| Next changeset 1:595ae1ba934a (2021-09-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb |
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added:
macros.xml samtools_fixmate.xml test-data/2_isize_overflow.bam.expected test-data/2_isize_overflow.sam test-data/2_isize_overflow.sam.expected test-data/3_reverse_read_pp_lt.bam.expected test-data/3_reverse_read_pp_lt.sam test-data/3_reverse_read_pp_lt.sam.expected test-data/4_reverse_read_pp_equal.bam.expected test-data/4_reverse_read_pp_equal.sam test-data/4_reverse_read_pp_equal.sam.expected test-data/5_ct.bam.expected test-data/5_ct.sam test-data/5_ct.sam.expected test-data/6_ct_replace.bam.expected test-data/6_ct_replace.sam test-data/6_ct_replace.sam.expected test-data/7_two_read_mapped.bam.expected test-data/7_two_read_mapped.sam test-data/7_two_read_mapped.sam.expected |
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| diff -r 000000000000 -r bc0cc7bfbfe9 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 28 04:28:45 2018 -0400 |
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| b'@@ -0,0 +1,172 @@\n+<macros>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <token name="@TOOL_VERSION@">1.9</token>\n+ <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(\',\')))</token>\n+ <token name="@PREPARE_IDX@"><![CDATA[\n+ ##prepare input and indices \n+ ln -s \'$input\' infile &&\n+ #if $input.is_of_type(\'bam\'):\n+ #if str( $input.metadata.bam_index ) != "None":\n+ ln -s \'${input.metadata.bam_index}\' infile.bai &&\n+ #else:\n+ samtools index infile infile.bai &&\n+ #end if\n+ #elif $input.is_of_type(\'cram\'):\n+ #if str( $input.metadata.cram_index ) != "None":\n+ ln -s \'${input.metadata.cram_index}\' infile.crai &&\n+ #else:\n+ samtools index infile infile.crai &&\n+ #end if\n+ #end if\n+ ]]></token>\n+ <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[\n+ ##prepare input and indices \n+ #for $i, $bam in enumerate( $input_bams ):\n+ ln -s \'$bam\' \'${i}\' &&\n+ #if $bam.is_of_type(\'bam\'):\n+ #if str( $bam.metadata.bam_index ) != "None":\n+ ln -s \'${bam.metadata.bam_index}\' \'${i}.bai\' &&\n+ #else:\n+ samtools index \'${i}\' \'${i}.bai\' &&\n+ #end if\n+ #elif $bam.is_of_type(\'cram\'):\n+ #if str( $bam.metadata.cram_index ) != "None":\n+ ln -s \'${bam.metadata.cram_index}\' \'${i}.crai\' &&\n+ #else:\n+ samtools index \'${i}\' \'${i}.crai\' &&\n+ #end if\n+ #end if\n+ #end for\n+ ]]></token>\n+ <token name="@PREPARE_FASTA_IDX@"><![CDATA[\n+ ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")\n+ ##and sets the -t/-T parameters accordingly:\n+ ##- in case of history a symbolic link is used because samtools (view) will generate\n+ ## the index which might not be possible in the directory containing the fasta file\n+ ##- in case of cached the absolute path is used which allows to read the cram file\n+ ## without specifying the reference\n+ #if $addref_cond.addref_select == "history":\n+ ln -s \'${addref_cond.ref}\' reference.fa &&\n+ samtools faidx reference.fa &&\n+ #set reffa="reference.fa"\n+ #set reffai="reference.fa.fai"\n+ #elif $addref_cond.addref_select == "cached":\n+ #set reffa=str($addref_cond.ref.fields.path)\n+ #set reffai=str($addref_cond.ref.fields.path)+".fai"\n+ #else\n+ #set reffa=None\n+ #set reffai=None\n+ #end if\n+ ]]></token>\n+ <token name="@ADDTHREADS@"><![CDATA[\n+ ##compute the number of ADDITIONAL threads to be used by samtools (-@)\n+ addthreads=\\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&\n+ ]]></token>\n+ <token name="@ADDMEMORY@"><![CDATA[\n+ ##compute the number of memory available to samtools sort (-m)\n+ ##use only 75% of available: https://github.com/samtools/samtools/issues/831\n+ addmemory=\\${GALAXY_MEMORY_MB_PER_SLOT:-768} && \n+ ((addmemory=addmemory*75/100)) &&\n+ ]]></token>\n+ <xml name="seed_input">\n+ <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> \n+ </xml>\n+ <xml name="flag_options">\n+ <option value="1">read is paired</option>\n+ <option value="2">read is mapped in a proper pair</option>\n+ <option value="4">read is unmapped</option>\n+ <option value="8">mate is unmapped</option>\n+ <option value="16">read reverse strand</option>\n+ <option value="32">mate reverse strand</option>\n+ <option value="64">read is the'..b'on>\n+ <option value="1024">read is a PCR or optical duplicate</option>\n+ <option value="2048">supplementary alignment</option>\n+ </xml>\n+\n+ <!