| Previous changeset 0:a0d039fa9771 (2018-03-12) Next changeset 2:720217c23995 (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_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83 |
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modified:
macros.xml samtools_fastx.xml test-data/samtools_fastx-out2-2.fastq test-data/samtools_fastx-out2-3.fastq test-data/samtools_fastx-out3-2.fasta test-data/samtools_fastx-out3-3.fasta |
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added:
test-data/1.1.fq.expected test-data/1.2.fq.expected test-data/1.stdout.expected test-data/10.1.fq.expected test-data/10.2.fq.expected test-data/10.s.fq.expected test-data/2.1.fq.expected test-data/2.2.fq.expected test-data/2.s.fq.expected test-data/2.stdout.expected test-data/3.1.fq.expected test-data/3.2.fq.expected test-data/3.s.fq.expected test-data/3.stdout.expected test-data/4.1.fq.expected test-data/4.2.fq.expected test-data/4.s.fq.expected test-data/4.stdout.expected test-data/5.1.fq.expected test-data/5.2.fq.expected test-data/5.s.fq.expected test-data/6.1.fq.expected test-data/6.2.fq.expected test-data/6.s.fq.expected test-data/7.1.fq.expected test-data/7.2.fq.expected test-data/7.s.fq.expected test-data/8.1.fq.expected test-data/8.2.fq.expected test-data/8.i.fq.expected test-data/8.s.fq.expected test-data/9.1.fq.expected test-data/9.2.fq.expected test-data/bam2fq.001.sam test-data/bam2fq.002.sam test-data/bam2fq.003.sam test-data/bam2fq.004.sam test-data/bam2fq.005.sam test-data/bam2fq.010.sam test-data/bc.fq.expected test-data/bc10.fq.expected test-data/bc_split.fq.expected test-data/samtools_fastx-out1-1.fasta.gz test-data/samtools_fastx-out1-2.fasta.gz test-data/samtools_fastx-out1-3.fasta.gz test-data/samtools_fastx-out1.fasta test-data/samtools_fastx-out1.fasta.gz test-data/samtools_fastx-out2-1.fastq.gz test-data/samtools_fastx-out2-2.fastq.gz test-data/samtools_fastx-out2-3.fastq.gz test-data/samtools_fastx-out3-1.fasta.gz test-data/samtools_fastx-out3-2.fasta.gz test-data/samtools_fastx-out3-3.fasta.gz |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e macros.xml --- a/macros.xml Mon Mar 12 12:53:10 2018 -0400 +++ b/macros.xml Fri Sep 28 04:39:19 2018 -0400 |
| [ |
| b'@@ -1,26 +1,131 @@\n <macros>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.3.1">samtools</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>\n <yield/>\n </requirements>\n </xml>\n- <token name="@TOOL_VERSION@">1.3.1</token>\n+ <token name="@TOOL_VERSION@">1.9</token>\n <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(\',\')))</token>\n- <xml name="filter_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">The read is unmapped</option>\n- <option value="8">The mate is unmapped</option>\n- <option value="16">Read strand</option>\n- <option value="32">Mate strand</option>\n- <option value="48">Read is the first in a pair</option>\n- <option value="64">Read is the second in a pair</option>\n- <option value="256">The alignment or this read is not primary</option>\n- <option value="512">The read fails platform/vendor quality checks</option>\n- <option value="768">The read is a PCR or optical duplicate</option>\n- <option value="1024">Supplementary alignment</option>\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-- )) &'..b'+ ]]></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 first in a pair</option>\n+ <option value="128">read is the second in a pair</option>\n+ <option value="256">alignment or read is not primary</option>\n+ <option value="512">read fails platform/vendor quality checks</option>\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@@ -64,21 +169,4 @@\n <exit_code range="1:" level="fatal" description="Error" />\n </stdio>\n </xml>\n- <token name="@no-chrom-options@">\n------\n-\n-.. class:: warningmark\n-\n-**No options available? How to re-detect metadata**\n-\n-If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:\n-\n-1. Click on the **pencil** icon adjacent to the dataset in the history\n-2. A new menu will appear in the center pane of the interface\n-3. Click **Datatype** tab\n-4. Set **New Type** to **BAM**\n-5. Click **Save**\n-\n-The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.\n- </token>\n </macros>\n' |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e samtools_fastx.xml --- a/samtools_fastx.xml Mon Mar 12 12:53:10 2018 -0400 +++ b/samtools_fastx.xml Fri Sep 28 04:39:19 2018 -0400 |
| [ |
| b'@@ -1,104 +1,515 @@\n-<?xml version="1.0"?>\n-<tool id="samtools_fastx" name="Samtools extract" version="@TOOL_VERSION@">\n- <description>FASTA or FASTQ from a SAM file</description>\n+<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy1">\n+ <description>extract FASTA or FASTQ from alignment files</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements" />\n+ <expand macro="stdio"/>\n <expand macro="version_command" />\n- <command detect_errors="exit_code">\n- <![CDATA[\n- samtools $output.output_format\n- #if $output.output_format == \'fastq\':\n- -v $output.default_quality $output.output_quality\n- #end if\n- #if $reference:\n- --reference \'$reference\'\n- #end if\n- $copy_flags $omit_read_number\n- -0 \'$nonspecific\'\n- -1 \'$forward\'\n- -2 \'$reverse\'\n- #if str($inclusive_filter) != \'None\':\n- #set $filter = $inclusive_filter\n- @FLAGS@\n- -f $flags\n- #end if\n- #if str($exclusive_filter) != \'None\':\n- #set $filter = $exclusive_filter\n- @FLAGS@\n- -F $flags\n- #end if\n- \'$input\'\n+ <command><![CDATA[\n+@ADDTHREADS@ \n+## name sort input file if neccessary\n+#if not $input.is_of_type(\'qname_sorted.bam\', \'qname_input_sorted.bam\'):\n+ samtools sort -@ \\$addthreads -n \'$input\' > input &&\n+#else:\n+ ln -s \'$input\' input &&\n+#end if\n+\n+#set command=str($output_fmt_cond.output_fmt_select)[:5]\n+\n+samtools $command\n+#if str($output_fmt_cond.output_fmt_select).startswith(\'fastq\'):\n+ #if str($output_fmt_cond.default_quality) != \'\':\n+ -v $output_fmt_cond.default_quality\n+ #end if\n+ $output_fmt_cond.output_quality\n+ $output_fmt_cond.ilumina_casava\n+#end if\n+$copy_tags\n+#if str($copy_arb_tags) != \'\':\n+ -T \'$copy_arb_tags\'\n+#end if\n+$read_numbering\n+#if \'r0\' in str($outputs):\n+ -0 nonspecific.$output_fmt_cond.output_fmt_select\n+#end if\n+#if \'r1\' in str($outputs):\n+ -1 forward.$output_fmt_cond.output_fmt_select\n+#end if\n+#if \'r2\' in str($outputs):\n+ -2 reverse.$output_fmt_cond.output_fmt_select\n+#end if\n+#if str($inclusive_filter) != \'None\':\n+ #set $filter = $inclusive_filter\n+ @FLAGS@\n+ -f $flags\n+#end if\n+#if str($exclusive_filter) != \'None\':\n+ #set $filter = $exclusive_filter\n+ @FLAGS@\n+ -F $flags\n+#end if\n+#if str($exclusive_filter) != \'None\':\n+ #set $filter = $exclusive_filter_all\n+ @FLAGS@\n+ -G $flags\n+#end if\n+#if \'s\' in str($outputs):\n+ -s singletons.$output_fmt_cond.output_fmt_select\n+#end if\n+#if str($idxout_cond.idxout_select) == \'yes\':\n+ #if str($idxout_cond.write1st) == \'yes\':\n+ --i1 i1.$output_fmt_cond.output_fmt_select\n+ #end if\n+ #if str($idxout_cond.write2nd) == \'yes\':\n+ --i2 i2.$output_fmt_cond.output_fmt_select\n+ #end if\n+ #if str($idxout_cond.index_format) != \'\':\n+ --index-format $idxout_cond.index_format\n+ #end if\n+ #if str($idxout_cond.barcode_tag) != \'\':\n+ --barcode-tag $idxout_cond.barcode_tag\n+ #end if\n+ #if str($idxout_cond.quality_tag) != \'\':\n+ --quality-tag $idxout_cond.quality_tag\n+ #end if\n+#end if\n+\n+input \n+\n+#if str($outputs)==\'None\' or \'other\' in str($outputs):\n+ ## since currently stdout in not zipped (samtools doesn\'t know about the extension)\n+ #if str($output_fmt_cond.output_fmt_select).endswith(\'.gz\'):\n+ | gzip - \n+ #end if\n+ > output.$output_fmt_cond.output_fmt_select\n+ && ln -s output.$output_fmt_cond.output_fmt_select output\n+#else\n+ ## otherwise the remaining sequences would show up in the datasets info box\n+ > /dev/null\n+#end if\n+#if \'r0\' in str($outputs):\n+ && ln -s nonspecific.$output_fmt_cond.output_fmt_select nonspecific\n+#end if\n+#if \'r1\' in str($outputs):\n+ && ln -s forward.$output_fmt_cond.out'..b' <param name="input" value="bam2fq.005.sam" ftype="sam" />\n+ <conditional name="output_fmt_cond">\n+ <param name="output_fmt_select" value="fastqsanger" />\n+ </conditional>\n+ <param name="outputs" value="r1,r2,s,other" />\n+ <param name="copy_tags" value="-t" />\n+ <param name="copy_arb_tags" value="MD,ia" />\n+ <param name="read_numbering" value="-N"/>\n+ <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />\n+ <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />\n+ <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />\n+ <output name="output" file="2.stdout.expected" ftype="fastqsanger" />\n+ </test>\n+ <!