Mercurial > repos > mvdbeek > test_upload
changeset 0:12bc610792b2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
| author | mvdbeek |
|---|---|
| date | Tue, 25 Sep 2018 04:09:34 -0400 |
| parents | |
| children | |
| files | macros.xml samtools_stats.xml test-data/phiX.bam test-data/samtools_stats_input.bam 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_ref.fa tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 12 files changed, 3498 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Sep 25 04:09:34 2018 -0400 @@ -0,0 +1,103 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> + <yield/> + </requirements> + </xml> + <token name="@TOOL_VERSION@">1.9</token> + <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ + ##prepare input and indices + #for $i, $bam in enumerate( $input_bams ): + ln -s '$bam' '${i}' && + #if $bam.is_of_type('bam'): + #if str( $bam.metadata.bam_index ) != "None": + ln -s '${bam.metadata.bam_index}' '${i}.bai' && + #else: + samtools index '${i}' '${i}.bai' && + #end if + #elif $bam.is_of_type('cram'): + #if str( $bam.metadata.cram_index ) != "None": + ln -s '${bam.metadata.cram_index}' '${i}.crai' && + #else: + samtools index '${i}' '${i}.crai' && + #end if + #end if + #end for + ]]></token> + <xml name="flag_options"> + <option value="1">read is paired</option> + <option value="2">read is mapped in a proper pair</option> + <option value="4">read is unmapped</option> + <option value="8">mate is unmapped</option> + <option value="16">read reverse strand</option> + <option value="32">mate reverse strand</option> + <option value="64">read is the first in a pair</option> + <option value="128">read is the second in a pair</option> + <option value="256">alignment or read is not primary</option> + <option value="512">read fails platform/vendor quality checks</option> + <option value="1024">read is a PCR or optical duplicate</option> + <option value="2048">supplementary alignment</option> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @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},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. 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. + </token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_stats.xml Tue Sep 25 04:09:34 2018 -0400 @@ -0,0 +1,306 @@ +<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 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 '${use_reference.reference_source.ref_file}'` && + #end if + #end if + + samtools stats + '${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(',')])} + #end if + #end if + + --GC-depth ${gc_depth} + --insert-size ${insert_size} + + ## The code below is commented out because using -I/--id options causes the following exception + ## Samtools-htslib: init_group_id() header parsing not yet implemented + ##if str($read_group) != "": + ## -I "${read_group}" + ##end if + + #if str($read_length): + --read-length ${read_length} + #end if + + --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} + + #if 'sn' in $outputs_to_split: + && echo "# Summary Numbers" > 'split/Summary numbers.tab' && + echo "" >> 'split/Summary numbers.tab' && + if grep -q ^SN '${output}'; then + grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab'; + fi + #end if + + #if 'ffq' in $outputs_to_split: + && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' && + if grep -q ^FFQ '${output}'; then + grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab'; + fi + #end if + + #if 'lfq' in $outputs_to_split: + && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' && + if grep -q ^LFQ '${output}'; then + grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab'; + fi + #end if + + #if 'mpc' in $outputs_to_split: + && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' && + if grep -q ^MPC '${output}'; then + grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab'; + fi + #end if + + #if 'gcf' in $outputs_to_split: + && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' && + if grep -q ^GCF '${output}'; then + grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab'; + fi + #end if + + #if 'gcl' in $outputs_to_split: + && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' && + if grep -q ^GCL '${output}'; then + grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab'; + fi + #end if + + #if 'gcc' in $outputs_to_split: + && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' && + if grep -q ^GCC '${output}'; then + grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab'; + fi + #end if + + #if 'is' in $outputs_to_split: + && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' && + if grep -q ^IS '${output}'; then + grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab'; + fi + #end if + + #if 'rl' in $outputs_to_split: + && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' && + if grep -q ^RL '${output}'; then + grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab'; + fi + #end if + + #if 'id' in $outputs_to_split: + && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' && + if grep -q ^ID '${output}'; then + grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab'; + fi + #end if + + #if 'ic' in $outputs_to_split: + && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' && + if grep -q ^IC '${output}'; then + grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab'; + fi + #end if + + #if 'cov' in $outputs_to_split: + && echo "# Coverage distribution" > 'split/Coverage distribution.tab' && + if grep -q ^COV '${output}'; then + grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab'; + fi + #end if + + #if 'gcd' in $outputs_to_split: + && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' && + if grep -q ^GCD '${output}'; then + grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab'; + fi + #end if + #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" /> + <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 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="Desired output files"> + <option value="sn">Summary numbers</option> + <option value="ffq">First Fragment Qualities</option> + <option value="lfq">Last Fragment Qualities</option> + <option value="mpc">Mismatches per cycle</option> + <option value="gcf">GC Content of first fragments</option> + <option value="gcl">GC Content of last fragments</option> + <option value="gcc">ACGT content per cycle</option> + <option value="is">Insert sizes</option> + <option value="rl">Read lengths</option> + <option value="id">Indel distribution</option> + <option value="ic">Indels per cycle</option> + <option value="cov">Coverage distribution</option> + <option value="gcd">GC depth</option> + </param> + </when> + </conditional> + <conditional name="filter_by_flags"> + <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" 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> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate strand</option> + <option value="64">Read is the first in a pair</option> + <option value="128">Read is the second in a pair</option> + <option value="256">The alignment or this read is not primary</option> + <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" 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> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate strand</option> + <option value="64">Read is the first in a pair</option> + <option value="128">Read is the second in a pair</option> + <option value="256">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="1024">The read is a PCR or optical duplicate</option> + </param> + </when> + <when value="nofilter" /> + + </conditional> + <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" > + <options> + <filter type="data_meta" ref="input_file" key="read_groups" /> + </options> + </param> + + --> + + <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" 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> + <when value="yes"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose a reference sequence for GC depth"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </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> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using file" /> + </when> + </conditional> + </when> + <when value="no" /> + </conditional> + + </inputs> + + <outputs> + <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> + <tests> + <test> + <param name="input_file" value="samtools_stats_input.bam" ftype="bam" /> + <param name="use_ref_selector" value="yes" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" /> + <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" /> + </test> + <test> + <param name="input_file" value="samtools_stats_input.bam" ftype="bam" /> + <param name="use_ref_selector" value="yes" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" /> + <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" /> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool runs the ``samtools stats`` command. + ]]></help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out1.tab Tue Sep 25 04:09:34 2018 -0400 @@ -0,0 +1,1138 @@ +# 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 +# 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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quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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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; 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 +# 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2.tab Tue Sep 25 04:09:34 2018 -0400 @@ -0,0 +1,1138 @@ +# 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 +# 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. 