-- region specification macros and tokens for tools that allow the specification \n+ of region by bed file / space separated list of regions -->\n+ <token name="@REGIONS_FILE@"><![CDATA[\n+ #if $cond_region.select_region == \'tab\':\n+ -t \'$cond_region.targetregions\'\n+ #end if\n+ ]]></token>\n+ <token name="@REGIONS_MANUAL@"><![CDATA[\n+ #if $cond_region.select_region == \'text\':\n+ #for $i, $x in enumerate($cond_region.regions_repeat):\n+ \'${x.region}\'\n+ #end for\n+ #end if\n+ ]]></token>\n+ <xml name="regions_macro">\n+ <conditional name="cond_region">\n+ <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">\n+ <option value="no" selected="True">No</option>\n+ <option value="text">Manualy specify regions</option>\n+ <option value="tab">Regions from tabular file</option>\n+ </param>\n+ <when value="no"/>\n+ <when value="text">\n+ <repeat name="regions_repeat" min="1" default="1" title="Regions">\n+ <param name="region" type="text" label="region" help="format chr:from-to">\n+ <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\\s\'\\":]+(:\\d+(-\\d+){0,1}){0,1}$</validator>\n+ </param>\n+ </repeat>\n+ </when>\n+ <when value="tab">\n+ <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{SAM_def,\n+ title={Definition of SAM/BAM format},\n+ url = {https://samtools.github.io/hts-specs/},}\n+ </citation>\n+ <citation type="doi">10.1093/bioinformatics/btp352</citation>\n+ <citation type="doi">10.1093/bioinformatics/btr076</citation>\n+ <citation type="doi">10.1093/bioinformatics/btr509</citation>\n+ <citation type="bibtex">\n+ @misc{Danecek_et_al,\n+ Author={Danecek, P., Schiffels, S., Durbin, R.},\n+ title={Multiallelic calling model in bcftools (-m)},\n+ url = {http://samtools.github.io/bcftools/call-m.pdf},}\n+ </citation>\n+ <citation type="bibtex">\n+ @misc{Durbin_VCQC,\n+ Author={Durbin, R.},\n+ title={Segregation based metric for variant call QC},\n+ url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}\n+ </citation>\n+ <citation type="bibtex">\n+ @misc{Li_SamMath,\n+ Author={Li, H.},\n+ title={Mathematical Notes on SAMtools Algorithms},\n+ url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}\n+ </citation>\n+ <citation type="bibtex">\n+ @misc{SamTools_github,\n+ title={SAMTools GitHub page},\n+ url = {https://github.com/samtools/samtools},}\n+ </citation>\n+ </citations>\n+ </xml>\n+ <xml name="version_command">\n+ <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>\n+ </xml>\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Error" />\n+ </stdio>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r bc0cc7bfbfe9 samtools_fixmate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_fixmate.xml Fri Sep 28 04:28:45 2018 -0400 |
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| @@ -0,0 +1,86 @@ +<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@"> + <description>fill mate coordinates, ISIZE and mate related flags</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @ADDTHREADS@ + ## name sort input + #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): + samtools sort + -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp + -n + -O BAM + -o namesorted.bam + '$bamfile' && + #else: + ln -s '$bamfile' namesorted.bam && + #end if + + samtools fixmate + -@ \$addthreads + $remsec + $noprop + $tempcigar + $addms + -O BAM + namesorted.bam + '$output' + ]]></command> + <inputs> + <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." /> + <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" /> + <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" /> + <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" /> + <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." /> + </inputs> + <outputs> + <!--<data name="output" format="sam" />--> + <data name="output" format="qname_sorted.bam"/> + </outputs> + <tests> +<!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> +<!-- test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);--> +<test> + <param name="bamfile" value="2_isize_overflow.sam" /> + <output name="output" file="2_isize_overflow.bam.expected" /> +</test> +<!-- test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");--> +<test> + <param name="bamfile" value="3_reverse_read_pp_lt.sam" /> + <output name="output" file="3_reverse_read_pp_lt.bam.expected" /> +</test> +<!-- test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");--> +<test> + <param name="bamfile" value="4_reverse_read_pp_equal.sam" /> + <output name="output" file="4_reverse_read_pp_equal.bam.expected" /> +</test> +<!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");--> +<test> + <param name="bamfile" value="5_ct.sam" /> + <param name="tempcigar" value="-c" /> + <output name="output" file="5_ct.bam.expected" /> +</test> +<!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> +<test> + <param name="bamfile" value="6_ct_replace.sam" /> + <param name="tempcigar" value="-c" /> + <output name="output" file="6_ct_replace.bam.expected" /> +</test> +<!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");--> +<test> + <param name="bamfile" value="7_two_read_mapped.sam" /> + <output name="output" file="7_two_read_mapped.bam.expected" /> +</test> +<!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");--> + </tests> + <help> +**What it does** + +Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment. + </help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/2_isize_overflow.bam.expected |
