| Previous changeset 7:145f6d74ff5e (2019-10-17) Next changeset 9:1cc79f49b8d5 (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b" |
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modified:
macros.xml samtools_stats.xml test-data/1.stats.expected test-data/11.stats.expected test-data/11.stats.g4.expected test-data/12.2reads.nooverlap.expected test-data/12.2reads.overlap.expected test-data/12.3reads.nooverlap.expected test-data/12.3reads.overlap.expected test-data/2.stats.expected test-data/6.stats.expected test-data/samtools_stats_out1.tab test-data/samtools_stats_out1__sn.tab |
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| diff -r 145f6d74ff5e -r e28839a4b932 macros.xml --- a/macros.xml Thu Oct 17 02:21:23 2019 -0400 +++ b/macros.xml Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -5,10 +5,16 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.9</token> - <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@TOOL_VERSION@">1.13</token> + <token name="@PROFILE@">20.05</token> + <token name="@FLAGS@"><![CDATA[ + #set $flags = 0 + #if $filter + #set $flags = sum(map(int, str($filter).split(','))) + #end if + ]]></token> <token name="@PREPARE_IDX@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": @@ -25,7 +31,7 @@ #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): @@ -63,6 +69,51 @@ #set reffai=None #end if ]]></token> + + <xml name="optional_reference"> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="no">No</option> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="no"/> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + </options> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> + </param> + </when> + </conditional> + </xml> + <xml name="mandatory_reference" token_help="" token_argument=""> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + </xml> + + <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && @@ -70,28 +121,28 @@ <token name="@ADDMEMORY@"><![CDATA[ ##compute the number of memory available to samtools sort (-m) ##use only 75% of available: https://github.com/samtools/samtools/issues/831 - addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && + addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ]]></token> <xml name="seed_input"> - <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> + <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> - <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 name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> + <option value="1" selected="@S1@">Read is paired</option> + <option value="2" selected="@S2@">Read is mapped in a proper pair</option> + <option value="4" selected="@S4@">Read is unmapped</option> + <option value="8" selected="@S8@">Mate is unmapped</option> + <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> + <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> + <option value="64" selected="@S64@">Read is the first in a pair</option> + <option value="128" selected="@S128@">Read is the second in a pair</option> + <option value="256" selected="@S256@">Alignment of the read is not primary</option> + <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> + <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> + <option value="2048" selected="@S2048@">Alignment is supplementary</option> </xml> - <!-- region specification macros and tokens for tools that allow the specification + <!-- region specification macros and tokens for tools that allow the specification of region by bed file / space separated list of regions --> <token name="@REGIONS_FILE@"><![CDATA[ #if $cond_region.select_region == 'tab': |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 samtools_stats.xml --- a/samtools_stats.xml Thu Oct 17 02:21:23 2019 -0400 +++ b/samtools_stats.xml Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy2">\n+<tool id="samtools_stats" name="Samtools stats" version="2.0.3" profile="@PROFILE@">\n <description>generate statistics for BAM dataset</description>\n <macros>\n <import>macros.xml</import>\n@@ -16,16 +16,12 @@\n #end if\n ${remove_dups}\n #if str( $filter_by_flags.filter_flags ) == "filter":\n- #if $filter_by_flags.require_flags:\n- #set $filter = $filter_by_flags.require_flags\n- @FLAGS@\n- --required-flag $flags\n- #end if\n- #if $filter_by_flags.exclude_flags:\n- #set $filter = $filter_by_flags.exclude_flags\n- @FLAGS@\n- --filtering-flag $flags\n- #end if\n+ #set $filter = $filter_by_flags.require_flags\n+ @FLAGS@\n+ --required-flag $flags\n+ #set $filter = $filter_by_flags.exclude_flags\n+ @FLAGS@\n+ --filtering-flag $flags\n #end if\n #if str($gc_depth):\n --GC-depth ${gc_depth}\n@@ -33,12 +29,9 @@\n #if str($insert_size):\n --insert-size ${insert_size}\n #end if\n- ## The code below is commented out because using -I/--id options causes \n- ## in samtools up to 1.9 the following exception\n- ## Samtools-htslib: init_group_id() header parsing not yet implemented\n- ##if str($read_group) != "":\n- ## -I "${read_group}"\n- ##end if\n+ ## #if $read_group\n+ ## -I \'$read_group\'\n+ ## #end if\n #if str($read_length):\n --read-length ${read_length}\n #end if\n@@ -63,7 +56,7 @@\n #if str($cov_threshold):\n -g $cov_threshold\n #end if\n- -@ \\$addthreads \n+ -@ \\$addthreads\n infile\n @REGIONS_MANUAL@\n > \'$output\'\n@@ -139,40 +132,19 @@\n <!-- TODO I would like to set the default values of float and int parameters as on the samtools stats help page, but then the tests don\'t work. Hence I leave the optional and give the defaults in the help -->\n <param name="gc_depth" argument="--GC-depth" type="float" optional="True" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement. default=2e4" />\n <param name="insert_size" argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />\n- <!--\n- The -I option of samtools stats returns the following message up to version 1.9:\n- Samtools-htslib: init_group_id() header parsing not yet implemented\n- Because of this the section below is commented out until this stats bug is fixed\n- <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >\n- <options>\n- <filter type="data_meta" ref="input" key="read_groups" />\n- </options>\n- </param>\n- -->\n+ <!