--# -i flag with no index-->\n+ <!--test_cmd($opts, out=>\'bam2fq/2.stdout.expected\', out_map=>{\'1.fq\' => \'bam2fq/7.1.fq.expected\', \'2.fq\' => \'bam2fq/7.2.fq.expected\', \'s.fq\' => \'bam2fq/7.s.fq.expected\'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->\n+ <test>\n+ <param name="input" value="bam2fq.005.sam" ftype="sam" />\n+ <conditional name="output_fmt_cond">\n+ <param name="output_fmt_select" value="fastqsanger" />\n+ <param name="ilumina_casava" value="-i" />\n+ </conditional>\n+ <param name="outputs" value="r1,r2,s,other" />\n+ <param name="copy_tags" value="-t" />\n+ <param name="copy_arb_tags" value="MD,ia" />\n+ <param name="read_numbering" value="-N"/>\n+ <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />\n+ <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />\n+ <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />\n+ <output name="output" file="2.stdout.expected" ftype="fastqsanger" />\n+ </test>\n+ <!--# -i flag with index-->\n+ <!--test_cmd($opts, out=>\'bam2fq/2.stdout.expected\', out_map=>{\'1.fq\' => \'bam2fq/8.1.fq.expected\', \'2.fq\' => \'bam2fq/8.2.fq.expected\', \'s.fq\' => \'bam2fq/8.s.fq.expected\', \'i.fq\' => \'bam2fq/8.i.fq.expected\'}, cmd=>"$$opts{bin}/samtools fastq @$threads \\-\\-barcode-tag BC -i \\-\\-index-format \'n2i2\' \\-\\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->\n+ <test>\n+ <param name="input" value="bam2fq.004.sam" ftype="sam" />\n+ <conditional name="output_fmt_cond">\n+ <param name="output_fmt_select" value="fastqsanger" />\n+ <param name="ilumina_casava" value="-i" />\n+ </conditional>\n+ <param name="outputs" value="r1,r2,s,other" />\n+ <conditional name="idxout_cond">\n+ <param name="idxout_select" value="yes"/>\n+ <param name="write1st" value="yes"/>\n+ <param name="barcode_tag" value="BC"/>\n+ <param name="index_format" value="n2i2"/>\n+ </conditional>\n+ <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" />\n+ <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" />\n+ <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />\n+ <output name="output" file="2.stdout.expected" ftype="fastqsanger" />\n+ <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" />\n </test>\n </tests>\n- <help>\n- <![CDATA[\n- This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a SAM or BAM file in FASTA or FASTQ format.\n- ]]>\n+ <help><![CDATA[\n+This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a\n+SAM or BAM file in FASTA or FASTQ format.\n+ ]]>\n </help>\n <expand macro="citations" />\n </tool>\n' |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/1.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,72 @@ +@ref1_grp1_p001 +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002 +CTCGGTACCC ++ +########## +@ref1_grp1_p003 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001 +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001 +CAAGCTTGAG ++ +AAAAAAAAAA +@unaligned_grp3_p001 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/1.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,72 @@ +@ref1_grp1_p001 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001 +ATTTAGGTGA ++ +BBBBBBBBBB +@unaligned_grp3_p001 +GAAAGTGAGGAGGTG ++ +edcba9876543210 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/10.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001 +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002 +CTCGGTACCC ++ +########## +@ref1_grp1_p003 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001 +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006 +TCTAGAGTCG ++ +1111111111 +@ref2_grp3_p001 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001 +CAAGCTTGAG ++ +AAAAAAAAAA |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/10.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004 +TTGCATGCCT ++ +9999999999 +@ref1_grp2_p005 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001 +ATTTAGGTGA ++ +BBBBBBBBBB |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/10.s.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +@ref1_grp2_p002a +CGGTACCCGG ++ +$$$$$$$$$$ +@unaligned_grp3_p001 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/2.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,72 @@ +@ref1_grp1_p001 +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002 +CTCGGTACCC ++ +########## +@ref1_grp1_p003 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001 +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001 +CAAGCTTGAG ++ +AAAAAAAAAA +@unaligned_grp3_p001 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/2.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,72 @@ +@ref1_grp1_p001 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001 +ATTTAGGTGA ++ +BBBBBBBBBB +@unaligned_grp3_p001 +GAAAGTGAGGAGGTG ++ +edcba9876543210 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/3.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,72 @@ +@ref1_grp1_p001 +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002 +CTCGGTACCC ++ +########## +@ref1_grp1_p003 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001 +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001 +CAAGCTTGAG ++ +AAAAAAAAAA +@unaligned_grp3_p001 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/3.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,72 @@ +@ref1_grp1_p001 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001 +ATTTAGGTGA ++ +BBBBBBBBBB +@unaligned_grp3_p001 +GAAAGTGAGGAGGTG ++ +edcba9876543210 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/3.s.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +@ref1_grp2_p002a +CGGTACCCGG ++ +$$$$$$$$$$ |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/4.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001 +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002 +CTCGGTACCC ++ +########## +@ref1_grp1_p003 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001 +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001 +CAAGCTTGAG ++ +AAAAAAAAAA |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/4.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001 +ATTTAGGTGA ++ +BBBBBBBBBB |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/4.s.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +@ref1_grp2_p002a +CGGTACCCGG ++ +$$$$$$$$$$ +@unaligned_grp3_p001 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/5.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001/1 +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002/1 +CTCGGTACCC ++ +########## +@ref1_grp1_p003/1 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004/1 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005/1 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006/1 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001/1 +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002/1 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003/1 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004/1 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005/1 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006/1 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001/1 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002/1 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003/1 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/1 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001/1 +CAAGCTTGAG ++ +AAAAAAAAAA |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/5.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001/2 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002/2 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003/2 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004/2 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005/2 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006/2 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001/2 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002/2 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003/2 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004/2 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005/2 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006/2 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001/2 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002/2 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003/2 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/2 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001/2 +ATTTAGGTGA ++ +BBBBBBBBBB |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/5.s.