Tool Test Results (powered by Planemo)

# HG changeset patch # User devteam # Date 1429712975 14400 # Node ID 0d71d94678474c28a7aafe8579024efbfbe5a58a Uploaded diff -r 000000000000 -r 0d71d9467847 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,70 @@ + + + + samtools + + + + + + + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + + 10.1093/bioinformatics/btp352 + 10.1093/bioinformatics/btr076 + 10.1093/bioinformatics/btr509 + + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + + + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + + + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + + + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + + + + + samtools --version | head -n 1 | awk '{ print $2 }' + + + + + + + +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + + + diff -r 000000000000 -r 0d71d9467847 samtools_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_stats.xml Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,296 @@ + + generate statistics for BAM dataset + + macros.xml + + + + + "${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} && + + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #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 && + #end if + + ## Unix true command below + + true + + #end if + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ,, 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. + + + ]]> + + + diff -r 000000000000 -r 0d71d9467847 samtools_stats_tool_test_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_stats_tool_test_output.html Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,372 @@ + + + + + + + Tool Test Results (powered by Planemo) + + + + + + + + + + + + + + +

+ +

Overview

Tests

The remainder of this contains a description for each test executed to run these jobs.

+ + + + + + + diff -r 000000000000 -r 0d71d9467847 test-data/phiX.bam Binary file test-data/phiX.bam has changed diff -r 000000000000 -r 0d71d9467847 test-data/samtools_stats_input.bam Binary file test-data/samtools_stats_input.bam has changed diff -r 000000000000 -r 0d71d9467847 test-data/samtools_stats_out1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out1.tab Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,1137 @@ +# 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 +# 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 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 200 +SN filtered sequences: 0 +SN sequences: 200 +SN is sorted: 1 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 200 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 6 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3 2 0 20 38 32 1 0 0 0 0 0 0 +FFQ 2 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 3 0 0 18 36 36 6 0 0 0 0 0 0 +FFQ 3 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 2 1 0 14 31 46 5 0 0 0 0 0 0 +FFQ 4 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 1 1 0 8 36 42 11 0 0 0 0 0 0 +FFQ 5 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 0 0 0 0 1 0 0 12 35 43 6 0 0 0 0 0 0 +FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 7 8 0 0 81 0 0 0 0 +FFQ 7 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 9 13 1 0 76 0 0 0 0 +FFQ 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 1 0 11 15 4 0 69 0 0 0 0 +FFQ 9 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 1 0 0 1 6 20 3 0 68 0 0 0 0 +FFQ 10 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 1 7 11 5 0 75 0 0 0 0 +FFQ 11 0 0 0 0 0 0 0 0 0 0 0 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0 +LFQ 243 0 0 0 0 0 0 0 0 0 0 0 0 2 2 17 14 0 0 0 0 0 0 0 0 6 5 5 0 0 0 0 0 6 13 0 2 3 25 0 0 0 0 +LFQ 244 0 0 0 0 0 0 0 0 0 0 0 0 1 3 18 11 0 0 0 0 0 0 0 0 6 5 5 1 0 0 1 0 2 12 0 5 1 29 0 0 0 0 +LFQ 245 0 0 0 0 0 0 0 0 0 0 0 0 1 8 14 11 0 0 0 0 0 0 0 0 8 5 3 1 0 0 1 0 1 15 1 1 3 27 0 0 0 0 +LFQ 246 0 0 0 0 0 0 0 0 0 0 0 0 4 6 15 12 0 0 0 0 0 0 0 0 5 2 8 1 0 1 1 0 1 13 0 2 1 28 0 0 0 0 +LFQ 247 0 0 0 0 0 0 0 0 0 0 0 0 8 3 16 14 0 0 0 0 0 0 0 0 10 4 6 0 0 0 0 0 2 15 1 2 2 17 0 0 0 0 +LFQ 248 0 0 0 0 0 0 0 0 0 0 0 0 5 6 21 8 0 0 0 0 0 0 0 0 7 8 6 2 0 0 0 1 1 14 0 2 2 17 0 0 0 0 +LFQ 249 0 0 0 0 0 0 0 0 0 0 0 0 5 6 20 8 0 0 0 0 0 0 0 0 5 7 10 0 1 0 0 0 1 15 0 2 0 20 0 0 0 0 +LFQ 250 0 0 0 0 0 0 0 0 0 0 0 0 2 10 15 10 0 0 0 0 0 0 0 0 9 5 8 1 0 0 0 2 6 10 0 0 2 20 0 0 0 0 +LFQ 251 0 0 0 0 0 0 0 0 0 0 0 0 7 20 21 17 0 0 0 0 0 0 0 0 7 7 6 0 0 0 0 1 2 4 0 0 0 8 0 0 0 0 +LFQ 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 +# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 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0 0 0 0 +MPC 184 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 185 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 186 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 187 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 188 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 189 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 190 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 192 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 0 +MPC 193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 195 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 196 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 +MPC 197 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 198 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 199 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 201 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 203 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 204 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 205 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 +MPC 206 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 207 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 208 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 209 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 +MPC 210 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 211 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 +MPC 212 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 213 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 +MPC 214 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 +MPC 215 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 216 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 217 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 218 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 219 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 220 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 221 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 222 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 223 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 224 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 226 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 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 +MPC 227 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 +MPC 228 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 229 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 230 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 +MPC 231 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 232 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 1 0 0 0 0 +MPC 233 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 +MPC 234 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 1 0 0 0 +MPC 235 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 +MPC 236 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 1 0 0 0 +MPC 237 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 1 0 0 0 +MPC 238 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 0 +MPC 239 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 1 0 0 0 +MPC 240 0 0 0 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 0 0 0 0 0 0 0 0 0 0 0 +MPC 241 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 0 +MPC 242 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 1 0 0 0 +MPC 243 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +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 +# 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 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 000000000000 -r 0d71d9467847 test-data/samtools_stats_out2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2.tab Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,1137 @@ +# 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 +# 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 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 200 +SN filtered sequences: 0 +SN sequences: 200 +SN is sorted: 1 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 200 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 6 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3 2 0 20 38 32 1 0 0 0 0 0 0 +FFQ 2 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 3 0 0 18 36 36 6 0 0 0 0 0 0 +FFQ 3 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 2 1 0 14 31 46 5 0 0 0 0 0 0 +FFQ 4 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 1 1 0 8 36 42 11 0 0 0 0 0 0 +FFQ 5 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 0 0 0 0 1 0 0 12 35 43 6 0 0 0 0 0 0 +FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 7 8 0 0 81 0 0 0 0 +FFQ 7 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 9 13 1 0 76 0 0 0 0 +FFQ 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 1 0 11 15 4 0 69 0 0 0 0 +FFQ 9 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 1 0 0 1 6 20 3 0 68 0 0 0 0 +FFQ 10 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 1 7 11 5 0 75 0 0 0 0 +FFQ 11 0 0 0 0 0 0 0 0 0 0 0 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0 +LFQ 243 0 0 0 0 0 0 0 0 0 0 0 0 2 2 17 14 0 0 0 0 0 0 0 0 6 5 5 0 0 0 0 0 6 13 0 2 3 25 0 0 0 0 +LFQ 244 0 0 0 0 0 0 0 0 0 0 0 0 1 3 18 11 0 0 0 0 0 0 0 0 6 5 5 1 0 0 1 0 2 12 0 5 1 29 0 0 0 0 +LFQ 245 0 0 0 0 0 0 0 0 0 0 0 0 1 8 14 11 0 0 0 0 0 0 0 0 8 5 3 1 0 0 1 0 1 15 1 1 3 27 0 0 0 0 +LFQ 246 0 0 0 0 0 0 0 0 0 0 0 0 4 6 15 12 0 0 0 0 0 0 0 0 5 2 8 1 0 1 1 0 1 13 0 2 1 28 0 0 0 0 +LFQ 247 0 0 0 0 0 0 0 0 0 0 0 0 8 3 16 14 0 0 0 0 0 0 0 0 10 4 6 0 0 0 0 0 2 15 1 2 2 17 0 0 0 0 +LFQ 248 0 0 0 0 0 0 0 0 0 0 0 0 5 6 21 8 0 0 0 0 0 0 0 0 7 8 6 2 0 0 0 1 1 14 0 2 2 17 0 0 0 0 +LFQ 249 0 0 0 0 0 0 0 0 0 0 0 0 5 6 20 8 0 0 0 0 0 0 0 0 5 7 10 0 1 0 0 0 1 15 0 2 0 20 0 0 0 0 +LFQ 250 0 0 0 0 0 0 0 0 0 0 0 0 2 10 15 10 0 0 0 0 0 0 0 0 9 5 8 1 0 0 0 2 6 10 0 0 2 20 0 0 0 0 +LFQ 251 0 0 0 0 0 0 0 0 0 0 0 0 7 20 21 17 0 0 0 0 0 0 0 0 7 7 6 0 0 0 0 1 2 4 0 0 0 8 0 0 0 0 +LFQ 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 +# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 217 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 218 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 219 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 220 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 221 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 222 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 223 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 224 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 226 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 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 +MPC 227 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 +MPC 228 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 229 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 230 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 +MPC 231 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 232 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 1 0 0 0 0 +MPC 233 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 +MPC 234 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 1 0 0 0 +MPC 235 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 +MPC 236 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 1 0 0 0 +MPC 237 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 1 0 0 0 +MPC 238 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 0 +MPC 239 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 1 0 0 0 +MPC 240 0 0 0 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 0 0 0 0 0 0 0 0 0 0 0 +MPC 241 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 0 +MPC 242 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 1 0 0 0 +MPC 243 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +MPC 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 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +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 +# 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 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 000000000000 -r 0d71d9467847 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 Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,252 @@ +# 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 000000000000 -r 0d71d9467847 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 Wed Apr 22 10:29:35 2015 -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 +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 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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 +66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +68 0 0 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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 000000000000 -r 0d71d9467847 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 Wed Apr 22 10:29:35 2015 -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 000000000000 -r 0d71d9467847 test-data/samtools_stats_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_ref.fa Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,239 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG +GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC +CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA +ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC +ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC +TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA +CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC +AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC +ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC +AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA +ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA +TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT +CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC +AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC +CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA +CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC +AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA +AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA +TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA +GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA +GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA +ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC +AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA +AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT +AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG +TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC +ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG +TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC +AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC +ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA +AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT +TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA +TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG +TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA +GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG +ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG +AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA +ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT +TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA +TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC +CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC +CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG +CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC +AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC +TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC +CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC +ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC +CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC +AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT +GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA +GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC +AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT +GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC +GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT +CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA +ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG +GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA +GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA +TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC +CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC +CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA +TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG +CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC +AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA +CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC +GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA +AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA +GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC +GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT +TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT +AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC +CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC +CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC +CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG +CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG +AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA +TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG +AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA +GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG +GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC +ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC +ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT +GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC +ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA +AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA +CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT +TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT +ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA +AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC +ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG +AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA +CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC +TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC +AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT +ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT +AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA +CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT +GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT +CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC +TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA +TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA +AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA +AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC +CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC +ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA +AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT +TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG +CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG +CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA +GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA +TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT +CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC +AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT +AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT +ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA +TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA +TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG +CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG +TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT +GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA +AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT +ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA +TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA +ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC +AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC +ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT +CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC +CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC +TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT +AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT +AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT +ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA +TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG +GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA +CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT +TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC +CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA +CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC +CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA +CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA +ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC +ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT +CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA +CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC +CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA +CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA +TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT +TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT +CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA +TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC +TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC +AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC +CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC +ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA +AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC +TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC +TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA +CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC +AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA +TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA +ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA +TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA +CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA +CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC +CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC +CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG +ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC +CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC +CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA +ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA +CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC +ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC +AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC +TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA +GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT +CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT +TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC +TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA +GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC +AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC +TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC +CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA +GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC +ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA +ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA +ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG +TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC +TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC +ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG + diff -r 000000000000 -r 0d71d9467847 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Wed Apr 22 10:29:35 2015 -0400 @@ -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): +# +# +# +#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 0d71d9467847 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +

+ diff -r 000000000000 -r 0d71d9467847 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 22 10:29:35 2015 -0400 @@ -0,0 +1,6 @@ + + + + + +