-- TOOD https://github.com/samtools/samtools/issues/1489 --> \n+ <param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" >\n+ <options>\n+ <filter type="data_meta" ref="input" key="read_groups" />\n+ </options>\n+ </param>\n <param name="read_length" argument="--read-length" type="integer" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty" />\n <param name="most_inserts" argument="--most-inserts" type="float" optional="true" label="Report only the main part of inserts" help="default=0.99" />\n <param name="trim_quality" argument="--trim-quality" type="i'..b' <param name="regions_repeat_2|region" value="ref1:39-56"/>\n </conditional>\n <param name="cov_threshold" value="4" />\n- <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" />\n+ <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="2" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/11.stats.g4.expected\',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->\n <test>\n@@ -292,7 +264,7 @@\n <param name="select_region" value="tab"/>\n <param name="targetregions" value="12_3reads.bed" ftype="tabular" />\n </conditional>\n- <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="3" />\n+ <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.3reads.overlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test>\n@@ -305,7 +277,7 @@\n <param name="targetregions" value="12_3reads.bed" ftype="tabular" />\n </conditional>\n <param name="remove_overlaps" value="-p"/>\n- <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="3" />\n+ <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.3reads.nooverlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test>\n@@ -317,7 +289,7 @@\n <param name="select_region" value="tab"/>\n <param name="targetregions" value="12_2reads.bed" ftype="tabular" />\n </conditional>\n- <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="3" />\n+ <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.2reads.overlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test>\n@@ -330,7 +302,7 @@\n <param name="targetregions" value="12_2reads.bed" ftype="tabular" />\n </conditional>\n <param name="remove_overlaps" value="-p"/>\n- <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="3" />\n+ <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.2reads.nooverlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test>\n@@ -357,6 +329,18 @@\n <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />\n </output_collection>\n </test>\n+ <!-- test filtering by read group -->\n+ <!-- <test>\n+ <param name="input" value="11_target.sam" ftype="sam" />\n+ <conditional name="addref_cond">\n+ <param name="addref_select" value="no" />\n+ </conditional>\n+ <param name="read_group" value="grp1" />\n+ <output name="output" file="11.stats.read_groups.expected" ftype="tabular" lines_diff="2" />\n+ <assert_command>\n+ <has_text text="-I \'grp1\'"/>\n+ </assert_command>\n+ </test> -->\n </tests>\n <help><![CDATA[\n **What it does**\n@@ -367,4 +351,3 @@\n ]]></help>\n <expand macro="citations"/>\n </tool>\n-\n' |
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| diff -r 145f6d74ff5e -r e28839a4b932 test-data/1.stats.expected --- a/test-data/1.stats.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/1.stats.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats --ref-seq reference.fa -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 1a1c1362 29c426ae 7bab45da # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 2 +SN raw total sequences: 2 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 2 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 70 # ignores clipping SN total first fragment length: 35 # ignores clipping SN total last fragment length: 35 # ignores clipping @@ -195,6 +199,42 @@ GCC 33 50.00 0.00 0.00 50.00 0.00 0.00 GCC 34 50.00 0.00 50.00 0.00 0.00 0.00 GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 0.00 50.00 0.00 50.00 +GCT 2 50.00 0.00 50.00 0.00 +GCT 3 0.00 0.00 50.00 50.00 +GCT 4 0.00 0.00 100.00 0.00 +GCT 5 0.00 0.00 50.00 50.00 +GCT 6 0.00 50.00 0.00 50.00 +GCT 7 0.00 0.00 50.00 50.00 +GCT 8 0.00 0.00 0.00 100.00 +GCT 9 0.00 50.00 50.00 0.00 +GCT 10 50.00 0.00 50.00 0.00 +GCT 11 50.00 0.00 0.00 50.00 +GCT 12 50.00 0.00 50.00 0.00 +GCT 13 50.00 0.00 50.00 0.00 +GCT 14 0.00 0.00 0.00 100.00 +GCT 15 100.00 0.00 0.00 0.00 +GCT 16 50.00 0.00 0.00 50.00 +GCT 17 0.00 0.00 50.00 50.00 +GCT 18 0.00 50.00 50.00 0.00 +GCT 19 0.00 100.00 0.00 0.00 +GCT 20 0.00 0.00 50.00 50.00 +GCT 21 0.00 0.00 100.00 0.00 +GCT 22 0.00 50.00 0.00 50.00 +GCT 23 50.00 0.00 0.00 50.00 +GCT 24 50.00 0.00 50.00 0.00 +GCT 25 50.00 0.00 50.00 0.00 +GCT 26 0.00 0.00 100.00 0.00 +GCT 27 50.00 0.00 0.00 50.00 +GCT 28 0.00 0.00 50.00 50.00 +GCT 29 0.00 50.00 0.00 50.00 +GCT 30 0.00 50.00 0.00 50.00 +GCT 31 0.00 50.00 50.00 0.00 +GCT 32 0.00 0.00 100.00 0.00 +GCT 33 100.00 0.00 0.00 0.00 +GCT 34 0.00 0.00 50.00 50.00 +GCT 35 50.00 0.00 50.00 0.00 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -231,6 +271,8 @@ FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 FBC 34 0.00 0.00 100.00 0.00 0.00 0.00 FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 6 5 15 9 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 LBC 2 0.00 0.00 0.00 100.00 0.00 0.00 @@ -267,6 +309,8 @@ LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 11 10 5 9 0 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
