.00 26.00 31.00 0.00 0.00
+82 31.00 30.00 23.00 16.00 0.00 0.00
+83 31.50 26.50 12.50 29.50 0.00 0.00
+84 19.00 41.00 21.00 19.00 0.00 0.00
+85 37.50 24.50 16.50 21.50 0.00 0.00
+86 15.00 48.00 15.00 22.00 0.00 0.00
+87 41.00 16.00 18.00 25.00 0.00 0.00
+88 23.50 27.50 27.50 21.50 0.00 0.00
+89 26.50 27.50 26.50 19.50 0.00 0.00
+90 18.50 23.50 24.50 33.50 0.00 0.00
+91 27.00 32.00 22.00 19.00 0.00 0.00
+92 23.50 17.50 27.50 31.50 0.00 0.00
+93 25.50 37.50 15.50 21.50 0.00 0.00
+94 27.00 17.00 24.00 32.00 0.00 0.00
+95 26.77 37.88 14.65 20.71 1.01 0.00
+96 29.50 25.50 16.50 28.50 0.00 0.00
+97 29.00 31.00 21.00 19.00 0.00 0.00
+98 18.18 33.33 22.22 26.26 1.01 0.00
+99 24.50 33.50 24.50 17.50 0.00 0.00
+100 24.50 16.50 24.50 34.50 0.00 0.00
+101 25.00 40.00 19.00 16.00 0.00 0.00
+102 17.50 17.50 32.50 32.50 0.00 0.00
+103 31.00 26.00 16.00 27.00 0.00 0.00
+104 26.50 29.50 20.50 23.50 0.00 0.00
+105 34.00 33.00 21.00 12.00 0.00 0.00
+106 23.00 31.00 26.00 20.00 0.00 0.00
+107 17.68 35.86 23.74 22.73 1.01 0.00
+108 24.75 30.81 23.74 20.71 1.01 0.00
+109 17.00 31.00 22.00 30.00 0.00 0.00
+110 16.16 35.35 24.24 24.24 1.01 0.00
+111 24.24 32.32 23.23 20.20 1.01 0.00
+112 37.37 28.28 16.16 18.18 1.01 0.00
+113 19.70 22.73 32.83 24.75 1.01 0.00
+114 17.00 31.00 35.00 17.00 0.00 0.00
+115 29.50 24.50 23.50 22.50 0.00 0.00
+116 22.00 30.00 34.00 14.00 0.00 0.00
+117 27.00 23.00 19.00 31.00 0.00 0.00
+118 25.50 14.50 34.50 25.50 0.00 0.00
+119 22.50 34.50 20.50 22.50 0.00 0.00
+120 17.50 24.50 26.50 31.50 0.00 0.00
+121 27.78 33.84 22.73 15.66 1.01 0.00
+122 17.00 23.00 25.00 35.00 0.00 0.00
+123 23.50 46.50 11.50 18.50 0.00 0.00
+124 9.00 32.00 34.00 25.00 0.00 0.00
+125 24.00 27.00 19.00 30.00 0.00 0.00
+126 26.00 17.00 28.00 29.00 0.00 0.00
+127 26.50 16.50 21.50 35.50 0.00 0.00
+128 18.00 34.00 31.00 17.00 0.00 0.00
+129 25.50 25.50 27.50 21.50 0.00 0.00
+130 25.00 20.00 22.00 33.00 0.00 0.00
+131 17.50 39.50 24.50 18.50 0.00 0.00
+132 21.00 28.00 23.00 28.00 0.00 0.00
+133 13.50 31.50 35.50 19.50 0.00 0.00
+134 24.50 19.50 30.50 25.50 0.00 0.00
+135 16.50 23.50 30.50 29.50 0.00 0.00
+136 28.00 32.00 15.00 25.00 0.00 0.00
+137 22.50 21.50 30.50 25.50 0.00 0.00
+138 14.50 34.50 24.50 26.50 0.00 0.00
+139 20.50 29.50 24.50 25.50 0.00 0.00
+140 17.00 23.00 30.00 30.00 0.00 0.00
+141 20.50 23.50 25.50 30.50 0.00 0.00
+142 18.00 29.00 38.00 15.00 0.00 0.00
+143 22.00 24.00 27.00 27.00 0.00 0.00
+144 21.50 30.50 26.50 21.50 0.00 0.00
+145 22.00 21.00 29.00 28.00 0.00 0.00
+146 25.00 16.00 39.00 20.00 0.00 0.00
+147 26.50 22.50 30.50 20.50 0.00 0.00
+148 12.50 28.50 36.50 22.50 0.00 0.00
+149 26.50 23.50 23.50 26.50 0.00 0.00
+150 14.00 29.00 24.00 33.00 0.00 0.00
+151 19.50 30.50 32.50 17.50 0.00 0.00
+152 18.50 17.50 29.50 34.50 0.00 0.00
+153 22.50 22.50 31.50 23.50 0.00 0.00
+154 22.00 21.00 29.00 28.00 0.00 0.00
+155 21.00 26.00 19.00 34.00 0.00 0.00