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +@ref1_grp2_p002a/1 +CGGTACCCGG ++ +$$$$$$$$$$ +@unaligned_grp3_p001/1 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/6.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001/1 RG:Z:grp1 BC:Z:AC-GT +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002/1 RG:Z:grp1 BC:Z:AATT+CCGG +CTCGGTACCC ++ +########## +@ref1_grp1_p003/1 RG:Z:grp1 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004/1 RG:Z:grp1 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005/1 RG:Z:grp1 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006/1 RG:Z:grp1 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001/1 RG:Z:grp2 BC:Z:TG+CA QT:Z:ab+cd +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002/1 RG:Z:grp2 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003/1 RG:Z:grp2 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004/1 RG:Z:grp2 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005/1 RG:Z:grp2 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006/1 RG:Z:grp2 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001/1 RG:Z:grp3 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002/1 RG:Z:grp3 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003/1 RG:Z:grp3 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/1 RG:Z:grp1 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001/1 RG:Z:grp2 +CAAGCTTGAG ++ +AAAAAAAAAA |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/6.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001/2 RG:Z:grp1 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002/2 RG:Z:grp1 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003/2 RG:Z:grp1 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004/2 RG:Z:grp1 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005/2 RG:Z:grp1 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006/2 RG:Z:grp1 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001/2 RG:Z:grp2 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002/2 RG:Z:grp2 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003/2 RG:Z:grp2 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004/2 RG:Z:grp2 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005/2 RG:Z:grp2 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006/2 RG:Z:grp2 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001/2 RG:Z:grp3 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002/2 RG:Z:grp3 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003/2 RG:Z:grp3 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/2 RG:Z:grp1 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001/2 RG:Z:grp2 +ATTTAGGTGA ++ +BBBBBBBBBB |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/6.s.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +@ref1_grp2_p002a/1 RG:Z:grp2 +CGGTACCCGG ++ +$$$$$$$$$$ +@unaligned_grp3_p001/1 RG:Z:grp3 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/7.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001/1 RG:Z:grp1 BC:Z:AC-GT MD:Z:10 +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002/1 RG:Z:grp1 BC:Z:AATT+CCGG MD:Z:10 +CTCGGTACCC ++ +########## +@ref1_grp1_p003/1 RG:Z:grp1 MD:Z:10 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004/1 RG:Z:grp1 MD:Z:10 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005/1 RG:Z:grp1 MD:Z:10 ia:i:40000 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006/1 RG:Z:grp1 MD:Z:10 ia:i:255 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001/1 RG:Z:grp2 BC:Z:TG+CA QT:Z:ab+cd MD:Z:8 +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002/1 RG:Z:grp2 MD:Z:10 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003/1 RG:Z:grp2 MD:Z:10 ia:i:4294967295 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004/1 RG:Z:grp2 MD:Z:10 ia:i:-2147483648 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005/1 RG:Z:grp2 MD:Z:10 ia:i:-1000 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006/1 RG:Z:grp2 MD:Z:10 ia:i:-1 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001/1 RG:Z:grp3 MD:Z:15 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002/1 RG:Z:grp3 MD:Z:15 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003/1 RG:Z:grp3 MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/1 RG:Z:grp1 MD:Z:10 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001/1 RG:Z:grp2 MD:Z:10 +CAAGCTTGAG ++ +AAAAAAAAAA |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/7.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001/2 RG:Z:grp1 MD:Z:10 +GTCGACTCTA ++ +---------- +@ref1_grp1_p002/2 RG:Z:grp1 MD:Z:10 +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003/2 RG:Z:grp1 MD:Z:10 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004/2 RG:Z:grp1 MD:Z:10 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005/2 RG:Z:grp1 MD:Z:10 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006/2 RG:Z:grp1 MD:Z:10 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001/2 RG:Z:grp2 MD:Z:10 +AGGTCGACTC ++ +.......... +@ref1_grp2_p002/2 RG:Z:grp2 MD:Z:10 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003/2 RG:Z:grp2 MD:Z:10 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004/2 RG:Z:grp2 MD:Z:10 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005/2 RG:Z:grp2 MD:Z:10 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006/2 RG:Z:grp2 MD:Z:10 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001/2 RG:Z:grp3 MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002/2 RG:Z:grp3 MD:Z:15 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003/2 RG:Z:grp3 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/2 RG:Z:grp1 MD:Z:10 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001/2 RG:Z:grp2 MD:Z:10 +ATTTAGGTGA ++ +BBBBBBBBBB |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/7.s.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +@ref1_grp2_p002a/1 RG:Z:grp2 MD:Z:10 +CGGTACCCGG ++ +$$$$$$$$$$ +@unaligned_grp3_p001/1 RG:Z:grp3 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/8.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001 1:N:0:GT +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002 1:N:0:TT +CTCGGTACCC ++ +########## +@ref1_grp1_p003 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001 1:N:0:CA +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001 +CAAGCTTGAG ++ +AAAAAAAAAA |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/8.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +@ref1_grp1_p001 1:N:0:GT +GTCGACTCTA ++ +---------- +@ref1_grp1_p002 1:N:0:TT +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001 1:N:0:CA +AGGTCGACTC ++ +.......... +@ref1_grp2_p002 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001 +ATTTAGGTGA ++ +BBBBBBBBBB |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/8.i.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8.i.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ +@ref1_grp1_p001 1:N:0:GT +GT ++ +"" +@ref1_grp1_p002 1:N:0:TT +TT ++ +"" +@ref1_grp2_p001 1:N:0:CA +CA ++ +cd |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/8.s.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +@ref1_grp2_p002a +CGGTACCCGG ++ +$$$$$$$$$$ +@unaligned_grp3_p001 +CACTCGTTCATGACG ++ +0123456789abcde |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/9.1.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/9.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,28 @@ +@HS2000-355_269:2:1108:12969:26408 +CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ++ +BCBFFFFFGGHHHJJJJIIJGIIIJIJIJIJII990?G=)?0?FH<GEF=CCFEE@G2=C?EE(;CB9;6@6(5??(559<?,9?AB239<2<8<928?8 +@HS2000-355_269:2:2312:2459:22449 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCTAACCGTAACTCTAACCCTAACCCTATCTCAA ++ +@@@FFBFD8CDHHIBBHIIHIFHH3811)?:)?9):B)B############################################################# +@HS2000-355_269:1:2307:11945:73421 +TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCATAACCCTAACCCTAACCCTAACCCTAACC ++ +@@@DFFDEHFHFHHGIJJGIJGHIGEGGHIIFEEHEGHHBBAA;?B@F(B(;;=)==66=?EE>?@7;;A############################## +@HS2000-355_269:1:1114:7529:75240 +TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTCACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTACCC ++ +@CCFFFFFDDAFB@GGHFGH@FHIFECBGAEC9CBBF?GFGDGIEGG>GCGI;=(8.6@=A)=???;?6;;66=2;;(,5<AB@5??