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| diff -r 145f6d74ff5e -r e28839a4b932 test-data/11.stats.expected --- a/test-data/11.stats.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/11.stats.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK cb2d2d82 bcd83869 62ec814e # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 26 +SN raw total sequences: 26 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 26 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 1 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 260 # ignores clipping SN total first fragment length: 140 # ignores clipping SN total last fragment length: 120 # ignores clipping @@ -89,6 +93,17 @@ GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 26.92 26.92 30.77 15.38 +GCT 2 7.69 38.46 26.92 26.92 +GCT 3 26.92 26.92 30.77 15.38 +GCT 4 11.54 34.62 26.92 26.92 +GCT 5 23.08 26.92 38.46 11.54 +GCT 6 11.54 34.62 23.08 30.77 +GCT 7 19.23 23.08 38.46 19.23 +GCT 8 11.54 38.46 23.08 26.92 +GCT 9 23.08 19.23 34.62 23.08 +GCT 10 11.54 34.62 26.92 26.92 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 @@ -100,6 +115,8 @@ FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 24 43 45 28 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 @@ -111,6 +128,19 @@ LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 30 33 36 21 0 +# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%] +BCC1 1 50.00 0.00 0.00 50.00 0.00 +BCC1 2 0.00 50.00 50.00 0.00 0.00 +BCC1 3 0.00 50.00 50.00 0.00 0.00 +BCC1 4 50.00 0.00 0.00 50.00 0.00 +# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. +QTQ1 1 +QTQ1 2 +QTQ1 3 +QTQ1 4 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
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| diff -r 145f6d74ff5e -r e28839a4b932 test-data/11.stats.g4.expected --- a/test-data/11.stats.g4.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/11.stats.g4.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats -g 4 -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK cb2d2d82 bcd83869 62ec814e # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 26 +SN raw total sequences: 26 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 26 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 1 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 260 # ignores clipping SN total first fragment length: 140 # ignores clipping SN total last fragment length: 120 # ignores clipping @@ -89,6 +93,17 @@ GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 26.92 26.92 30.77 15.38 +GCT 2 7.69 38.46 26.92 26.92 +GCT 3 26.92 26.92 30.77 15.38 +GCT 4 11.54 34.62 26.92 26.92 +GCT 5 23.08 26.92 38.46 11.54 +GCT 6 11.54 34.62 23.08 30.77 +GCT 7 19.23 23.08 38.46 19.23 +GCT 8 11.54 38.46 23.08 26.92 +GCT 9 23.08 19.23 34.62 23.08 +GCT 10 11.54 34.62 26.92 26.92 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 @@ -100,6 +115,8 @@ FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 24 43 45 28 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 @@ -111,6 +128,19 @@ LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 30 33 36 21 0 +# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%] +BCC1 1 50.00 0.00 0.00 50.00 0.00 +BCC1 2 0.00 50.00 50.00 0.00 0.00 +BCC1 3 0.00 50.00 50.00 0.00 0.00 +BCC1 4 50.00 0.00 0.00 50.00 0.00 +# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. +QTQ1 1 +QTQ1 2 +QTQ1 3 +QTQ1 4 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/12.2reads.nooverlap.expected --- a/test-data/12.2reads.nooverlap.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/12.2reads.nooverlap.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats -t /tmp/tmp0r5zs075/files/b/2/1/dataset_b2175431-044e-449d-8f60-1bfd33679b61.dat -p -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 5b31676a b0edee94 471895da # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 2 +SN raw total sequences: 2 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 2 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 200 # ignores clipping SN total first fragment length: 100 # ignores clipping SN total last fragment length: 100 # ignores clipping @@ -353,6 +357,107 @@ GCC 98 50.00 50.00 0.00 0.00 0.00 0.00 GCC 99 50.00 50.00 0.00 0.00 0.00 0.00 GCC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 50.00 0.00 50.00 0.00 +GCT 2 0.00 50.00 50.00 0.00 +GCT 3 0.00 50.00 0.00 50.00 +GCT 4 0.00 50.00 50.00 0.00 +GCT 5 0.00 0.00 50.00 50.00 +GCT 6 0.00 0.00 50.00 50.00 +GCT 7 0.00 50.00 0.00 50.00 +GCT 8 0.00 0.00 50.00 50.00 +GCT 9 0.00 50.00 0.00 50.00 +GCT 10 50.00 0.00 50.00 0.00 +GCT 11 0.00 0.00 100.00 0.00 +GCT 12 50.00 0.00 0.00 50.00 +GCT 13 0.00 50.00 50.00 0.00 +GCT 14 50.00 0.00 0.00 50.00 +GCT 15 0.00 0.00 50.00 50.00 +GCT 16 0.00 50.00 50.00 0.00 +GCT 17 0.00 50.00 0.00 50.00 +GCT 18 100.00 0.00 0.00 0.00 +GCT 19 50.00 0.00 0.00 50.00 +GCT 20 0.00 50.00 50.00 0.00 +GCT 21 50.00 0.00 0.00 50.00 +GCT 22 0.00 50.00 0.00 50.00 +GCT 23 0.00 0.00 0.00 100.00 +GCT 24 0.00 50.00 50.00 0.00 +GCT 25 0.00 0.00 0.00 100.00 +GCT 26 0.00 0.00 50.00 50.00 +GCT 27 0.00 100.00 0.00 0.00 +GCT 28 0.00 0.00 0.00 100.00 +GCT 29 50.00 0.00 50.00 0.00 +GCT 30 0.00 50.00 0.00 50.00 +GCT 31 0.00 50.00 0.00 50.00 +GCT 32 0.00 0.00 50.00 50.00 +GCT 33 0.00 50.00 0.00 50.00 +GCT 34 50.00 0.00 0.00 50.00 +GCT 35 0.00 50.00 0.00 50.00 +GCT 36 0.00 100.00 0.00 0.00 +GCT 37 0.00 50.00 0.00 50.00 +GCT 38 50.00 50.00 0.00 0.00 +GCT 39 100.00 0.00 0.00 0.00 +GCT 40 0.00 0.00 100.00 0.00 +GCT 41 0.00 50.00 0.00 50.00 +GCT 42 50.00 50.00 0.00 0.00 +GCT 43 0.00 0.00 50.00 50.00 +GCT 44 50.00 0.00 50.00 0.00 +GCT 45 50.00 0.00 50.00 0.00 +GCT 46 50.00 0.00 50.00 0.00 +GCT 47 50.00 0.00 50.00 0.00 +GCT 48 0.00 50.00 50.00 0.00 +GCT 49 50.00 0.00 0.00 50.00 +GCT 50 0.00 0.00 50.00 50.00 +GCT 51 0.00 0.00 100.00 0.00 +GCT 52 50.00 0.00 50.00 0.00 +GCT 53 0.00 50.00 0.00 50.00 +GCT 54 50.00 0.00 50.00 0.00 +GCT 55 50.00 0.00 0.00 50.00 +GCT 56 0.00 50.00 50.00 0.00 +GCT 57 100.00 0.00 0.00 0.00 +GCT 58 50.00 0.00 50.00 0.00 +GCT 59 100.00 0.00 0.00 0.00 +GCT 60 50.00 0.00 50.00 0.00 +GCT 61 0.00 0.00 0.00 100.00 +GCT 62 0.00 50.00 50.00 0.00 +GCT 63 50.00 0.00 0.00 50.00 +GCT 64 0.00 0.00 100.00 0.00 +GCT 65 50.00 50.00 0.00 0.00 +GCT 66 0.00 50.00 0.00 50.00 +GCT 67 0.00 0.00 0.00 100.00 +GCT 68 0.00 50.00 0.00 50.00 +GCT 69 0.00 50.00 0.00 50.00 +GCT 70 50.00 0.00 0.00 50.00 +GCT 71 0.00 0.00 0.00 100.00 +GCT 72 0.00 50.00 0.00 50.00 +GCT 73 0.00 0.00 0.00 100.00 +GCT 74 0.00 50.00 0.00 50.00 +GCT 75 50.00 0.00 0.00 50.00 +GCT 76 0.00 50.00 0.00 50.00 +GCT 77 50.00 0.00 0.00 50.00 +GCT 78 50.00 0.00 0.00 50.00 +GCT 79 50.00 0.00 0.00 50.00 +GCT 80 50.00 0.00 0.00 50.00 +GCT 81 50.00 0.00 0.00 50.00 +GCT 82 50.00 0.00 0.00 50.00 +GCT 83 50.00 0.00 0.00 50.00 +GCT 84 50.00 0.00 0.00 50.00 +GCT 85 50.00 0.00 0.00 50.00 +GCT 86 50.00 0.00 0.00 50.00 +GCT 87 50.00 0.00 0.00 50.00 +GCT 88 50.00 0.00 0.00 50.00 +GCT 89 50.00 0.00 0.00 50.00 +GCT 90 50.00 0.00 0.00 50.00 +GCT 91 50.00 0.00 50.00 0.00 +GCT 92 50.00 0.00 50.00 0.00 +GCT 93 50.00 0.00 50.00 0.00 +GCT 94 50.00 0.00 0.00 50.00 +GCT 95 50.00 0.00 50.00 0.00 +GCT 96 50.00 0.00 50.00 0.00 +GCT 97 50.00 0.00 50.00 0.00 +GCT 98 50.00 0.00 50.00 0.00 +GCT 99 50.00 0.00 50.00 0.00 +GCT 100 50.00 0.00 0.00 50.00 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -454,6 +559,8 @@ FBC 98 0.00 100.00 0.00 0.00 0.00 0.00 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 FBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 50 21 14 15 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 LBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -555,6 +662,26 @@ LBC 98 100.00 0.00 0.00 0.00 0.00 0.00 LBC 99 100.00 0.00 0.00 0.00 0.00 0.00 LBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 41 20 23 16 0 +# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%] +BCC1 2 0.00 0.00 100.00 0.00 0.00 +BCC1 3 0.00 0.00 0.00 100.00 0.00 +BCC1 4 0.00 100.00 0.00 0.00 0.00 +BCC1 5 0.00 0.00 0.00 100.00 0.00 +BCC1 6 100.00 0.00 0.00 0.00 0.00 +BCC1 7 0.00 0.00 0.00 100.00 0.00 +BCC1 8 0.00 100.00 0.00 0.00 0.00 +# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. +QTQ1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +QTQ1 2 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 +QTQ1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 +QTQ1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/12.2reads.overlap.expected --- a/test-data/12.2reads.overlap.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/12.2reads.overlap.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats -t /tmp/tmp0r5zs075/files/2/a/2/dataset_2a2a3ee9-3133-4880-a37c-50b6354c9000.dat -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 5b31676a b0edee94 471895da # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 2 +SN raw total sequences: 2 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 2 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 200 # ignores clipping SN total first fragment length: 100 # ignores clipping SN total last fragment length: 100 # ignores clipping @@ -353,6 +357,107 @@ GCC 98 50.00 50.00 0.00 0.00 0.00 0.00 GCC 99 50.00 50.00 0.00 0.00 0.00 0.00 GCC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 50.00 0.00 50.00 0.00 +GCT 2 0.00 50.00 50.00 0.00 +GCT 3 0.00 50.00 0.00 50.00 +GCT 4 0.00 50.00 50.00 0.00 +GCT 5 0.00 0.00 50.00 50.00 +GCT 6 0.00 0.00 50.00 50.00 +GCT 7 0.00 50.00 0.00 50.00 +GCT 8 0.00 0.00 50.00 50.00 +GCT 9 0.00 50.00 0.00 50.00 +GCT 10 50.00 0.00 50.00 0.00 +GCT 11 0.00 0.00 100.00 0.00 +GCT 12 50.00 0.00 0.00 50.00 +GCT 13 0.00 50.00 50.00 0.00 +GCT 14 50.00 0.00 0.00 50.00 +GCT 15 0.00 0.00 50.00 50.00 +GCT 16 0.00 50.00 50.00 0.00 +GCT 17 0.00 50.00 0.00 50.00 +GCT 18 100.00 0.00 0.00 0.00 +GCT 19 50.00 0.00 0.00 50.00 +GCT 20 0.00 50.00 50.00 0.00 +GCT 21 50.00 0.00 0.00 50.00 +GCT 22 0.00 50.00 0.00 50.00 +GCT 23 0.00 0.00 0.00 100.00 +GCT 24 0.00 50.00 50.00 0.00 +GCT 25 0.00 0.00 0.00 100.00 +GCT 26 0.00 0.00 50.00 50.00 +GCT 27 0.00 100.00 0.00 0.00 +GCT 28 0.00 0.00 0.00 100.00 +GCT 29 50.00 0.00 50.00 0.00 +GCT 30 0.00 50.00 0.00 50.00 +GCT 31 0.00 50.00 0.00 50.00 +GCT 32 0.00 0.00 50.00 50.00 +GCT 33 0.00 50.00 0.00 50.00 +GCT 34 50.00 0.00 0.00 50.00 +GCT 35 0.00 50.00 0.00 50.00 +GCT 36 0.00 100.00 0.00 0.00 +GCT 37 0.00 50.00 0.00 50.00 +GCT 38 50.00 50.00 0.00 0.00 +GCT 39 100.00 0.00 0.00 0.00 +GCT 40 0.00 0.00 100.00 0.00 +GCT 41 0.00 50.00 0.00 50.00 +GCT 42 50.00 50.00 0.00 0.00 +GCT 43 0.00 0.00 50.00 50.00 +GCT 44 50.00 0.00 50.00 0.00 +GCT 45 50.00 0.00 50.00 0.00 +GCT 46 50.00 0.00 50.00 0.00 +GCT 47 50.00 0.00 50.00 0.00 +GCT 48 0.00 50.00 50.00 0.00 +GCT 49 50.00 0.00 0.00 50.00 +GCT 50 0.00 0.00 50.00 50.00 +GCT 51 0.00 0.00 100.00 0.00 +GCT 52 50.00 0.00 50.00 0.00 +GCT 53 0.00 50.00 0.00 50.00 +GCT 54 50.00 0.00 50.00 0.00 +GCT 55 50.00 0.00 0.00 50.00 +GCT 56 0.00 50.00 50.00 0.00 +GCT 57 100.00 0.00 0.00 0.00 +GCT 58 50.00 0.00 50.00 0.00 +GCT 59 100.00 0.00 0.00 0.00 +GCT 60 50.00 0.00 50.00 0.00 +GCT 61 0.00 0.00 0.00 100.00 +GCT 62 0.00 50.00 50.00 0.00 +GCT 63 50.00 0.00 0.00 50.00 +GCT 64 0.00 0.00 100.00 0.00 +GCT 65 50.00 50.00 0.00 0.00 +GCT 66 0.00 50.00 0.00 50.00 +GCT 67 0.00 0.00 0.00 100.00 +GCT 68 0.00 50.00 0.00 50.00 +GCT 69 0.00 50.00 0.00 50.00 +GCT 70 50.00 0.00 0.00 50.00 +GCT 71 0.00 0.00 0.00 100.00 +GCT 72 0.00 50.00 0.00 50.00 +GCT 73 0.00 0.00 0.00 100.00 +GCT 74 0.00 50.00 0.00 50.00 +GCT 75 50.00 0.00 0.00 50.00 +GCT 76 0.00 50.00 0.00 50.00 +GCT 77 50.00 0.00 0.00 50.00 +GCT 78 50.00 0.00 0.00 50.00 +GCT 79 50.00 0.00 0.00 50.00 +GCT 80 50.00 0.00 0.00 50.00 +GCT 81 50.00 0.00 0.00 50.00 +GCT 82 50.00 0.00 0.00 50.00 +GCT 83 50.00 0.00 0.00 50.00 +GCT 84 50.00 0.00 0.00 50.00 +GCT 85 50.00 0.00 0.00 50.00 +GCT 86 50.00 0.00 0.00 50.00 +GCT 87 50.00 0.00 0.00 50.00 +GCT 88 50.00 0.00 0.00 50.00 +GCT 89 50.00 0.00 0.00 50.00 +GCT 90 50.00 0.00 0.00 50.00 +GCT 91 50.00 0.00 50.00 0.00 +GCT 92 50.00 0.00 50.00 0.00 +GCT 93 50.00 0.00 50.00 0.00 +GCT 94 50.00 0.00 0.00 50.00 +GCT 95 50.00 0.00 50.00 0.00 +GCT 96 50.00 0.00 50.00 0.00 +GCT 97 50.00 0.00 50.00 0.00 +GCT 98 50.00 0.00 50.00 0.00 +GCT 99 50.00 0.00 50.00 0.00 +GCT 100 50.00 0.00 0.00 50.00 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -454,6 +559,8 @@ FBC 98 0.00 100.00 0.00 0.00 0.00 0.00 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 FBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 50 21 14 15 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 LBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -555,6 +662,26 @@ LBC 98 100.00 0.00 0.00 0.00 0.00 0.00 LBC 99 100.00 0.00 0.00 0.00 0.00 0.00 LBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 41 20 23 16 0 +# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%] +BCC1 2 0.00 0.00 100.00 0.00 0.00 +BCC1 3 0.00 0.00 0.00 100.00 0.00 +BCC1 4 0.00 100.00 0.00 0.00 0.00 +BCC1 5 0.00 0.00 0.00 100.00 0.00 +BCC1 6 100.00 0.00 0.00 0.00 0.00 +BCC1 7 0.00 0.00 0.00 100.00 0.00 +BCC1 8 0.00 100.00 0.00 0.00 0.00 +# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. +QTQ1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +QTQ1 2 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 +QTQ1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 +QTQ1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/12.3reads.nooverlap.expected --- a/test-data/12.3reads.nooverlap.