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| Binary file test-data/2_isize_overflow.bam.expected has changed |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/2_isize_overflow.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_isize_overflow.sam Fri Sep 28 04:28:45 2018 -0400 |
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| @@ -0,0 +1,20 @@ +@HD VN:1.4 SO:queryname +@SQ SN:ref1 LN:45 +@SQ SN:ref2 LN:40 +of1 99 ref1 10 30 23M = 8 2 AAGTCGGCAGCGTCAGATGTGTA ??????????????????????? +of1 147 ref1 8 30 23M = 10 -2 CTGTCTCTTATACACATCTCCTT ??????????????????????? +r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * +r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 +r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 +r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * +r003 16 ref1 29 30 6H5M * 0 0 TAGGC * +r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * +r007 8 ref1 9 30 5H6M * 0 0 AGCTAA * +r007 4 ref1 9 30 * * 0 0 GGGGGG * +u1 4 * 0 30 * * 0 0 TAATTGGGTCTTCAGAGCACCTA ??????????????????????? +x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * +x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? +x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? +x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? +x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? +x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/2_isize_overflow.sam.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_isize_overflow.sam.expected Fri Sep 28 04:28:45 2018 -0400 |
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| @@ -0,0 +1,20 @@ +@HD VN:1.4 SO:queryname +@SQ SN:ref1 LN:45 +@SQ SN:ref2 LN:40 +of1 99 ref1 10 30 23M = 8 21 AAGTCGGCAGCGTCAGATGTGTA ??????????????????????? MQ:i:30 MC:Z:23M +of1 147 ref1 8 30 23M = 10 -21 CTGTCTCTTATACACATCTCCTT ??????????????????????? MQ:i:30 MC:Z:23M +r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * MQ:i:30 MC:Z:8M4I4M1D3M +r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 MQ:i:30 MC:Z:9M +r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 +r003 33 ref1 9 30 5H6M = 29 25 AGCTAA * MQ:i:30 MC:Z:6H5M +r003 17 ref1 29 30 6H5M = 9 -25 TAGGC * MQ:i:30 MC:Z:5H6M +r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * +r007 9 ref1 9 30 5H6M = 9 0 AGCTAA * MC:Z:* +r007 5 ref1 9 30 * = 9 0 GGGGGG * MQ:i:30 MC:Z:5H6M +u1 4 * 0 30 * * 0 0 TAATTGGGTCTTCAGAGCACCTA ??????????????????????? +x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * +x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? +x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? +x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? +x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? +x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/3_reverse_read_pp_lt.bam.expected |
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| Binary file test-data/3_reverse_read_pp_lt.bam.expected has changed |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/3_reverse_read_pp_lt.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_reverse_read_pp_lt.sam Fri Sep 28 04:28:45 2018 -0400 |
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| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40340 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U +MS0_12500:1:2114:20577:3664#6 147 1 40340 23 75M = 40346 -75 CAAAATCTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/3_reverse_read_pp_lt.sam.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_reverse_read_pp_lt.sam.expected Fri Sep 28 04:28:45 2018 -0400 |
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| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40340 69 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M +MS0_12500:1:2114:20577:3664#6 147 1 40340 23 75M = 40346 -69 CAAAATCTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/4_reverse_read_pp_equal.bam.expected |
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| Binary file test-data/4_reverse_read_pp_equal.bam.expected has changed |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/4_reverse_read_pp_equal.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_reverse_read_pp_equal.sam Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U +MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/4_reverse_read_pp_equal.sam.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_reverse_read_pp_equal.sam.expected Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M +MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M |
