Mercurial > repos > devteam > samtools_stats
changeset 3:45c568e7f1f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:17:02 -0400 |
| parents | b02596e3d7a3 |
| children | 8d500e0e0dbe |
| files | macros.xml samtools_stats.xml test-data/samtools_stats_out1.tab test-data/samtools_stats_out2.tab test-data/samtools_stats_out2/gcc.tab test-data/samtools_stats_out2/mpc.tab test-data/samtools_stats_out2/sn.tab test-data/samtools_stats_out2__gcc.tab test-data/samtools_stats_out2__mpc.tab test-data/samtools_stats_out2__sn.tab tool_dependencies.xml |
| diffstat | 11 files changed, 1182 insertions(+), 1177 deletions(-) [+] |
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--- 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 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> <yield/> </requirements> </xml> + <token name="@TOOL_VERSION@">1.3.1</token> <xml name="citations"> <citations> <citation type="bibtex"> @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/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> @@ -41,7 +42,7 @@ </citations> </xml> <xml name="version_command"> - <version_command>echo $(samtools --version | head -n 1)", "$(samtools --version | grep -o -E "htslib.*?")</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -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. - </token> - </macros>
--- 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 @@ -<tool id="samtools_stats" name="Stats" version="2.0"> +<tool id="samtools_stats" name="Stats" version="2.0.1"> <description>generate statistics for BAM dataset</description> <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> <command><![CDATA[ #if $use_reference.use_ref_selector == "yes": #if $use_reference.reference_source.reference_source_selector == "history": - ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats - #else: - samtools stats - #end if - #else: - samtools stats - #end if - "${input_file}" - --coverage ${coverage_min},${coverage_max},${coverage_step} - ${remove_dups} - #if str( $filter_by_flags.filter_flags ) == "filter": - #if $filter_by_flags.require_flags: - --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])} - #end if - #if $filter_by_flags.exclude_flags: - --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])} + ln -s '${use_reference.reference_source.ref_file}' && + samtools faidx `basename '${use_reference.reference_source.ref_file}'` && #end if #end if - --GC-depth ${gc_depth} - --insert-size ${insert_size} + + samtools stats + '${input_file}' + --coverage ${coverage_min},${coverage_max},${coverage_step} + ${remove_dups} - ## The code below is commented out because using -I/--id options causes the following exception - ## Samtools-htslib: init_group_id() header parsing not yet implemented + #if str( $filter_by_flags.filter_flags ) == "filter": + #if $filter_by_flags.require_flags: + --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])} + #end if + #if $filter_by_flags.exclude_flags: + --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])} + #end if + #end if - ##if str($read_group) != "": - ## -I "${read_group}" - ##end if + --GC-depth ${gc_depth} + --insert-size ${insert_size} - #if str($read_length) != "0": - --read-length "${read_length}" - #end if - --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 "${use_reference.reference_source.ref_file}" + ## The code below is commented out because using -I/--id options causes the following exception + ## Samtools-htslib: init_group_id() header parsing not yet implemented + ##if str($read_group) != "": + ## -I "${read_group}" + ##end if + + #if str($read_length): + --read-length ${read_length} #end if - #end if - > "${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 ]]></command> <inputs> <param name="input_file" type="data" format="sam,bam" label="BAM file" /> - <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="minimum coverage value for --coverage option"/> - <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/> - <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/> - <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/> + <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" /> + <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" /> + <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" /> + <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" + label="Exclude reads marked as duplicates" /> <conditional name="split_output"> - <param name="split_output_selector" type="select" label="Output" help="Select between a single output or separate outputs for each statistics"> - <option value="no" selected="True">a single summary file</option> - <option value="yes">separate datasets for each statistics</option> + <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics"> + <option value="no" selected="True">One single summary file</option> + <option value="yes">Separate datasets for each statistic</option> </param> <when value="no" /> <when value="yes"> - <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Statistics to extract"> + <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files"> <option value="sn">Summary numbers</option> <option value="ffq">First Fragment Qualities</option> <option value="lfq">Last Fragment Qualities</option> @@ -156,12 +183,12 @@ </when> </conditional> <conditional name="filter_by_flags"> - <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options"> + <param name="filter_flags" type="select" label="Filter by SAM flags" help="More info on the flags: https://samtools.github.io/hts-specs/SAMv1.pdf"> <option value="nofilter" selected="True">Do not filter</option> <option value="filter">Filter by flags to exclude or require</option> </param> <when value="filter"> - <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f"> + <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" label="Require"> <option