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/12.3reads.nooverlap.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats -t /tmp/tmp0r5zs075/files/1/3/0/dataset_13082855-efe1-437e-8a91-ff7d013770db.dat -p -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 09f8b87f 140798ec 2b989f07 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 3 +SN raw total sequences: 3 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 3 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 300 # ignores clipping SN total first fragment length: 100 # ignores clipping SN total last fragment length: 200 # ignores clipping @@ -355,6 +359,107 @@ GCC 98 0.00 66.67 0.00 33.33 0.00 0.00 GCC 99 0.00 100.00 0.00 0.00 0.00 0.00 GCC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 33.33 0.00 0.00 66.67 +GCT 2 0.00 33.33 33.33 33.33 +GCT 3 0.00 33.33 33.33 33.33 +GCT 4 33.33 66.67 0.00 0.00 +GCT 5 0.00 66.67 33.33 0.00 +GCT 6 33.33 0.00 0.00 66.67 +GCT 7 33.33 0.00 0.00 66.67 +GCT 8 0.00 33.33 33.33 33.33 +GCT 9 0.00 66.67 33.33 0.00 +GCT 10 33.33 33.33 0.00 33.33 +GCT 11 33.33 33.33 0.00 33.33 +GCT 12 0.00 33.33 33.33 33.33 +GCT 13 0.00 0.00 33.33 66.67 +GCT 14 0.00 66.67 33.33 0.00 +GCT 15 33.33 66.67 0.00 0.00 +GCT 16 33.33 0.00 0.00 66.67 +GCT 17 33.33 0.00 0.00 66.67 +GCT 18 0.00 33.33 33.33 33.33 +GCT 19 0.00 33.33 33.33 33.33 +GCT 20 0.00 66.67 33.33 0.00 +GCT 21 33.33 66.67 0.00 0.00 +GCT 22 33.33 0.00 0.00 66.67 +GCT 23 0.00 0.00 33.33 66.67 +GCT 24 0.00 33.33 33.33 33.33 +GCT 25 33.33 66.67 0.00 0.00 +GCT 26 33.33 33.33 0.00 33.33 +GCT 27 0.00 33.33 33.33 33.33 +GCT 28 0.00 33.33 33.33 33.33 +GCT 29 0.00 0.00 33.33 66.67 +GCT 30 33.33 66.67 0.00 0.00 +GCT 31 33.33 66.67 0.00 0.00 +GCT 32 33.33 0.00 0.00 66.67 +GCT 33 0.00 0.00 33.33 66.67 +GCT 34 0.00 33.33 33.33 33.33 +GCT 35 33.33 33.33 0.00 33.33 +GCT 36 0.00 66.67 33.33 0.00 +GCT 37 33.33 66.67 0.00 0.00 +GCT 38 33.33 0.00 0.00 66.67 +GCT 39 0.00 0.00 33.33 66.67 +GCT 40 0.00 33.33 33.33 33.33 +GCT 41 33.33 66.67 0.00 0.00 +GCT 42 33.33 33.33 0.00 33.33 +GCT 43 0.00 33.33 33.33 33.33 +GCT 44 0.00 33.33 33.33 33.33 +GCT 45 0.00 33.33 33.33 33.33 +GCT 46 33.33 66.67 0.00 0.00 +GCT 47 33.33 33.33 0.00 33.33 +GCT 48 33.33 0.00 0.00 66.67 +GCT 49 0.00 0.00 33.33 66.67 +GCT 50 0.00 66.67 33.33 0.00 +GCT 51 33.33 66.67 0.00 0.00 +GCT 52 0.00 66.67 33.33 0.00 +GCT 53 33.33 0.00 0.00 66.67 +GCT 54 33.33 0.00 0.00 66.67 +GCT 55 0.00 33.33 33.33 33.33 +GCT 56 0.00 66.67 33.33 0.00 +GCT 57 33.33 33.33 0.00 33.33 +GCT 58 33.33 33.33 0.00 33.33 +GCT 59 0.00 33.33 33.33 33.33 +GCT 60 0.00 0.00 33.33 66.67 +GCT 61 0.00 66.67 33.33 0.00 +GCT 62 33.33 66.67 0.00 0.00 +GCT 63 33.33 0.00 0.00 66.67 +GCT 64 33.33 0.00 0.00 66.67 +GCT 65 0.00 33.33 33.33 33.33 +GCT 66 0.00 33.33 33.33 33.33 +GCT 67 33.33 66.67 0.00 0.00 +GCT 68 0.00 66.67 33.33 0.00 +GCT 69 33.33 0.00 0.00 66.67 +GCT 70 33.33 0.00 0.00 66.67 +GCT 71 0.00 33.33 33.33 33.33 +GCT 72 0.00 66.67 33.33 0.00 +GCT 73 33.33 33.33 0.00 33.33 +GCT 74 33.33 33.33 0.00 33.33 +GCT 75 0.00 33.33 33.33 33.33 +GCT 76 0.00 0.00 33.33 66.67 +GCT 77 0.00 66.67 33.33 0.00 +GCT 78 33.33 66.67 0.00 0.00 +GCT 79 33.33 0.00 0.00 66.67 +GCT 80 33.33 0.00 0.00 66.67 +GCT 81 0.00 33.33 33.33 33.33 +GCT 82 0.00 66.67 33.33 0.00 +GCT 83 0.00 66.67 33.33 0.00 +GCT 84 33.33 33.33 0.00 33.33 +GCT 85 33.33 0.00 0.00 66.67 +GCT 86 0.00 0.00 33.33 66.67 +GCT 87 0.00 66.67 33.33 0.00 +GCT 88 33.33 66.67 0.00 0.00 +GCT 89 33.33 33.33 0.00 33.33 +GCT 90 0.00 0.00 33.33 66.67 +GCT 91 0.00 33.33 33.33 33.33 +GCT 92 0.00 66.67 33.33 0.00 +GCT 93 33.33 66.67 0.00 0.00 +GCT 94 33.33 33.33 0.00 33.33 +GCT 95 33.33 0.00 0.00 66.67 +GCT 96 0.00 33.33 33.33 33.33 +GCT 97 33.33 0.00 33.33 33.33 +GCT 98 33.33 66.67 0.00 0.00 +GCT 99 0.00 66.67 33.33 0.00 +GCT 100 33.33 0.00 0.00 66.67 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 100.00 0.00 0.00 0.00 0.00 @@ -456,6 +561,8 @@ FBC 98 0.00 0.00 0.00 100.00 0.00 0.00 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 FBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 0 51 0 49 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 0.00 0.00 0.00 100.00 0.00 0.00 LBC 2 0.00 50.00 0.00 50.00 0.00 0.00 @@ -557,6 +664,26 @@ LBC 98 0.00 100.00 0.00 0.00 0.00 0.00 LBC 99 0.00 100.00 0.00 0.00 0.00 0.00 LBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 1 102 0 97 0 +# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%] +BCC1 2 0.00 0.00 100.00 0.00 0.00 +BCC1 3 0.00 0.00 0.00 100.00 0.00 +BCC1 4 0.00 100.00 0.00 0.00 0.00 +BCC1 5 0.00 0.00 0.00 100.00 0.00 +BCC1 6 100.00 0.00 0.00 0.00 0.00 +BCC1 7 0.00 0.00 0.00 100.00 0.00 +BCC1 8 0.00 100.00 0.00 0.00 0.00 +# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. +QTQ1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +QTQ1 2 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 +QTQ1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 +QTQ1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/12.3reads.overlap.expected --- a/test-data/12.3reads.overlap.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/12.3reads.overlap.