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| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/5_ct.bam.expected |
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| Binary file test-data/5_ct.bam.expected has changed |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/5_ct.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5_ct.sam Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U +MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/5_ct.sam.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5_ct.sam.expected Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M ct:Z:1F75M-75T2R75M +MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/6_ct_replace.bam.expected |
| b |
| Binary file test-data/6_ct_replace.bam.expected has changed |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/6_ct_replace.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6_ct_replace.sam Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 +MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 ct:Z:1F70M-75T2R70M |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/6_ct_replace.sam.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6_ct_replace.sam.expected Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.4 SO:queryname +@SQ SN:1 LN:4569345 +@RG ID:1#6 LB:1 SM:a +MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M ct:Z:1F75M-75T2R75M +MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 MC:Z:75M |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/7_two_read_mapped.bam.expected |
| b |
| Binary file test-data/7_two_read_mapped.bam.expected has changed |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/7_two_read_mapped.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7_two_read_mapped.sam Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,22 @@ +@HD VN:1.4 SO:queryname +@SQ SN:ref1 LN:45 +@SQ SN:ref2 LN:40 +of1 99 ref1 10 30 23M = 8 2 AAGTCGGCAGCGTCAGATGTGTA ??????????????????????? +of1 147 ref1 8 30 23M = 10 -2 CTGTCTCTTATACACATCTCCTT ??????????????????????? +r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * +r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 +r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 +r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * +r003 16 ref1 29 30 6H5M * 0 0 TAGGC * +r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * +r007 8 ref1 9 30 5H6M * 0 0 AGCTAA * +r007 4 ref1 9 30 * * 0 0 GGGGGG * +r008 12 ref1 9 30 5H6M * 0 0 AGCTAA * +r008 4 ref1 9 30 * * 0 0 GGGGGG * +uu1 4 * 0 30 * * 0 0 TAATTGGGTCTTCAGAGCACCTA ??????????????????????? +x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * +x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? +x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? +x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? +x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? +x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? |
| b |
| diff -r 000000000000 -r bc0cc7bfbfe9 test-data/7_two_read_mapped.sam.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7_two_read_mapped.sam.expected Fri Sep 28 04:28:45 2018 -0400 |
| b |
| @@ -0,0 +1,22 @@ +@HD VN:1.4 SO:queryname +@SQ SN:ref1 LN:45 +@SQ SN:ref2 LN:40 +of1 99 ref1 10 30 23M = 8 21 AAGTCGGCAGCGTCAGATGTGTA ??????????????????????? MQ:i:30 MC:Z:23M +of1 147 ref1 8 30 23M = 10 -21 CTGTCTCTTATACACATCTCCTT ??????????????????????? MQ:i:30 MC:Z:23M +r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * MQ:i:30 MC:Z:8M4I4M1D3M +r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 MQ:i:30 MC:Z:9M +r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 +r003 33 ref1 9 30 5H6M = 29 25 AGCTAA * MQ:i:30 MC:Z:6H5M +r003 17 ref1 29 30 6H5M = 9 -25 TAGGC * MQ:i:30 MC:Z:5H6M +r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * +r007 9 ref1 9 30 5H6M = 9 0 AGCTAA * MC:Z:* +r007 5 ref1 9 30 * = 9 0 GGGGGG * MQ:i:30 MC:Z:5H6M +r008 13 ref1 9 30 5H6M = 9 0 AGCTAA * +r008 13 ref1 9 30 * = 9 0 GGGGGG * +uu1 4 * 0 30 * * 0 0 TAATTGGGTCTTCAGAGCACCTA ??????????????????????? +x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * +x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? +x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? +x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? +x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? +x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? |