############# +@HS2000-355_269:2:2302:12695:6571 +CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCACA ++ +@@@FBEFDDHHHHIIIIIFFAHGGHHGE??C8C;;FFB>;D>;@DEC@H(=FA@(==@)6=22)7;;?A>AA2;;;?@A##################### +@HS2000-690_130:8:2104:17804:42012 +ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCCACCCCCACCC ++ +CCCFFFFFHGDFHIIJJIIJJIGFHEHIIIJIGIEGDHHIIJJJHIHI=D(BC@FG2;=CEECH@CDF################################ +@HS2000-355_269:2:2213:5874:97462 +ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCAAACCCTAACCCTAACCACAACCCACACCCATATCT ++ +@@@FDFADHDDBFG;CGB;BFHDHGGIG3CGGCC;9?GDF939BFG(B#################################################### |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/9.2.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/9.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ +@HS2000-355_269:1:2307:11945:73421 +AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTGGGGTTGGGG ++ +?@@DBDBDFAAC;CBG<CGGII@GHCHGGEHAH@?DGDG2*??DFF*=BFCH'55@;??;6;@##################################### +@HS2000-355_269:2:1108:12969:26408 +AGGGTTGGGTTAGGGTTGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTGGGGTTTGGGGTGGGGTTGGGGGT ++ +@@@FDDFFFFFADHIEHGII@G?GIG?DAHII9B@DFG8BBFCG)=BGEHAAA=AH76?@CC','5=B59(9?A########################## +@HS2000-690_130:8:1215:11245:58923 +ACACTAACCCGAACCCTAACACAAACCCTAACCCTAACCCTAACCCTAACCCTAACGCGAACACCAACCATAACCCTAACCAACACACTAACGCTAACCC ++ +=>;AAA+AAB6AA12?22?@*:)?1??ABB###################################################################### |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bam2fq.001.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2fq.001.sam Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,65 @@ +@HD VN:1.4 SO:queryname +@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample +@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample +@RG ID:grp3 DS:Group 3 LB:Library 3 SM:Sample +@PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 +@CO The MIT License +@CO +@CO Copyright (c) 2014, 2015 Genome Research Ltd. +@CO +@CO Permission is hereby granted, free of charge, to any person obtaining a copy +@CO of this software and associated documentation files (the "Software"), to deal +@CO in the Software without restriction, including without limitation the rights +@CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +@CO copies of the Software, and to permit persons to whom the Software is +@CO furnished to do so, subject to the following conditions: +@CO +@CO The above copyright notice and this permission notice shall be included in +@CO all copies or substantial portions of the Software. +@CO +@CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +@CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +@CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +@CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +@CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +@CO THE SOFTWARE. +@SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 +@SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 +ref1_grp1_p001 99 ref1 1 0 10M = 25 34 CGAGCTCGGT !!!!!!!!!! MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:ACGT H0:i:1 aa:A:! ab:A:~ fa:f:3.14159 za:Z:Hello world! ha:H:DEADBEEF ba:B:c,-128,0,127 bb:B:C,0,127,255 bc:B:s,-32768,0,32767 bd:B:S,0,32768,65535 be:B:i,-2147483648,0,2147483647 bf:B:I,0,2147483648,4294967295 bg:B:f,2.71828,6.626e-34,2.9979e+09 +ref1_grp1_p001 147 ref1 25 12 10M = 1 -34 TAGAGTCGAC ---------- MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p002 99 ref1 5 2 10M = 29 34 CTCGGTACCC ########## MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:AATTCCGG H0:i:1 aa:A:a ab:A:z fa:f:4.3597e-18 za:Z:Another string ha:H:2000AD +ref1_grp1_p002 147 ref1 29 14 10M = 5 -34 GTCGACCTGC ////////// MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p003 99 ref1 9 4 10M = 33 34 GTACCCGGGG %%%%%%%%%% MD:Z:10 NM:i:0 fa:f:1.66e-27 RG:Z:grp1 +ref1_grp1_p003 147 ref1 33 16 10M = 9 -34 ACCTGCAGGC 1111111111 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p004 99 ref1 13 6 10M = 37 34 CCGGGGATCC '''''''''' MD:Z:10 NM:i:0 fa:f:1.38e-23 za:Z:xRG:Z:grp2 RG:Z:grp1 +ref1_grp1_p004 147 ref1 37 18 10M = 13 -34 GCAGGCATGC 3333333333 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p005 99 ref1 17 8 10M = 41 34 GGATCCTCTA )))))))))) MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:40000 +ref1_grp1_p005 147 ref1 41 20 10M = 17 -34 GCATGCAAGC 5555555555 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p006 99 ref1 21 10 10M = 45 34 CCTCTAGAGT ++++++++++ MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:255 +ref1_grp1_p006 147 ref1 45 22 10M = 21 -34 GCAAGCTTGA 7777777777 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp2_p001 99 ref1 3 1 8M2S = 27 34 AGCTCGGTAC """""""""" MD:Z:8 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 2147 ref1 11 1 8H2M = 27 34 AC "" MD:Z:2 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 147 ref1 27 13 10M = 3 -34 GAGTCGACCT .......... MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p002 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 147 ref1 31 15 10M = 7 -34 CGACCTGCAG 0000000000 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p003 99 ref1 11 5 10M = 35 34 ACCCGGGGAT &&&&&&&&&& MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:4294967295 +ref1_grp2_p003 147 ref1 35 17 10M = 11 -34 CTGCAGGCAT 2222222222 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p004 99 ref1 15 7 10M = 39 34 GGGGATCCTC (((((((((( MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-2147483648 +ref1_grp2_p004 147 ref1 39 19 10M = 15 -34 AGGCATGCAA 4444444444 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p005 99 ref1 19 9 10M = 43 34 ATCCTCTAGA ********** MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1000 +ref1_grp2_p005 147 ref1 43 21 10M = 19 -34 ATGCAAGCTT 6666666666 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p006 99 ref1 23 11 10M = 47 34 TCTAGAGTCG ,,,,,,,,,, MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1 +ref1_grp2_p006 147 ref1 47 23 10M = 23 -34 AAGCTTGAGT 8888888888 MD:Z:10 NM:i:0 RG:Z:grp2 +ref2_grp3_p001 83 ref2 1 99 15M = 31 45 ATTCTATAGTGTCAC ~~~~~~~~~~~~~~~ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p001 163 ref2 31 99 15M = 1 -45 CTGTTTCCTGTGTGA ||||||||||||||| MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 NM:i:13 RG:Z:grp3 +ref2_grp3_p002 99 ref2 46 99 15M = 16 -45 CTGTTTCCTGTGTGA {{{{{{{{{{{{{{{ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p002 147 ref2 16 99 15M = 46 45 CTAAATAGCTTGGCG }}}}}}}}}}}}}}} MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p003 99 ref2 1 99 15M = 1 15 ACGTMRWSYKVHDBN 0123456789abcd! MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 NM:i:14 RG:Z:grp3 +ref2_grp3_p003 147 ref2 1 99 15M = 1 -15 NVHDBMRSWYKACGT !dcba9876543210 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 NM:i:14 RG:Z:grp3 +ref12_grp1_p001 97 ref1 36 50 10M ref2 2 0 TGCAGGCATG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp1_p001 145 ref2 2 50 10M ref1 36 0 TTCTATAGTG BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp2_p001 97 ref1 46 50 10M ref2 12 0 CAAGCTTGAG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp2 +ref12_grp2_p001 145 ref2 12 50 10M ref1 46 0 TCACCTAAAT BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp2 +unaligned_grp3_p001 77 * 0 0 * * 0 0 CACTCGTTCATGACG 0123456789abcde RG:Z:grp3 +unaligned_grp3_p001 141 * 0 0 * * 0 0 GAAAGTGAGGAGGTG edcba9876543210 RG:Z:grp3 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bam2fq.002.