+156 14.50 23.50 35.50 26.50 0.00 0.00
+157 22.00 31.00 23.00 24.00 0.00 0.00
+158 22.50 29.50 24.50 23.50 0.00 0.00
+159 17.50 12.50 46.50 23.50 0.00 0.00
+160 24.50 26.50 26.50 22.50 0.00 0.00
+161 13.00 23.00 45.00 19.00 0.00 0.00
+162 31.50 16.50 22.50 29.50 0.00 0.00
+163 19.50 21.50 35.50 23.50 0.00 0.00
+164 29.00 18.00 21.00 32.00 0.00 0.00
+165 14.50 17.50 35.50 32.50 0.00 0.00
+166 17.50 37.50 28.50 16.50 0.00 0.00
+167 16.50 21.50 31.50 30.50 0.00 0.00
+168 14.00 25.00 30.00 31.00 0.00 0.00
+169 18.50 20.50 23.50 37.50 0.00 0.00
+170 19.00 23.00 28.00 30.00 0.00 0.00
+171 20.00 28.00 33.00 19.00 0.00 0.00
+172 19.00 20.00 32.00 29.00 0.00 0.00
+173 24.50 16.50 33.50 25.50 0.00 0.00
+174 17.50 23.50 33.50 25.50 0.00 0.00
+175 33.50 17.50 35.50 13.50 0.00 0.00
+176 16.50 32.50 28.50 22.50 0.00 0.00
+177 19.00 22.00 27.00 32.00 0.00 0.00
+178 16.00 26.00 30.00 28.00 0.00 0.00
+179 18.00 18.00 22.00 42.00 0.00 0.00
+180 21.00 22.00 34.00 23.00 0.00 0.00
+181 20.50 19.50 35.50 24.50 0.00 0.00
+182 32.50 18.50 22.50 26.50 0.00 0.00
+183 24.50 13.50 28.50 33.50 0.00 0.00
+184 15.00 29.00 30.00 26.00 0.00 0.00
+185 15.00 32.00 33.00 20.00 0.00 0.00
+186 22.50 23.50 34.50 19.50 0.00 0.00
+187 19.00 14.00 40.00 27.00 0.00 0.00
+188 27.50 21.50 27.50 23.50 0.00 0.00
+189 17.00 22.00 34.00 27.00 0.00 0.00
+190 23.00 30.00 23.00 24.00 0.00 0.00
+191 25.00 22.00 28.00 25.00 0.00 0.00
+192 34.50 24.50 13.50 27.50 0.00 0.00
+193 18.50 25.50 25.50 30.50 0.00 0.00
+194 18.50 33.50 24.50 23.50 0.00 0.00
+195 16.00 26.00 23.00 35.00 0.00 0.00
+196 21.50 25.50 24.50 28.50 0.00 0.00
+197 20.00 21.00 23.00 36.00 0.00 0.00
+198 17.00 21.00 37.00 25.00 0.00 0.00
+199 20.50 18.50 25.50 35.50 0.00 0.00
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+201 27.00 21.00 23.00 29.00 0.00 0.00
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+205 19.50 21.50 22.50 36.50 0.00 0.00
+206 26.50 24.50 21.50 27.50 0.00 0.00
+207 22.50 21.50 19.50 36.50 0.00 0.00
+208 14.00 35.00 29.00 22.00 0.00 0.00
+209 16.00 23.00 12.00 49.00 0.00 0.00
+210 18.50 19.50 40.50 21.50 0.00 0.00
+211 26.00 20.00 22.00 32.00 0.00 0.00
+212 21.00 31.00 18.00 30.00 0.00 0.00
+213 24.00 15.00 31.00 30.00 0.00 0.00
+214 17.50 24.50 25.50 32.50 0.00 0.00
+215 26.00 24.00 23.00 27.00 0.00 0.00
+216 21.50 17.50 25.50 35.50 0.00 0.00
+217 26.00 29.00 17.00 28.00 0.00 0.00
+218 20.00 27.00 21.00 32.00 0.00 0.00
+219 17.00 21.00 21.00 41.00 0.00 0.00
+220 25.50 23.50 23.50 27.50 0.00 0.00
+221 21.50 23.50 20.50 34.50 0.00 0.00
+222 21.50 21.50 18.50 38.50 0.00 0.00
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+228 33.00 19.00 26.00 22.00 0.00 0.00
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+230 21.00 32.00 16.00 31.00 0.00 0.00
+231 23.00 28.00 30.00 19.00 0.00 0.00
+232 23.50 21.50 12.50 42.50 0.00 0.00
+233 21.00 27.00 25.00 27.00 0.00 0.00
+234 16.50 27.50 22.50 33.50 0.00 0.00