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quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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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; 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 +# 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2__gcc.tab Tue Sep 25 04:09:34 2018 -0400 @@ -0,0 +1,252 @@ +# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent) +1 21.94 30.10 34.18 13.78 2.04 0.00 +2 30.00 16.00 11.00 43.00 0.00 0.00 +3 33.00 25.00 9.00 33.00 0.00 0.00 +4 17.00 29.00 13.00 41.00 0.00 0.00 +5 37.00 22.00 12.00 29.00 0.00 0.00 +6 36.00 26.00 17.00 21.00 0.00 0.00 +7 29.50 13.50 31.50 25.50 0.00 0.00 +8 50.50 14.50 19.50 15.50 0.00 0.00 +9 17.00 33.00 18.00 32.00 0.00 0.00 +10 37.00 14.00 21.00 28.00 0.00 0.00 +11 20.50 14.50 29.50 35.50 0.00 0.00 +12 30.00 24.00 22.00 24.00 0.00 0.00 +13 27.00 15.00 21.00 37.00 0.00 0.00 +14 24.24 22.22 26.26 27.27 1.01 0.00 +15 25.50 20.50 24.50 29.50 0.00 0.00 +16 31.00 15.00 20.00 34.00 0.00 0.00 +17 28.00 25.00 14.00 33.00 0.00 0.00 +18 30.50 28.50 19.50 21.50 0.00 0.00 +19 29.00 26.00 21.00 24.00 0.00 0.00 +20 22.50 23.50 17.50 36.50 0.00 0.00 +21 35.50 17.50 19.50 27.50 0.00 0.00 +22 37.50 28.50 15.50 18.50 0.00 0.00 +23 31.31 19.19 13.13 36.36 1.01 0.00 +24 37.00 12.00 22.00 29.00 0.00 0.00 +25 35.50 22.50 17.50 24.50 0.00 0.00 +26 33.50 18.50 15.50 32.50 0.00 0.00 +27 34.50 14.50 25.50 25.50 0.00 0.00 +28 31.00 14.00 24.00 31.00 0.00 0.00 +29 30.00 27.00 24.00 19.00 0.00 0.00 +30 31.00 20.00 14.00 35.00 0.00 0.00 +31 33.50 29.50 13.50 23.50 0.00 0.00 +32 42.50 20.50 19.50 17.50 0.00 0.00 +33 25.50 23.50 14.50 36.50 0.00 0.00 +34 39.50 16.50 20.50 23.50 0.00 0.00 +35 32.50 23.50 21.50 22.50 0.00 0.00 +36 42.00 25.00 16.00 17.00 0.00 0.00 +37 38.00 17.00 19.00 26.00 0.00 0.00 +38 24.00 26.00 25.00 25.00 0.00 0.00 +39 22.50 41.50 18.50 17.50 0.00 0.00 +40 32.00 16.00 21.00 31.00 0.00 0.00 +41 33.00 28.00 19.00 20.00 0.00 0.00 +42 30.50 25.50 19.50 24.50 0.00 0.00 +43 35.00 29.00 15.00 21.00 0.00 0.00 +44 20.00 27.00 22.00 31.00 0.00 0.00 +45 40.50 21.50 21.50 16.50 0.00 0.00 +46 26.50 20.50 22.50 30.50 0.00 0.00 +47 38.50 29.50 16.50 15.50 0.00 0.00 +48 27.50 24.50 17.50 30.50 0.00 0.00 +49 28.50 32.50 10.50 28.50 0.00 0.00 +50 46.50 20.50 9.50 23.50 0.00 0.00 +51 34.50 28.50 13.50 23.50 0.00 0.00 +52 41.50 23.50 20.50 14.50 0.00 0.00 +53 20.00 28.00 26.00 26.00 0.00 0.00 +54 31.50 18.50 24.50 25.50 0.00 0.00 +55 30.50 22.50 16.50 30.50 0.00 0.00 +56 33.50 22.50 13.50 30.50 0.00 0.00 +57 23.00 24.00 23.00 30.00 0.00 0.00 +58 25.00 37.00 19.00 19.00 0.00 0.00 +59 34.00 23.00 24.00 19.00 0.00 0.00 +60 29.00 28.00 17.00 26.00 0.00 0.00 +61 25.50 23.50 24.50 26.50 0.00 0.00 +62 31.50 22.50 16.50 29.50 0.00 0.00 +63 27.50 28.50 25.50 18.50 0.00 0.00 +64 33.50 21.50 25.50 19.50 0.00 0.00 +65 35.50 19.50 18.50 26.50 0.00 0.00 +66 34.00 25.00 15.00 26.00 0.00 0.00 +67 37.00 23.00 19.00 21.00 0.00 0.00 +68 36.50 29.50 13.50 20.50 0.00 0.00 +69 38.50 19.50 20.50 21.50 0.00 0.00 +70 38.50 16.50 18.50 26.50 0.00 0.00 +71 25.50 38.50 21.50 14.50 0.00 0.00 +72 29.00 29.00 25.00 17.00 0.00 0.00 +73 32.50 20.50 21.50 25.50 0.00 0.00 +74 28.50 32.50 12.50 26.50 0.00 0.00 +75 41.50 12.50 18.50 27.50 0.00 0.00 +76 24.50 29.50 23.50 22.50 0.00 0.00 +77 36.00 21.00 18.00 25.00 0.00 0.00 +78 27.00 34.00 22.00 17.00 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2__mpc.tab Tue Sep 25 04:09:34 2018 -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 Sep 25 04:09:34 2018 -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_ref.fa Tue Sep 25 04:09:34 2018 -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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Tue Sep 25 04:09:34 2018 -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): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Sep 25 04:09:34 2018 -0400 @@ -0,0 +1,7 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>