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2fq.002.sam Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,66 @@ +@HD VN:1.4 SO:queryname +@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample +@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample +@RG ID:grp3 DS:Group 3 LB:Library 3 SM:Sample +@PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 +@CO The MIT License +@CO +@CO Copyright (c) 2014, 2015 Genome Research Ltd. +@CO +@CO Permission is hereby granted, free of charge, to any person obtaining a copy +@CO of this software and associated documentation files (the "Software"), to deal +@CO in the Software without restriction, including without limitation the rights +@CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +@CO copies of the Software, and to permit persons to whom the Software is +@CO furnished to do so, subject to the following conditions: +@CO +@CO The above copyright notice and this permission notice shall be included in +@CO all copies or substantial portions of the Software. +@CO +@CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +@CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +@CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +@CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +@CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +@CO THE SOFTWARE. +@SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 +@SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 +ref1_grp1_p001 99 ref1 1 0 10M = 25 34 CGAGCTCGGT !!!!!!!!!! MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:ACGT H0:i:1 aa:A:! ab:A:~ fa:f:3.14159 za:Z:Hello world! ha:H:DEADBEEF ba:B:c,-128,0,127 bb:B:C,0,127,255 bc:B:s,-32768,0,32767 bd:B:S,0,32768,65535 be:B:i,-2147483648,0,2147483647 bf:B:I,0,2147483648,4294967295 bg:B:f,2.71828,6.626e-34,2.9979e+09 +ref1_grp1_p001 147 ref1 25 12 10M = 1 -34 TAGAGTCGAC ---------- MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p002 99 ref1 5 2 10M = 29 34 CTCGGTACCC ########## MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:AATTCCGG H0:i:1 aa:A:a ab:A:z fa:f:4.3597e-18 za:Z:Another string ha:H:2000AD +ref1_grp1_p002 147 ref1 29 14 10M = 5 -34 GTCGACCTGC ////////// MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p003 99 ref1 9 4 10M = 33 34 GTACCCGGGG %%%%%%%%%% MD:Z:10 NM:i:0 fa:f:1.66e-27 RG:Z:grp1 +ref1_grp1_p003 147 ref1 33 16 10M = 9 -34 ACCTGCAGGC 1111111111 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p004 99 ref1 13 6 10M = 37 34 CCGGGGATCC '''''''''' MD:Z:10 NM:i:0 fa:f:1.38e-23 za:Z:xRG:Z:grp2 RG:Z:grp1 +ref1_grp1_p004 147 ref1 37 18 10M = 13 -34 GCAGGCATGC 3333333333 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p005 99 ref1 17 8 10M = 41 34 GGATCCTCTA )))))))))) MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:40000 +ref1_grp1_p005 147 ref1 41 20 10M = 17 -34 GCATGCAAGC 5555555555 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p006 99 ref1 21 10 10M = 45 34 CCTCTAGAGT ++++++++++ MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:255 +ref1_grp1_p006 147 ref1 45 22 10M = 21 -34 GCAAGCTTGA 7777777777 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp2_p001 99 ref1 3 1 8M2S = 27 34 AGCTCGGTAC """""""""" MD:Z:8 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 2147 ref1 11 1 8H2M = 27 34 AC "" MD:Z:2 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 147 ref1 27 13 10M = 3 -34 GAGTCGACCT .......... MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p002a 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 147 ref1 31 15 10M = 7 -34 CGACCTGCAG 0000000000 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p003 99 ref1 11 5 10M = 35 34 ACCCGGGGAT &&&&&&&&&& MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:4294967295 +ref1_grp2_p003 147 ref1 35 17 10M = 11 -34 CTGCAGGCAT 2222222222 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p004 99 ref1 15 7 10M = 39 34 GGGGATCCTC (((((((((( MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-2147483648 +ref1_grp2_p004 147 ref1 39 19 10M = 15 -34 AGGCATGCAA 4444444444 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p005 99 ref1 19 9 10M = 43 34 ATCCTCTAGA ********** MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1000 +ref1_grp2_p005 147 ref1 43 21 10M = 19 -34 ATGCAAGCTT 6666666666 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p006 99 ref1 23 11 10M = 47 34 TCTAGAGTCG ,,,,,,,,,, MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1 +ref1_grp2_p006 147 ref1 47 23 10M = 23 -34 AAGCTTGAGT 8888888888 MD:Z:10 NM:i:0 RG:Z:grp2 +ref2_grp3_p001 83 ref2 1 99 15M = 31 45 ATTCTATAGTGTCAC ~~~~~~~~~~~~~~~ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p001 163 ref2 31 99 15M = 1 -45 CTGTTTCCTGTGTGA ||||||||||||||| MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 NM:i:13 RG:Z:grp3 +ref2_grp3_p002 99 ref2 46 99 15M = 16 -45 CTGTTTCCTGTGTGA {{{{{{{{{{{{{{{ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p002 147 ref2 16 99 15M = 46 45 CTAAATAGCTTGGCG }}}}}}}}}}}}}}} MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p003 99 ref2 1 99 15M = 1 15 ACGTMRWSYKVHDBN 0123456789abcd! MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 NM:i:14 RG:Z:grp3 +ref2_grp3_p003 147 ref2 1 99 15M = 1 -15 NVHDBMRSWYKACGT !dcba9876543210 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 NM:i:14 RG:Z:grp3 +ref12_grp1_p001 97 ref1 36 50 10M ref2 2 0 TGCAGGCATG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp1_p001 145 ref2 2 50 10M ref1 36 0 TTCTATAGTG BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp2_p001 97 ref1 46 50 10M ref2 12 0 CAAGCTTGAG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp2 +ref12_grp2_p001 145 ref2 12 50 10M ref1 46 0 TCACCTAAAT BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp2 +unaligned_grp3_p001 77 * 0 0 * * 0 0 CACTCGTTCATGACG 0123456789abcde RG:Z:grp3 +unaligned_grp3_p001 141 * 0 0 * * 0 0 GAAAGTGAGGAGGTG edcba9876543210 RG:Z:grp3 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bam2fq.003.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2fq.003.sam Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,65 @@ +@HD VN:1.4 SO:queryname +@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample +@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample +@RG ID:grp3 DS:Group 3 LB:Library 3 SM:Sample +@PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 +@CO The MIT License +@CO +@CO Copyright (c) 2014, 2015 Genome Research Ltd. +@CO +@CO Permission is hereby granted, free of charge, to any person obtaining a copy +@CO of this software and associated documentation files (the "Software"), to deal +@CO in the Software without restriction, including without limitation the rights +@CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +@CO copies of the Software, and to permit persons to whom the Software is +@CO furnished to do so, subject to the following conditions: +@CO +@CO The above copyright notice and this permission notice shall be included in +@CO all copies or substantial portions of the Software. +@CO +@CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +@CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +@CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +@CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +@CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +@CO THE SOFTWARE. +@SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 +@SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 +ref1_grp1_p001 99 ref1 1 0 10M = 25 34 CGAGCTCGGT !!!!!!!!!! MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:ACGT H0:i:1 aa:A:! ab:A:~ fa:f:3.14159 za:Z:Hello world! ha:H:DEADBEEF ba:B:c,-128,0,127 bb:B:C,0,127,255 bc:B:s,-32768,0,32767 bd:B:S,0,32768,65535 be:B:i,-2147483648,0,2147483647 bf:B:I,0,2147483648,4294967295 bg:B:f,2.71828,6.626e-34,2.9979e+09 +ref1_grp1_p001 147 ref1 25 12 10M = 1 -34 TAGAGTCGAC ---------- MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p002 99 ref1 5 2 10M = 29 34 CTCGGTACCC ########## MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:AATTCCGG H0:i:1 aa:A:a ab:A:z fa:f:4.3597e-18 za:Z:Another string ha:H:2000AD +ref1_grp1_p002 147 ref1 29 14 10M = 5 -34 GTCGACCTGC ////////// MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p003 99 ref1 9 4 10M = 33 34 GTACCCGGGG %%%%%%%%%% MD:Z:10 NM:i:0 fa:f:1.66e-27 RG:Z:grp1 +ref1_grp1_p003 147 ref1 33 16 10M = 9 -34 ACCTGCAGGC 1111111111 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p004 99 ref1 13 6 10M = 37 34 CCGGGGATCC '''''''''' MD:Z:10 NM:i:0 fa:f:1.38e-23 za:Z:xRG:Z:grp2 RG:Z:grp1 +ref1_grp1_p004 147 ref1 37 18 10M = 13 -34 GCAGGCATGC 3333333333 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p005 99 ref1 17 8 10M = 41 34 GGATCCTCTA )))))))))) MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:40000 +ref1_grp1_p005 147 ref1 41 20 10M = 17 -34 GCATGCAAGC 5555555555 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p006 99 ref1 21 10 10M = 45 34 CCTCTAGAGT ++++++++++ MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:255 +ref1_grp1_p006 147 ref1 45 22 10M = 21 -34 GCAAGCTTGA 7777777777 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp2_p001 99 ref1 3 1 8M2S = 27 34 AGCTCGGTAC """""""""" MD:Z:8 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 2147 ref1 11 1 8H2M = 27 34 AC "" MD:Z:2 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 147 ref1 27 13 10M = 3 -34 GAGTCGACCT .......... MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p002a 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 147 