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats -t /tmp/tmp0r5zs075/files/6/5/e/dataset_65ea4e4d-a70d-4001-911d-9d81ff2829a6.dat -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 09f8b87f 140798ec 2b989f07 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 3 +SN raw total sequences: 3 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 3 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 300 # ignores clipping SN total first fragment length: 100 # ignores clipping SN total last fragment length: 200 # ignores clipping @@ -355,6 +359,107 @@ GCC 98 0.00 66.67 0.00 33.33 0.00 0.00 GCC 99 0.00 100.00 0.00 0.00 0.00 0.00 GCC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 33.33 0.00 0.00 66.67 +GCT 2 0.00 33.33 33.33 33.33 +GCT 3 0.00 33.33 33.33 33.33 +GCT 4 33.33 66.67 0.00 0.00 +GCT 5 0.00 66.67 33.33 0.00 +GCT 6 33.33 0.00 0.00 66.67 +GCT 7 33.33 0.00 0.00 66.67 +GCT 8 0.00 33.33 33.33 33.33 +GCT 9 0.00 66.67 33.33 0.00 +GCT 10 33.33 33.33 0.00 33.33 +GCT 11 33.33 33.33 0.00 33.33 +GCT 12 0.00 33.33 33.33 33.33 +GCT 13 0.00 0.00 33.33 66.67 +GCT 14 0.00 66.67 33.33 0.00 +GCT 15 33.33 66.67 0.00 0.00 +GCT 16 33.33 0.00 0.00 66.67 +GCT 17 33.33 0.00 0.00 66.67 +GCT 18 0.00 33.33 33.33 33.33 +GCT 19 0.00 33.33 33.33 33.33 +GCT 20 0.00 66.67 33.33 0.00 +GCT 21 33.33 66.67 0.00 0.00 +GCT 22 33.33 0.00 0.00 66.67 +GCT 23 0.00 0.00 33.33 66.67 +GCT 24 0.00 33.33 33.33 33.33 +GCT 25 33.33 66.67 0.00 0.00 +GCT 26 33.33 33.33 0.00 33.33 +GCT 27 0.00 33.33 33.33 33.33 +GCT 28 0.00 33.33 33.33 33.33 +GCT 29 0.00 0.00 33.33 66.67 +GCT 30 33.33 66.67 0.00 0.00 +GCT 31 33.33 66.67 0.00 0.00 +GCT 32 33.33 0.00 0.00 66.67 +GCT 33 0.00 0.00 33.33 66.67 +GCT 34 0.00 33.33 33.33 33.33 +GCT 35 33.33 33.33 0.00 33.33 +GCT 36 0.00 66.67 33.33 0.00 +GCT 37 33.33 66.67 0.00 0.00 +GCT 38 33.33 0.00 0.00 66.67 +GCT 39 0.00 0.00 33.33 66.67 +GCT 40 0.00 33.33 33.33 33.33 +GCT 41 33.33 66.67 0.00 0.00 +GCT 42 33.33 33.33 0.00 33.33 +GCT 43 0.00 33.33 33.33 33.33 +GCT 44 0.00 33.33 33.33 33.33 +GCT 45 0.00 33.33 33.33 33.33 +GCT 46 33.33 66.67 0.00 0.00 +GCT 47 33.33 33.33 0.00 33.33 +GCT 48 33.33 0.00 0.00 66.67 +GCT 49 0.00 0.00 33.33 66.67 +GCT 50 0.00 66.67 33.33 0.00 +GCT 51 33.33 66.67 0.00 0.00 +GCT 52 0.00 66.67 33.33 0.00 +GCT 53 33.33 0.00 0.00 66.67 +GCT 54 33.33 0.00 0.00 66.67 +GCT 55 0.00 33.33 33.33 33.33 +GCT 56 0.00 66.67 33.33 0.00 +GCT 57 33.33 33.33 0.00 33.33 +GCT 58 33.33 33.33 0.00 33.33 +GCT 59 0.00 33.33 33.33 33.33 +GCT 60 0.00 0.00 33.33 66.67 +GCT 61 0.00 66.67 33.33 0.00 +GCT 62 33.33 66.67 0.00 0.00 +GCT 63 33.33 0.00 0.00 66.67 +GCT 64 33.33 0.00 0.00 66.67 +GCT 65 0.00 33.33 33.33 33.33 +GCT 66 0.00 33.33 33.33 33.33 +GCT 67 33.33 66.67 0.00 0.00 +GCT 68 0.00 66.67 33.33 0.00 +GCT 69 33.33 0.00 0.00 66.67 +GCT 70 33.33 0.00 0.00 66.67 +GCT 71 0.00 33.33 33.33 33.33 +GCT 72 0.00 66.67 33.33 0.00 +GCT 73 33.33 33.33 0.00 33.33 +GCT 74 33.33 33.33 0.00 33.33 +GCT 75 0.00 33.33 33.33 33.33 +GCT 76 0.00 0.00 33.33 66.67 +GCT 77 0.00 66.67 33.33 0.00 +GCT 78 33.33 66.67 0.00 0.00 +GCT 79 33.33 0.00 0.00 66.67 +GCT 80 33.33 0.00 0.00 66.67 +GCT 81 0.00 33.33 33.33 33.33 +GCT 82 0.00 66.67 33.33 0.00 +GCT 83 0.00 66.67 33.33 0.00 +GCT 84 33.33 33.33 0.00 33.33 +GCT 85 33.33 0.00 0.00 66.67 +GCT 86 0.00 0.00 33.33 66.67 +GCT 87 0.00 66.67 33.33 0.00 +GCT 88 33.33 66.67 0.00 0.00 +GCT 89 33.33 33.33 0.00 33.33 +GCT 90 0.00 0.00 33.33 66.67 +GCT 91 0.00 33.33 33.33 33.33 +GCT 92 0.00 66.67 33.33 0.00 +GCT 93 33.33 66.67 0.00 0.00 +GCT 94 33.33 33.33 0.00 33.33 +GCT 95 33.33 0.00 0.00 66.67 +GCT 96 0.00 33.33 33.33 33.33 +GCT 97 33.33 0.00 33.33 33.33 +GCT 98 33.33 66.67 0.00 0.00 +GCT 99 0.00 66.67 33.33 0.00 +GCT 100 33.33 0.00 0.00 66.67 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 100.00 0.00 0.00 0.00 0.00 @@ -456,6 +561,8 @@ FBC 98 0.00 0.00 0.00 100.00 0.00 0.00 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 FBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 0 51 0 49 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 0.00 0.00 0.00 100.00 0.00 0.00 LBC 2 0.00 50.00 0.00 50.00 0.00 0.00 @@ -557,6 +664,26 @@ LBC 98 0.00 100.00 0.00 0.00 0.00 0.00 LBC 99 0.00 100.00 0.00 0.00 0.00 0.00 LBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 1 102 0 97 0 +# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%] +BCC1 2 0.00 0.00 100.00 0.00 0.00 +BCC1 3 0.00 0.00 0.00 100.00 0.00 +BCC1 4 0.00 100.00 0.00 0.00 0.00 +BCC1 5 0.00 0.00 0.00 100.00 0.00 +BCC1 6 100.00 0.00 0.00 0.00 0.00 +BCC1 7 0.00 0.00 0.00 100.00 0.00 +BCC1 8 0.00 100.00 0.00 0.00 0.00 +# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. +QTQ1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +QTQ1 2 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 +QTQ1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 +QTQ1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/2.stats.expected --- a/test-data/2.stats.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/2.stats.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats --ref-seq reference.fa -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 1a1c1362 29c426ae 7bab45da # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 2 +SN raw total sequences: 2 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 2 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 70 # ignores clipping SN total first fragment length: 35 # ignores clipping SN total last fragment length: 35 # ignores clipping @@ -195,6 +199,42 @@ GCC 33 50.00 0.00 0.00 50.00 0.00 0.00 GCC 34 50.00 0.00 50.00 0.00 0.00 0.00 GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 0.00 50.00 0.00 50.00 +GCT 2 50.00 0.00 50.00 0.00 +GCT 3 0.00 0.00 50.00 50.00 +GCT 4 0.00 0.00 100.00 0.00 +GCT 5 0.00 0.00 50.00 50.00 +GCT 6 0.00 50.00 0.00 50.00 +GCT 7 0.00 0.00 50.00 50.00 +GCT 8 0.00 0.00 0.00 100.00 +GCT 9 0.00 50.00 50.00 0.00 +GCT 10 50.00 0.00 50.00 0.00 +GCT 11 50.00 0.00 0.00 50.00 +GCT 12 50.00 0.00 50.00 0.00 +GCT 13 50.00 0.00 50.00 0.00 +GCT 14 0.00 0.00 0.00 100.00 +GCT 15 100.00 0.00 0.00 0.00 +GCT 16 50.00 0.00 0.00 50.00 +GCT 17 0.00 0.00 50.00 50.00 +GCT 18 0.00 50.00 50.00 0.00 +GCT 19 0.00 100.00 0.00 0.00 +GCT 20 0.00 0.00 50.00 50.00 +GCT 21 0.00 0.00 100.00 0.00 +GCT 22 0.00 50.00 0.00 50.00 +GCT 23 50.00 0.00 0.00 50.00 +GCT 24 50.00 0.00 50.00 0.00 +GCT 25 50.00 0.00 50.00 0.00 +GCT 26 0.00 0.00 100.00 0.00 +GCT 27 50.00 0.00 0.00 50.00 +GCT 28 0.00 0.00 50.00 50.00 +GCT 29 0.00 50.00 0.00 50.00 +GCT 30 0.00 50.00 0.00 50.00 +GCT 31 0.00 50.00 50.00 0.00 +GCT 32 0.00 0.00 100.00 0.00 +GCT 33 100.00 0.00 0.00 0.00 +GCT 34 0.00 0.00 50.00 50.00 +GCT 35 50.00 0.00 50.00 0.00 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -231,6 +271,8 @@ FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 FBC 34 0.00 0.00 100.00 0.00 0.00 0.00 FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 6 5 15 9 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 LBC 2 0.00 0.00 0.00 100.00 0.00 0.00 @@ -267,6 +309,8 @@ LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 11 10 5 9 0 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/6.stats.expected --- a/test-data/6.stats.expected Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/6.stats.expected Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats --insert-size 0 --ref-seq reference.fa -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 1a1c1362 32507d92 7bab45da # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 2 +SN raw total sequences: 2 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 2 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 70 # ignores clipping SN total first fragment length: 35 # ignores clipping SN total last fragment length: 35 # ignores clipping @@ -195,6 +199,42 @@ GCC 33 0.00 0.00 50.00 50.00 0.00 0.00 GCC 34 100.00 0.00 0.00 0.00 0.00 0.00 GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%] +GCT 1 0.00 50.00 0.00 50.00 +GCT 2 50.00 0.00 50.00 0.00 +GCT 3 0.00 0.00 50.00 50.00 +GCT 4 0.00 0.00 100.00 0.00 +GCT 5 0.00 0.00 50.00 50.00 +GCT 6 0.00 50.00 50.00 0.00 +GCT 7 0.00 0.00 0.00 100.00 +GCT 8 0.00 0.00 50.00 50.00 +GCT 9 0.00 0.00 50.00 50.00 +GCT 10 0.00 50.00 50.00 0.00 +GCT 11 100.00 0.00 0.00 0.00 +GCT 12 0.00 0.00 50.00 50.00 +GCT 13 100.00 0.00 0.00 0.00 +GCT 14 0.00 0.00 50.00 50.00 +GCT 15 50.00 0.00 0.00 50.00 +GCT 16 50.00 0.00 0.00 50.00 +GCT 17 50.00 0.00 50.00 0.00 +GCT 18 0.00 0.00 50.00 50.00 +GCT 19 0.00 100.00 0.00 0.00 +GCT 20 0.00 50.00 0.00 50.00 +GCT 21 0.00 0.00 100.00 0.00 +GCT 22 0.00 50.00 50.00 0.00 +GCT 23 50.00 0.00 0.00 50.00 +GCT 24 50.00 0.00 0.00 50.00 +GCT 25 50.00 0.00 50.00 0.00 +GCT 26 0.00 0.00 100.00 0.00 +GCT 27 0.00 0.00 50.00 50.00 +GCT 28 50.00 0.00 0.00 50.00 +GCT 29 0.00 50.00 50.00 0.00 +GCT 30 0.00 0.00 0.00 100.00 +GCT 31 0.00 50.00 50.00 0.00 +GCT 32 0.00 50.00 50.00 0.00 +GCT 33 50.00 0.00 50.00 0.00 +GCT 34 50.00 0.00 0.00 50.00 +GCT 35 50.00 0.00 50.00 0.00 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -231,6 +271,8 @@ FBC 33 0.00 0.00 100.00 0.00 0.00 0.00 FBC 34 100.00 0.00 0.00 0.00 0.00 0.00 FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 6 5 15 9 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%] LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 LBC 2 0.00 0.00 0.00 100.00 0.00 0.00 @@ -267,6 +309,8 @@ LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 11 10 5 9 0 # 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 IS 0 0 0 0 0 IS 1 0 0 0 0 |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/samtools_stats_out1.tab --- a/test-data/samtools_stats_out1.tab Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/samtools_stats_out1.tab Tue Sep 28 16:17:39 2021 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-# This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats\n+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats\n # This file contains statistics for all reads.\n-# The command line was: stats --ref-seq reference.fa infile\n+# The command line was: stats --ref-seq reference.fa -@ 0 infile\n # CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n CHK\t1bd20fd8\t58ad2167\t29883386\n # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n-SN\traw total sequences:\t200\n+SN\traw total sequences:\t200\t# excluding supplementary and secondary reads\n SN\tfiltered sequences:\t0\n SN\tsequences:\t200\n SN\tis sorted:\t1\n@@ -20,6 +20,7 @@\n SN\treads MQ0:\t6\t# mapped and MQ=0\n SN\treads QC failed:\t0\n SN\tnon-primary alignments:\t0\n+SN\tsupplementary alignments:\t0\n SN\ttotal length:\t50200\t# ignores clipping\n SN\ttotal first fragment length:\t25100\t# ignores clipping\n SN\ttotal last fragment length:\t25100\t# ignores clipping\n@@ -1094,6 +1095,258 @@\n GCC\t249\t25.00\t23.00\t21.00\t31.00\t0.00\t0.00\n GCC\t250\t27.50\t22.50\t17.50\t32.50\t0.00\t0.00\n GCC\t251\t13.50\t20.50\t36.50\t29.50\t0.00\t0.00\n+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]\n+GCT\t1\t22.45\t32.65\t31.63\t13.27\n+GCT\t2\t26.00\t17.00\t10.00\t47.00\n+GCT\t3\t34.00\t25.00\t9.00\t32.00\n+GCT\t4\t13.00\t32.00\t10.00\t45.00\n+GCT\t5\t37.00\t24.00\t10.00\t29.00\n+GCT\t6\t44.00\t26.00\t17.00\t13.00\n+GCT\t7\t28.00\t13.00\t32.00\t27.00\n+GCT\t8\t49.00\t16.00\t18.00\t17.00\n+GCT\t9\t19.00\t35.00\t16.00\t30.00\n+GCT\t10\t35.00\t13.00\t22.00\t30.00\n+GCT\t11\t18.00\t15.00\t29.00\t38.00\n+GCT\t12\t28.00\t24.00\t22.00\t26.00\n+GCT\t13\t29.00\t17.00\t19.00\t35.00\n+GCT\t14\t21.21\t24.24\t24.24\t30.30\n+GCT\t15\t23.00\t20.00\t25.00\t32.00\n+GCT\t16\t35.00\t15.00\t20.00\t30.00\n+GCT\t17\t29.00\t26.00\t13.00\t32.00\n+GCT\t18\t31.00\t30.00\t18.00\t21.00\n+GCT\t19\t30.00\t26.00\t21.00\t23.00\n+GCT\t20\t23.00\t21.00\t20.00\t36.00\n+GCT\t21\t36.00\t18.00\t19.00\t27.00\n+GCT\t22\t39.00\t31.00\t13.00\t17.00\n+GCT\t23\t30.30\t21.21\t11.11\t37.37\n+GCT\t24\t36.00\t14.00\t20.00\t30.00\n+GCT\t25\t38.00\t23.00\t17.00\t22.00\n+GCT\t26\t36.00\t21.00\t13.00\t30.00\n+GCT\t27\t32.00\t18.00\t22.00\t28.00\n+GCT\t28\t30.00\t13.00\t25.00\t32.00\n+GCT\t29\t30.00\t28.00\t23.00\t19.00\n+GCT\t30\t34.00\t21.00\t13.00\t32.00\n+GCT\t31\t33.00\t29.00\t14.00\t24.00\n+GCT\t32\t38.00\t20.00\t20.00\t22.00\n+GCT\t33\t27.00\t23.00\t15.00\t35.00\n+GCT\t34\t43.00\t17.00\t20.00\t20.00\n+GCT\t35\t35.00\t23.00\t22.00\t20.00\n+GCT\t36\t41.00\t25.00\t16.00\t18.00\n+GCT\t37\t38.00\t18.00\t18.00\t26.00\n+GCT\t38\t23.00\t26.00\t25.00\t26.00\n+GCT\t39\t22.00\t41.00\t19.00\t18.00\n+GCT\t40\t29.00\t14.00\t23.00\t34.00\n+GCT\t41\t29.00\t27.00\t20.00\t24.00\n+GCT\