+235 20.00 15.00 28.00 37.00 0.00 0.00
+236 28.00 23.00 21.00 28.00 0.00 0.00
+237 20.50 19.50 22.50 37.50 0.00 0.00
+238 21.50 29.50 24.50 24.50 0.00 0.00
+239 20.00 8.00 17.00 55.00 0.00 0.00
+240 28.00 24.00 16.00 32.00 0.00 0.00
+241 22.50 22.50 16.50 38.50 0.00 0.00
+242 29.00 25.00 13.00 33.00 0.00 0.00
+243 22.50 15.50 23.50 38.50 0.00 0.00
+244 20.50 23.50 16.50 39.50 0.00 0.00
+245 28.00 23.00 19.00 30.00 0.00 0.00
+246 21.00 29.00 25.00 25.00 0.00 0.00
+247 32.00 14.00 13.00 41.00 0.00 0.00
+248 18.00 18.00 25.00 39.00 0.00 0.00
+249 25.00 23.00 21.00 31.00 0.00 0.00
+250 27.50 22.50 17.50 32.50 0.00 0.00
+251 13.50 20.50 36.50 29.50 0.00 0.00
diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out2__mpc.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2__mpc.tab Tue May 09 11:17:02 2017 -0400
@@ -0,0 +1,253 @@
+# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches
+1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0
+2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0
+3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0
+4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0
+5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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+20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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+22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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+27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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diff -r b02596e3d7a3 -r 45c568e7f1f9 test-data/samtools_stats_out2__sn.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2__sn.tab Tue May 09 11:17:02 2017 -0400
@@ -0,0 +1,33 @@
+# Summary Numbers
+
+raw total sequences: 200
+filtered sequences: 0
+sequences: 200
+is sorted: 1
+1st fragments: 100
+last fragments: 100
+reads mapped: 25
+reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
+reads unmapped: 175
+reads properly paired: 0 # proper-pair bit set
+reads paired: 200 # paired-end technology bit set
+reads duplicated: 0 # PCR or optical duplicate bit set
+reads MQ0: 6 # mapped and MQ=0
+reads QC failed: 0
+non-primary alignments: 0
+total length: 50200 # ignores clipping
+bases mapped: 6275 # ignores clipping
+bases mapped (cigar): 6275 # more accurate
+bases trimmed: 0
+bases duplicated: 0
+mismatches: 591 # from NM fields
+error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
+average length: 251
+maximum length: 251
+average quality: 34.7
+insert size average: 0.0
+insert size standard deviation: 0.0
+inward oriented pairs: 0
+outward oriented pairs: 0
+pairs with other orientation: 0
+pairs on different chromosomes: 0
diff -r b02596e3d7a3 -r 45c568e7f1f9 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Dec 18 19:47:08 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
-
-
-