ref1 31 15 10M = 7 -34 CGACCTGCAG 0000000000 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p003 99 ref1 11 5 10M = 35 34 ACCCGGGGAT &&&&&&&&&& MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:4294967295 +ref1_grp2_p003 147 ref1 35 17 10M = 11 -34 CTGCAGGCAT 2222222222 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p004 99 ref1 15 7 10M = 39 34 GGGGATCCTC (((((((((( MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-2147483648 +ref1_grp2_p004 147 ref1 39 19 10M = 15 -34 AGGCATGCAA 4444444444 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p005 99 ref1 19 9 10M = 43 34 ATCCTCTAGA ********** MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1000 +ref1_grp2_p005 147 ref1 43 21 10M = 19 -34 ATGCAAGCTT 6666666666 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p006 99 ref1 23 11 10M = 47 34 TCTAGAGTCG ,,,,,,,,,, MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1 +ref1_grp2_p006 147 ref1 47 23 10M = 23 -34 AAGCTTGAGT 8888888888 MD:Z:10 NM:i:0 RG:Z:grp2 +ref2_grp3_p001 83 ref2 1 99 15M = 31 45 ATTCTATAGTGTCAC ~~~~~~~~~~~~~~~ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p001 163 ref2 31 99 15M = 1 -45 CTGTTTCCTGTGTGA ||||||||||||||| MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 NM:i:13 RG:Z:grp3 +ref2_grp3_p002 99 ref2 46 99 15M = 16 -45 CTGTTTCCTGTGTGA {{{{{{{{{{{{{{{ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p002 147 ref2 16 99 15M = 46 45 CTAAATAGCTTGGCG }}}}}}}}}}}}}}} MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p003 99 ref2 1 99 15M = 1 15 ACGTMRWSYKVHDBN 0123456789abcd! MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 NM:i:14 RG:Z:grp3 +ref2_grp3_p003 147 ref2 1 99 15M = 1 -15 NVHDBMRSWYKACGT !dcba9876543210 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 NM:i:14 RG:Z:grp3 +ref12_grp1_p001 97 ref1 36 50 10M ref2 2 0 TGCAGGCATG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp1_p001 145 ref2 2 50 10M ref1 36 0 TTCTATAGTG BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp2_p001 97 ref1 46 50 10M ref2 12 0 CAAGCTTGAG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp2 +ref12_grp2_p001 145 ref2 12 50 10M ref1 46 0 TCACCTAAAT BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp2 +unaligned_grp3_p001 77 * 0 0 * * 0 0 CACTCGTTCATGACG 0123456789abcde RG:Z:grp3 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bam2fq.004.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2fq.004.sam Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,65 @@ +@HD VN:1.4 SO:queryname +@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample +@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample +@RG ID:grp3 DS:Group 3 LB:Library 3 SM:Sample +@PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 +@CO The MIT License +@CO +@CO Copyright (c) 2014, 2015 Genome Research Ltd. +@CO +@CO Permission is hereby granted, free of charge, to any person obtaining a copy +@CO of this software and associated documentation files (the "Software"), to deal +@CO in the Software without restriction, including without limitation the rights +@CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +@CO copies of the Software, and to permit persons to whom the Software is +@CO furnished to do so, subject to the following conditions: +@CO +@CO The above copyright notice and this permission notice shall be included in +@CO all copies or substantial portions of the Software. +@CO +@CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +@CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +@CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +@CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +@CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +@CO THE SOFTWARE. +@SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 +@SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 +ref1_grp1_p001 99 ref1 1 0 10M = 25 34 CGAGCTCGGT !!!!!!!!!! MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:ACGT H0:i:1 aa:A:! ab:A:~ fa:f:3.14159 za:Z:Hello world! ha:H:DEADBEEF ba:B:c,-128,0,127 bb:B:C,0,127,255 bc:B:s,-32768,0,32767 bd:B:S,0,32768,65535 be:B:i,-2147483648,0,2147483647 bf:B:I,0,2147483648,4294967295 bg:B:f,2.71828,6.626e-34,2.9979e+09 +ref1_grp1_p001 147 ref1 25 12 10M = 1 -34 TAGAGTCGAC ---------- MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p002 99 ref1 5 2 10M = 29 34 CTCGGTACCC ########## MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:AATTCCGG H0:i:1 aa:A:a ab:A:z fa:f:4.3597e-18 za:Z:Another string ha:H:2000AD +ref1_grp1_p002 147 ref1 29 14 10M = 5 -34 GTCGACCTGC ////////// MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p003 99 ref1 9 4 10M = 33 34 GTACCCGGGG %%%%%%%%%% MD:Z:10 NM:i:0 fa:f:1.66e-27 RG:Z:grp1 +ref1_grp1_p003 147 ref1 33 16 10M = 9 -34 ACCTGCAGGC 1111111111 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p004 99 ref1 13 6 10M = 37 34 CCGGGGATCC '''''''''' MD:Z:10 NM:i:0 fa:f:1.38e-23 za:Z:xRG:Z:grp2 RG:Z:grp1 +ref1_grp1_p004 147 ref1 37 18 10M = 13 -34 GCAGGCATGC 3333333333 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p005 99 ref1 17 8 10M = 41 34 GGATCCTCTA )))))))))) MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:40000 +ref1_grp1_p005 147 ref1 41 20 10M = 17 -34 GCATGCAAGC 5555555555 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p006 99 ref1 21 10 10M = 45 34 CCTCTAGAGT ++++++++++ MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:255 +ref1_grp1_p006 147 ref1 45 22 10M = 21 -34 GCAAGCTTGA 7777777777 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp2_p001 99 ref1 3 1 8M2S = 27 34 AGCTCGGTAC """""""""" MD:Z:8 NM:i:0 RG:Z:grp2 BC:Z:TGCA QT:Z:abcd H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 2147 ref1 11 1 8H2M = 27 34 AC "" MD:Z:2 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 147 ref1 27 13 10M = 3 -34 GAGTCGACCT .......... MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p002a 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 147 ref1 31 15 10M = 7 -34 CGACCTGCAG 0000000000 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p003 99 ref1 11 5 10M = 35 34 ACCCGGGGAT &&&&&&&&&& MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:4294967295 +ref1_grp2_p003 147 ref1 35 17 10M = 11 -34 CTGCAGGCAT 2222222222 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p004 99 ref1 15 7 10M = 39 34 GGGGATCCTC (((((((((( MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-2147483648 +ref1_grp2_p004 147 ref1 39 19 10M = 15 -34 AGGCATGCAA 4444444444 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p005 99 ref1 19 9 10M = 43 34 ATCCTCTAGA ********** MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1000 +ref1_grp2_p005 147 ref1 43 21 10M = 19 -34 ATGCAAGCTT 6666666666 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p006 99 ref1 23 11 10M = 47 34 TCTAGAGTCG ,,,,,,,,,, MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1 +ref1_grp2_p006 147 ref1 47 23 10M = 23 -34 AAGCTTGAGT 8888888888 MD:Z:10 NM:i:0 RG:Z:grp2 +ref2_grp3_p001 83 ref2 1 99 15M = 31 45 ATTCTATAGTGTCAC ~~~~~~~~~~~~~~~ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p001 163 ref2 31 99 15M = 1 -45 CTGTTTCCTGTGTGA ||||||||||||||| MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 NM:i:13 RG:Z:grp3 +ref2_grp3_p002 99 ref2 46 99 15M = 16 -45 CTGTTTCCTGTGTGA {{{{{{{{{{{{{{{ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p002 147 ref2 16 99 15M = 46 45 CTAAATAGCTTGGCG }}}}}}}}}}}}}}} MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p003 99 ref2 1 99 15M = 1 15 ACGTMRWSYKVHDBN 0123456789abcd! MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 NM:i:14 RG:Z:grp3 +ref2_grp3_p003 147 ref2 1 99 15M = 1 -15 NVHDBMRSWYKACGT !dcba9876543210 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 NM:i:14 RG:Z:grp3 +ref12_grp1_p001 97 ref1 36 50 10M ref2 2 0 TGCAGGCATG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp1_p001 145 ref2 2 50 10M ref1 36 0 TTCTATAGTG BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp2_p001 97 ref1 46 50 10M ref2 12 0 CAAGCTTGAG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp2 +ref12_grp2_p001 145 ref2 12 50 10M ref1 46 0 TCACCTAAAT BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp2 +unaligned_grp3_p001 77 * 0 0 * * 0 0 CACTCGTTCATGACG 0123456789abcde RG:Z:grp3 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bam2fq.005.