t42\t29.00\t27.00\t18.00\t26.00\n+GCT\t43\t38.00\t28.00\t16.00\t18.00\n+GCT\t44\t21.00\t26.00\t23.00\t30.00\n+GCT\t45\t38.00\t25.00\t18.00\t19.00\n+GCT\t46\t27.00\t21.00\t22.00\t30.00\n+GCT\t47\t40.00\t28.00\t18.00\t14.00\n+GCT\t48\t25.00\t22.00\t20.00\t33.00\n+GCT\t49\t26.00\t33.00\t10.00\t31.00\n+GCT\t50\t49.00\t20.00\t10.00\t21.00\n+GCT\t51\t29.00\t29.00\t13.00\t29.00\n+GCT\t52\t43.00\t22.00\t22.00\t13.00\n+GCT\t53\t19.00\t27.00\t27.00\t27.00\n+GCT\t54\t25.00\t18.00\t25.00\t32.00\n+GCT\t55\t32.00\t22.00\t17.00\t29.00\n+GCT\t56\t36.00\t20.00\t16.00\t28.00\n+GCT\t57\t28.00\t24.00\t23.00\t25.00\n+GCT\t58\t23.00\t39.00\t17.00\t21.00\n+GCT\t59\t33.00\t21.00\t26.00\t20.00\n+GCT\t60\t30.00\t26.00\t19.00\t25.00\n+GCT\t61\t23.00\t23.00\t25.00\t29.00\n+GCT\t62\t35.00\t19.00\t20.00\t26.00\n+GCT\t63\t26.00\t25.00\t29.00\t20.00\n+GCT\t64\t30.00\t20.00\t27.00\t23.00\n+GCT\t65\t38.00\t17.00\t21.00\t24.00\n+GCT\t66\t33.00\t26.00\t14.00\t27.00\n+GCT\t67\t35.00\t21.00\t21.00\t23.00\n+GCT\t68\t39.00\t28.00\t15.00\t18.00\n+GCT\t69\t38.00\t18.00\t22.00\t22.00\n+GCT\t70\t40.00\t13.00\t22.00\t25.00\n+GCT\t71\t29.00\t41.00\t19.00\t11.00\n+GCT\t72\t33.00\t26.00\t28.00\t13.00\n+GCT\t73\t31.00\t18.00\t24.00\t27.00\n+GCT\t74\t31.00\t32.00\t13.00\t24.00\n+GCT\t75\t46.00\t10.00\t21.00\t23.00\n+GCT\t76\t23.00\t28.00\t25.00\t24.00\n+GCT\t77\t35.00\t20.00\t19.00\t26.00\n+GCT\t78\t29.00\t30.00\t26.00\t15.00\n+GCT\t79\t24.00\t25.00\t27.00\t24.00\n+GCT\t80\t40.00\t18.00\t29.00\t13.00\n+GCT\t81\t18.00\t26.0'..b'.00\n+GCT\t178\t19.00\t26.00\t30.00\t25.00\n+GCT\t179\t24.00\t20.00\t20.00\t36.00\n+GCT\t180\t22.00\t25.00\t31.00\t22.00\n+GCT\t181\t21.00\t17.00\t38.00\t24.00\n+GCT\t182\t35.00\t21.00\t20.00\t24.00\n+GCT\t183\t28.00\t15.00\t27.00\t30.00\n+GCT\t184\t17.00\t30.00\t29.00\t24.00\n+GCT\t185\t16.00\t32.00\t33.00\t19.00\n+GCT\t186\t21.00\t22.00\t36.00\t21.00\n+GCT\t187\t24.00\t13.00\t41.00\t22.00\n+GCT\t188\t29.00\t19.00\t30.00\t22.00\n+GCT\t189\t19.00\t23.00\t33.00\t25.00\n+GCT\t190\t24.00\t28.00\t25.00\t23.00\n+GCT\t191\t28.00\t21.00\t29.00\t22.00\n+GCT\t192\t37.00\t25.00\t13.00\t25.00\n+GCT\t193\t18.00\t26.00\t25.00\t31.00\n+GCT\t194\t21.00\t34.00\t24.00\t21.00\n+GCT\t195\t16.00\t28.00\t21.00\t35.00\n+GCT\t196\t23.00\t23.00\t27.00\t27.00\n+GCT\t197\t18.00\t20.00\t24.00\t38.00\n+GCT\t198\t15.00\t19.00\t39.00\t27.00\n+GCT\t199\t23.00\t17.00\t27.00\t33.00\n+GCT\t200\t25.00\t27.00\t23.00\t25.00\n+GCT\t201\t26.00\t19.00\t25.00\t30.00\n+GCT\t202\t23.00\t23.00\t21.00\t33.00\n+GCT\t203\t21.00\t19.00\t32.00\t28.00\n+GCT\t204\t26.00\t29.00\t24.00\t21.00\n+GCT\t205\t16.00\t23.00\t21.00\t40.00\n+GCT\t206\t28.00\t25.00\t21.00\t26.00\n+GCT\t207\t22.00\t22.00\t19.00\t37.00\n+GCT\t208\t12.00\t32.00\t32.00\t24.00\n+GCT\t209\t18.00\t20.00\t15.00\t47.00\n+GCT\t210\t18.00\t15.00\t45.00\t22.00\n+GCT\t211\t28.00\t14.00\t28.00\t30.00\n+GCT\t212\t23.00\t27.00\t22.00\t28.00\n+GCT\t213\t22.00\t12.00\t34.00\t32.00\n+GCT\t214\t16.00\t24.00\t26.00\t34.00\n+GCT\t215\t28.00\t22.00\t25.00\t25.00\n+GCT\t216\t18.00\t17.00\t26.00\t39.00\n+GCT\t217\t27.00\t30.00\t16.00\t27.00\n+GCT\t218\t18.00\t24.00\t24.00\t34.00\n+GCT\t219\t19.00\t18.00\t24.00\t39.00\n+GCT\t220\t28.00\t23.00\t24.00\t25.00\n+GCT\t221\t20.00\t24.00\t20.00\t36.00\n+GCT\t222\t22.00\t21.00\t19.00\t38.00\n+GCT\t223\t19.00\t22.00\t33.00\t26.00\n+GCT\t224\t19.00\t20.00\t27.00\t34.00\n+GCT\t225\t14.00\t32.00\t34.00\t20.00\n+GCT\t226\t20.00\t20.00\t29.00\t31.00\n+GCT\t227\t17.00\t22.00\t26.00\t35.00\n+GCT\t228\t34.00\t20.00\t25.00\t21.00\n+GCT\t229\t22.00\t27.00\t16.00\t35.00\n+GCT\t230\t23.00\t33.00\t15.00\t29.00\n+GCT\t231\t20.00\t27.00\t31.00\t22.00\n+GCT\t232\t25.00\t23.00\t11.00\t41.00\n+GCT\t233\t22.00\t25.00\t27.00\t26.00\n+GCT\t234\t14.00\t27.00\t23.00\t36.00\n+GCT\t235\t17.00\t11.00\t32.00\t40.00\n+GCT\t236\t29.00\t20.00\t24.00\t27.00\n+GCT\t237\t16.00\t19.00\t23.00\t42.00\n+GCT\t238\t22.00\t25.00\t29.00\t24.00\n+GCT\t239\t18.00\t8.00\t17.00\t57.00\n+GCT\t240\t27.00\t26.00\t14.00\t33.00\n+GCT\t241\t21.00\t22.00\t17.00\t40.00\n+GCT\t242\t26.00\t28.00\t10.00\t36.00\n+GCT\t243\t25.00\t15.00\t24.00\t36.00\n+GCT\t244\t15.00\t24.00\t16.00\t45.00\n+GCT\t245\t24.00\t23.00\t19.00\t34.00\n+GCT\t246\t18.00\t25.00\t29.00\t28.00\n+GCT\t247\t30.00\t13.00\t14.00\t43.00\n+GCT\t248\t22.00\t17.00\t26.00\t35.00\n+GCT\t249\t25.00\t22.00\t22.00\t31.00\n+GCT\t250\t25.00\t20.00\t20.00\t35.00\n+GCT\t251\t13.00\t17.00\t40.00\t30.00\n # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]\n FBC\t1\t21.43\t27.55\t36.73\t14.29\t2.04\t0.00\n FBC\t2\t34.00\t15.00\t12.00\t39.00\t0.00\t0.00\n@@ -1346,6 +1599,8 @@\n FBC\t249\t25.00\t24.00\t20.00\t31.00\t0.00\t0.00\n FBC\t250\t30.00\t25.00\t15.00\t30.00\t0.00\t0.00\n FBC\t251\t14.00\t24.00\t33.00\t29.00\t0.00\t0.00\n+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n+FTC\t6178\t6247\t5821\t6841\t13\n # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]\n LBC\t1\t22.45\t32.65\t31.63\t13.27\t2.04\t0.00\n LBC\t2\t26.00\t17.00\t10.00\t47.00\t0.00\t0.00\n@@ -1598,6 +1853,8 @@\n LBC\t249\t25.00\t22.00\t22.00\t31.00\t0.00\t0.00\n LBC\t250\t25.00\t20.00\t20.00\t35.00\t0.00\t0.00\n LBC\t251\t13.00\t17.00\t40.00\t30.00\t0.00\t0.00\n+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n+LTC\t6413\t6102\t5966\t6606\t13\n # 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\n # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n RL\t251\t200\n' |
| b |
| diff -r 145f6d74ff5e -r e28839a4b932 test-data/samtools_stats_out1__sn.tab --- a/test-data/samtools_stats_out1__sn.tab Thu Oct 17 02:21:23 2019 -0400 +++ b/test-data/samtools_stats_out1__sn.tab Tue Sep 28 16:17:39 2021 +0000 |
| b |
| @@ -1,5 +1,5 @@ # Summary Numbers. -raw total sequences: 200 +raw total sequences: 200 # excluding supplementary and secondary reads filtered sequences: 0 sequences: 200 is sorted: 1 @@ -14,6 +14,7 @@ reads MQ0: 6 # mapped and MQ=0 reads QC failed: 0 non-primary alignments: 0 +supplementary alignments: 0 total length: 50200 # ignores clipping total first fragment length: 25100 # ignores clipping total last fragment length: 25100 # ignores clipping |