value="1">Read is paired</option> <option value="2">Read is mapped in a proper pair</option> <option value="4">The read is unmapped</option> @@ -174,7 +201,7 @@ <option value="512">The read fails platform/vendor quality checks</option> <option value="1024">The read is a PCR or optical duplicate</option> </param> - <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F"> + <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" label="Exclude"> <option value="1">Read is paired</option> <option value="2">Read is mapped in a proper pair</option> <option value="4">The read is unmapped</option> @@ -191,19 +218,18 @@ <when value="nofilter" /> </conditional> - <param name="gc_depth" type="float" value="20000" label="GC-depth bin size" help="--GC-depth; decreasing bin size increases memory requirement; default = 20000.0"/> - <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/> + <param name="gc_depth" argument="--GC-depth" type="float" value="20000" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement" /> + <param name="insert_size" argument="--insert-size" type="integer" value="8000" label="Maximum insert size" /> + <!-- - <!-- - The -I option of samtools stats returns the following message in version 1.2: Samtools-htslib: init_group_id() header parsing not yet implemented Abort trap: 6 - + Because of this the section below is commented out until this stats bug is fixed - <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > + <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > <options> <filter type="data_meta" ref="input_file" key="read_groups" /> </options> @@ -211,12 +237,12 @@ --> - <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/> - <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/> - <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/> - + <param name="read_length" argument="--read-length" type="integer" value="" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty"/> + <param name="most_inserts" argument="--most-inserts" type="float" value="0.99" label="Report only the main part of inserts" /> + <param name="trim_quality" argument="--trim-quality" type="integer" value="0" label="BWA trim parameter" /> + <conditional name="use_reference"> - <param name="use_ref_selector" type="select" label="Use reference sequence" help="--ref-seq; required for GC-depth and mismatches-per-cycle calculation"> + <param name="use_ref_selector" argument="--ref-seq" type="select" label="Use reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation"> <option value="yes">Use reference</option> <option selected="True" value="no">Do not use reference</option> </param> @@ -228,8 +254,9 @@ </param> <when value="cached"> <param name="ref_file" type="select" label="Using genome"> - <options from_data_table="fasta_indexes" /> - <filter type="data_meta" ref="input_file" key="dbkey" column="1" /> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input_file" key="dbkey" column="1" /> + </options> </param> </when> <when value="history"> @@ -243,7 +270,7 @@ </inputs> <outputs> - <data format="tabular" name="output" label="${tool.name} on ${on_string}"> + <data name="output" format="tabular" label="${tool.name} on ${on_string}"> <discover_datasets pattern="(?P<designation>.+)\.tab" ext="tabular" visible="true" directory="split" /> </data> </outputs> @@ -263,34 +290,17 @@ <param name="split_output_selector" value="yes" /> <param name="generate_tables" value="sn,mpc,gcc" /> <output name="output" file="samtools_stats_out2.tab" lines_diff="4"> - <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" /> - <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" /> - <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" /> + <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2__sn.tab" /> + <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2__gcc.tab" /> + <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2__mpc.tab" /> </output> </test> </tests> <help><![CDATA[ **What it does** -This tool runs the ``samtools stats`` command. It has the following options:: - - -c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1] - -d, --remove-dups Exclude from statistics reads marked as duplicates - -f, --required-flag <str|int> Required flag, 0 for unset. See also `samtools flags` [0] - -F, --filtering-flag <str|int> Filtering flag, 0 for unset. See also `samtools flags` [0] - --GC-depth <float> the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4] - -h, --help This help message - -i, --insert-size <int> Maximum insert size [8000] - -I, --id <string> Include only listed read group or sample name - -l, --read-length <int> Include in the statistics only reads with the given read length [] - -m, --most-inserts <float> Report only the main part of inserts [0.99] - -q, --trim-quality <int> The BWA trimming parameter [0] - -r, --ref-seq <file> 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. ]]></help> - <expand macro="citations"></expand> + <expand macro="citations"/> </tool>
--- 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
--- 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
--- 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 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--- 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
--- /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 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--- /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. 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--- /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
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="1.2"> - <repository changeset_revision="a55970300738" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>