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2fq.005.sam Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,65 @@ +@HD VN:1.4 SO:queryname +@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample +@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample +@RG ID:grp3 DS:Group 3 LB:Library 3 SM:Sample +@PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 +@CO The MIT License +@CO +@CO Copyright (c) 2014, 2015 Genome Research Ltd. +@CO +@CO Permission is hereby granted, free of charge, to any person obtaining a copy +@CO of this software and associated documentation files (the "Software"), to deal +@CO in the Software without restriction, including without limitation the rights +@CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +@CO copies of the Software, and to permit persons to whom the Software is +@CO furnished to do so, subject to the following conditions: +@CO +@CO The above copyright notice and this permission notice shall be included in +@CO all copies or substantial portions of the Software. +@CO +@CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +@CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +@CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +@CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +@CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +@CO THE SOFTWARE. +@SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 +@SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 +ref1_grp1_p001 99 ref1 1 0 10M = 25 34 CGAGCTCGGT !!!!!!!!!! MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:AC-GT H0:i:1 aa:A:! ab:A:~ fa:f:3.14159 za:Z:Hello world! ha:H:DEADBEEF ba:B:c,-128,0,127 bb:B:C,0,127,255 bc:B:s,-32768,0,32767 bd:B:S,0,32768,65535 be:B:i,-2147483648,0,2147483647 bf:B:I,0,2147483648,4294967295 bg:B:f,2.71828,6.626e-34,2.9979e+09 +ref1_grp1_p001 147 ref1 25 12 10M = 1 -34 TAGAGTCGAC ---------- MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p002 99 ref1 5 2 10M = 29 34 CTCGGTACCC ########## MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:AATT+CCGG H0:i:1 aa:A:a ab:A:z fa:f:4.3597e-18 za:Z:Another string ha:H:2000AD +ref1_grp1_p002 147 ref1 29 14 10M = 5 -34 GTCGACCTGC ////////// MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p003 99 ref1 9 4 10M = 33 34 GTACCCGGGG %%%%%%%%%% MD:Z:10 NM:i:0 fa:f:1.66e-27 RG:Z:grp1 +ref1_grp1_p003 147 ref1 33 16 10M = 9 -34 ACCTGCAGGC 1111111111 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p004 99 ref1 13 6 10M = 37 34 CCGGGGATCC '''''''''' MD:Z:10 NM:i:0 fa:f:1.38e-23 za:Z:xRG:Z:grp2 RG:Z:grp1 +ref1_grp1_p004 147 ref1 37 18 10M = 13 -34 GCAGGCATGC 3333333333 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p005 99 ref1 17 8 10M = 41 34 GGATCCTCTA )))))))))) MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:40000 +ref1_grp1_p005 147 ref1 41 20 10M = 17 -34 GCATGCAAGC 5555555555 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p006 99 ref1 21 10 10M = 45 34 CCTCTAGAGT ++++++++++ MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:255 +ref1_grp1_p006 147 ref1 45 22 10M = 21 -34 GCAAGCTTGA 7777777777 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp2_p001 99 ref1 3 1 8M2S = 27 34 AGCTCGGTAC """""""""" MD:Z:8 NM:i:0 RG:Z:grp2 BC:Z:TG+CA QT:Z:ab+cd H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 2147 ref1 11 1 8H2M = 27 34 AC "" MD:Z:2 NM:i:0 RG:Z:grp2 BC:Z:TG-CA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 147 ref1 27 13 10M = 3 -34 GAGTCGACCT .......... MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p002a 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 147 ref1 31 15 10M = 7 -34 CGACCTGCAG 0000000000 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p003 99 ref1 11 5 10M = 35 34 ACCCGGGGAT &&&&&&&&&& MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:4294967295 +ref1_grp2_p003 147 ref1 35 17 10M = 11 -34 CTGCAGGCAT 2222222222 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p004 99 ref1 15 7 10M = 39 34 GGGGATCCTC (((((((((( MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-2147483648 +ref1_grp2_p004 147 ref1 39 19 10M = 15 -34 AGGCATGCAA 4444444444 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p005 99 ref1 19 9 10M = 43 34 ATCCTCTAGA ********** MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1000 +ref1_grp2_p005 147 ref1 43 21 10M = 19 -34 ATGCAAGCTT 6666666666 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p006 99 ref1 23 11 10M = 47 34 TCTAGAGTCG ,,,,,,,,,, MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1 +ref1_grp2_p006 147 ref1 47 23 10M = 23 -34 AAGCTTGAGT 8888888888 MD:Z:10 NM:i:0 RG:Z:grp2 +ref2_grp3_p001 83 ref2 1 99 15M = 31 45 ATTCTATAGTGTCAC ~~~~~~~~~~~~~~~ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p001 163 ref2 31 99 15M = 1 -45 CTGTTTCCTGTGTGA ||||||||||||||| MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 NM:i:13 RG:Z:grp3 +ref2_grp3_p002 99 ref2 46 99 15M = 16 -45 CTGTTTCCTGTGTGA {{{{{{{{{{{{{{{ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p002 147 ref2 16 99 15M = 46 45 CTAAATAGCTTGGCG }}}}}}}}}}}}}}} MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p003 99 ref2 1 99 15M = 1 15 ACGTMRWSYKVHDBN 0123456789abcd! MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 NM:i:14 RG:Z:grp3 +ref2_grp3_p003 147 ref2 1 99 15M = 1 -15 NVHDBMRSWYKACGT !dcba9876543210 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 NM:i:14 RG:Z:grp3 +ref12_grp1_p001 97 ref1 36 50 10M ref2 2 0 TGCAGGCATG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp1_p001 145 ref2 2 50 10M ref1 36 0 TTCTATAGTG BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp2_p001 97 ref1 46 50 10M ref2 12 0 CAAGCTTGAG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp2 +ref12_grp2_p001 145 ref2 12 50 10M ref1 46 0 TCACCTAAAT BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp2 +unaligned_grp3_p001 77 * 0 0 * * 0 0 CACTCGTTCATGACG 0123456789abcde RG:Z:grp3 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bam2fq.010.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2fq.010.sam Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,65 @@ +@HD VN:1.4 SO:queryname +@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample +@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample +@RG ID:grp3 DS:Group 3 LB:Library 3 SM:Sample +@PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 +@CO The MIT License +@CO +@CO Copyright (c) 2014, 2015 Genome Research Ltd. +@CO +@CO Permission is hereby granted, free of charge, to any person obtaining a copy +@CO of this software and associated documentation files (the "Software"), to deal +@CO in the Software without restriction, including without limitation the rights +@CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +@CO copies of the Software, and to permit persons to whom the Software is +@CO furnished to do so, subject to the following conditions: +@CO +@CO The above copyright notice and this permission notice shall be included in +@CO all copies or substantial portions of the Software. +@CO +@CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +@CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +@CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +@CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +@CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +@CO THE SOFTWARE. +@SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 +@SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 +ref1_grp1_p001 99 ref1 1 0 10M = 25 34 CGAGCTCGGT !!!!!!!!!! MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:ACGT H0:i:1 aa:A:! ab:A:~ fa:f:3.14159 za:Z:Hello world! ha:H:DEADBEEF ba:B:c,-128,0,127 bb:B:C,0,127,255 bc:B:s,-32768,0,32767 bd:B:S,0,32768,65535 be:B:i,-2147483648,0,2147483647 bf:B:I,0,2147483648,4294967295 bg:B:f,2.71828,6.626e-34,2.9979e+09 +ref1_grp1_p001 147 ref1 25 12 10M = 1 -34 TAGAGTCGAC ---------- MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p002 99 ref1 5 2 10M = 29 34 CTCGGTACCC ########## MD:Z:10 NM:i:0 RG:Z:grp1 BC:Z:AATTCCGG H0:i:1 aa:A:a ab:A:z fa:f:4.3597e-18 za:Z:Another string ha:H:2000AD +ref1_grp1_p002 147 ref1 29 14 10M = 5 -34 GTCGACCTGC ////////// MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p003 99 ref1 9 4 10M = 33 34 GTACCCGGGG %%%%%%%%%% MD:Z:10 NM:i:0 fa:f:1.66e-27 RG:Z:grp1 +ref1_grp1_p003 147 ref1 33 16 10M = 9 -34 ACCTGCAGGC 1111111111 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p004 99 ref1 13 6 10M = 37 34 CCGGGGATCC '''''''''' MD:Z:10 NM:i:0 fa:f:1.38e-23 za:Z:xRG:Z:grp2 RG:Z:grp1 +ref1_grp1_p004 147 ref1 37 18 10M = 13 -34 GCAGGCATGC 3333333333 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p005 99 ref1 17 8 10M = 41 34 GGATCCTCTA )))))))))) MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:40000 +ref1_grp1_p005 147 ref1 41 20 10M = 17 -34 GCATGCAAGC 5555555555 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp1_p006 99 ref1 21 10 10M = 45 34 CCTCTAGAGT ++++++++++ MD:Z:10 NM:i:0 RG:Z:grp1 ia:i:255 +ref1_grp1_p006 147 ref1 45 22 10M = 21 -34 GCAAGCTTGA 7777777777 MD:Z:10 NM:i:0 RG:Z:grp1 +ref1_grp2_p001 99 ref1 3 1 8M2S = 27 34 AGCTCGGTAC """""""""" MD:Z:8 NM:i:0 RG:Z:grp2 BC:Z:TGCA QT:Z:abcd H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 2147 ref1 11 1 8H2M = 27 34 AC "" MD:Z:2 NM:i:0 RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE +ref1_grp2_p001 147 ref1 27 13 10M = 3 -34 GAGTCGACCT .......... MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p002a 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ MD:Z:10 NM:i:0 fa:f:6.022e+23 RG:Z:grp2 +ref1_grp2_p002 147 ref1 31 15 10M = 7 -34 CGACCTGCAG 0000000000 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p003 99 ref1 11 5 10M = 35 34 ACCCGGGGAT &&&&&&&&&& MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:4294967295 +ref1_grp2_p003 147 ref1 35 17 10M = 11 -34 CTGCAGGCAT 2222222222 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p004 99 ref1 15 7 10M = 39 34 GGGGATCCTC (((((((((( MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-2147483648 +ref1_grp2_p004 147 ref1 39 19 10M = 15 -34 AGGCATGCAA 4444444444 MD:Z:10 NM:i:0 RG:Z:grp2 OQ:Z:9999999999 +ref1_grp2_p005 99 ref1 19 9 10M = 43 34 ATCCTCTAGA ********** MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1000 +ref1_grp2_p005 147 ref1 43 21 10M = 19 -34 ATGCAAGCTT 6666666666 MD:Z:10 NM:i:0 RG:Z:grp2 +ref1_grp2_p006 99 ref1 23 11 10M = 47 34 TCTAGAGTCG ,,,,,,,,,, MD:Z:10 NM:i:0 RG:Z:grp2 ia:i:-1 OQ:Z:1111111111 +ref1_grp2_p006 147 ref1 47 23 10M = 23 -34 AAGCTTGAGT 8888888888 MD:Z:10 NM:i:0 RG:Z:grp2 +ref2_grp3_p001 83 ref2 1 99 15M = 31 45 ATTCTATAGTGTCAC ~~~~~~~~~~~~~~~ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p001 163 ref2 31 99 15M = 1 -45 CTGTTTCCTGTGTGA ||||||||||||||| MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 NM:i:13 RG:Z:grp3 +ref2_grp3_p002 99 ref2 46 99 15M = 16 -45 CTGTTTCCTGTGTGA {{{{{{{{{{{{{{{ MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p002 147 ref2 16 99 15M = 46 45 CTAAATAGCTTGGCG }}}}}}}}}}}}}}} MD:Z:15 NM:i:0 RG:Z:grp3 +ref2_grp3_p003 99 ref2 1 99 15M = 1 15 ACGTMRWSYKVHDBN 0123456789abcd! MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 NM:i:14 RG:Z:grp3 +ref2_grp3_p003 147 ref2 1 99 15M = 1 -15 NVHDBMRSWYKACGT !dcba9876543210 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 NM:i:14 RG:Z:grp3 +ref12_grp1_p001 97 ref1 36 50 10M ref2 2 0 TGCAGGCATG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp1_p001 145 ref2 2 50 10M ref1 36 0 TTCTATAGTG BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp1 +ref12_grp2_p001 97 ref1 46 50 10M ref2 12 0 CAAGCTTGAG AAAAAAAAAA MD:Z:10 NM:i:0 RG:Z:grp2 +ref12_grp2_p001 145 ref2 12 50 10M ref1 46 0 TCACCTAAAT BBBBBBBBBB MD:Z:10 NM:i:0 RG:Z:grp2 +unaligned_grp3_p001 77 * 0 0 * * 0 0 CACTCGTTCATGACG 0123456789abcde RG:Z:grp3 |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bc.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bc.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ +@ref1_grp1_p001 +GT ++ +"" +@ref1_grp1_p002 +TT ++ +"" +@ref1_grp2_p001 +CA ++ +cd |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bc10.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bc10.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ +@ref1_grp1_p001 +GT ++ +"" +@ref1_grp1_p002 +TT ++ +"" +@ref1_grp2_p001 +CA ++ +cd |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/bc_split.fq.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bc_split.fq.expected Fri Sep 28 04:39:19 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ +@ref1_grp1_p001/1 +GT ++ +"" +@ref1_grp1_p002/1 +CCGG ++ +"""" +@ref1_grp2_p001/1 +CA ++ +cd |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out1-1.fasta.gz |
| b |
| Binary file test-data/samtools_fastx-out1-1.fasta.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out1-2.fasta.gz |
| b |
| Binary file test-data/samtools_fastx-out1-2.fasta.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out1-3.fasta.gz |
| b |
| Binary file test-data/samtools_fastx-out1-3.fasta.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-out1.fasta Fri Sep 28 04:39:19 2018 -0400 |
| b |
| b'@@ -0,0 +1,800 @@\n+>chrM_101_581_3:0:0_1:0:0_45/1\n+GAGGTAAAATTACACATGCAAACCTCCATAGACCGGAGAAAAATCCCTTAAAGATTTACTTAAAATTTAA\n+>chrM_101_581_3:0:0_1:0:0_45/2\n+TTTTAAGCTATGGCTAGTAGTTCTCTGGCAAATATTTTTGTTAAATTTAATTATTTAGGTTTATGGCTAA\n+>chrM_271_788_1:2:0_0:1:0_73/1\n+TAGCCCATTTCTTCCCATTGCATTGGCTACACCTTGACCTAACGTTTTTATGTTTGATTCTTTTGCTTAC\n+>chrM_271_788_1:2:0_0:1:0_73/2\n+TGACTAAGTTATACCTCTTAGGGTTGGCAAATTTCGTGCCAGCCACCTCGTTCATACGATTAACCCAAAC\n+>chrM_296_703_3:1:0_0:1:0_b/1\n+GGGTTTGCTGAAGATGGCGGTATATAGGCTGAATTAGCAAGTGATGGTGAGGTAGAGCGGGGTTTATCGA\n+>chrM_296_703_3:1:0_0:1:0_b/2\n+TTTAAATTTCGTGCCAGCCACCTGGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGT\n+>chrM_317_794_1:3:0_0:1:0_18/1\n+CTCGGTCATACGATTAACCCAAACTAAATATTTTCGGCGTAAAACGTGTCATCTATAAATAAATAAATAG\n+>chrM_317_794_1:3:0_0:1:0_18/2\n+AAAATGTAGCCCATTTCTTCCCATTGCATTGGCTACACCTTGACCTAACGTTTTTATGTTTGATTCTTTT\n+>chrM_408_812_0:2:1_4:2:0_ad/1\n+TGAAAAATCATTGTTAGGACCTAAACCGTCAATAACGAAAGTAATTCTACTCATTTATAATACACGACAG\n+>chrM_408_812_0:2:1_4:2:0_ad/2\n+GAAATGTTCTGTTATAAGAAAATGACGCCCATTTCTTCCCATTGCATTGGCTCCACCTTGACCTAACGTT\n+>chrM_424_929_1:0:1_1:1:0_4a/1\n+GGACCTAAACCGTCAATAACGAAAGTAATTCTAGTCATTTATAATCCACGACAGCTAAGACCCAAACTGG\n+>chrM_424_929_1:0:1_1:1:0_4a/2\n+TAATTTGAGGAGGGTGACTGGCGGTGTGTGCGTACTTCATTGCTCAATTCAATTAAGCTCCCTATTCTTA\n+>chrM_769_1311_4:2:0_1:0:0_9b/1\n+CAAAGGGAAGACATGGGGTACATTTTCTTATAACAGAACATTACTATCCCCTTTATGAAACTAAAGGACT\n+>chrM_769_1311_4:2:0_1:0:0_9b/2\n+TTAGTTAGAAGTTTTCTAGTTAGTTCATTATGCAAAAGGAACAAGGTTTAATCTTTGCTTGTTCTTACTT\n+>chrM_826_1305_2:0:0_0:0:0_63/1\n+AGAAGTTTTCTAGTTAGTTCATTATGCAAAAGGTACAAGGTTTAATCTTTGCTTGTTCTTACTTTTAATT\n+>chrM_826_1305_2:0:0_0:0:0_63/2\n+AAACTAAAGGACTAAGGAGGATTTAGTAGTAACTTAAGAATAGAGAGCTTAATTGAATTGAGGAATGAAG\n+>chrM_946_1374_2:0:1_1:0:0_b7/1\n+GTTGATTCATAAAATTGTTTTTAGGTAGGTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTA\n+>chrM_946_1374_2:0:1_1:0:0_b7/2\n+CTTATTTCTAGACATCCGTTTCTGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTT\n+>chrM_1166_1638_1:0:0_3:1:0_54/1\n+AGAATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGAACTAGTACCGCAAGGGAAAGATGAAAGACT\n+>chrM_1166_1638_1:0:0_3:1:0_54/2\n+ATCGCATTCTTTATTGGTGGCTGCTTATAGGCCTCCAATGGTTAAAAGCTGTTTTGTTAATTATTCACTA\n+>chrM_1187_1670_2:0:0_1:1:0_5/1\n+TACATCTAGGAGCTATAGAACTAGAACCGCAAGGGAAAGATGAAAGCCTAATTAAAAGTAAGAACAAGCA\n+>chrM_1187_1670_2:0:0_1:1:0_5/2\n+ATGGAATTAATTGAAATTTTATTTTGAGCTTGATCGCTTTCTTTATTGGTGGCTGCTTTTAGGCCTACAA\n+>chrM_1366_1837_1:0:0_0:0:0_24/1\n+ATTTATAGTGTGATTATTGCCTATAGTCTGATTAACTAACAATGGTTATCCGAGTTGTTATACGCGTATG\n+>chrM_1366_1837_1:0:0_0:0:0_24/2\n+TGAATCAACTCGTCTATGTGGCAAAATAGTGAGACGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTT\n+>chrM_1396_1891_4:1:0_3:0:0_55/1\n+GAGAAGATTTTTAGGTAGAGGTGAAACGCCTACCGAGCTTGTTGATAGCTTGTTACCCAAAAAGTGAATT\n+>chrM_1396_1891_4:1:0_3:0:0_55/2\n+ATCTTTCCTATAGGCATTCCGGATTTGGGTTAACAGAGAAGTTATAGGTGGATTATTTATAGTGTGATTA\n+>chrM_1461_2059_1:2:0_0:0:0_8f/1\n+GAATTTAAGTTCAATTATAAACTTGCTGAAAAAAGAACAAAATCAAAAAGTAAGTTTAGATTATAGCCAA\n+>chrM_1461_2059_1:2:0_0:0:0_8f/2\n+CCCTAATTAAGGAACAAGTGATTATGCTACCTTTGCACGGTCAGGATACCGCGGCCGTTAAACTTTAGTC\n+>chrM_1654_2097_0:1:0_1:0:0_a8/1\n+AGAGACAGTTGGACCCTCGTTTAGCCGTTCATGCTAGTCCCTAATTAAGGACCAAGTGATTATGCTACCT\n+>chrM_1654_2097_0:1:0_1:0:0_a8/2\n+ATTTCAATTAATTCCATAATCTACACCAACTTCCTAAACTTAAAATTGGGTTAATCTATAACTTTATAGA\n+>chrM_1772_2275_1:0:0_1:0:0_3f/1\n+ATTTTTATTCTCCGAGGTCACCCCAACCGAAATTTCAAACTTATACTATAGTTTTTGGGCCATTAGGTTT\n+>chrM_1772_2275_1:0:0_1:0:0_3f/2\n+CGCGTATAACAACTCGGATAACCATTGTTAGTTAATCAGACTATAGGCAATAATCACACTATACATAATC\n+>chrM_2021_2595_3:0:0_2:0:0_22/1\n+AAGGTGGCTCTATTTCTCTTGACCTTTCGTACTGGGAGAAATCGTAAATAGATAGAAACCGACCAGGATT\n+>chrM_2021_2595_3:0:0_2:0:0_22/2\n+CGTGCAACGGTAGCATAATCACTTGTTCCTTAATTAGGGACTAGCATGAACGGCTCAACGAGGGTCCACC\n+>chrM_2195_2667_1:0:0_2:0:0_95/1\n+TTTAATTTATTAAACCTAATGGCCCAAAAACTATAGTCTAAGTTTGAAATTTCGGTTGGGGTGACCTCGG\n+>chrM_2195_2667_1:0:0_2:0:0_95/2\n+GTAGGTTAGAGGGTGTACGTATATATTTTATTTAGATTTTATTCATAAATTAAGTTGAGAGCGCTTATAT\n+>chrM_2674_3159_3:1:0_1:1:1_e/1\n+CTACGGCTCGTAAAGCTCCGATTAGTGAGAATTTGGAGTTTGAGGCTCATCCTGATCAAGAATGGAGTAA\n+>chrM_2674_3159_3:1:0_1:1:1_e/2\n+TTATTGGGGTGGCAGAGCCATGAAATTGCGTAAGACTAAAAACCTTGTTCCCAGAGGTTC'..b'TAAAAT\n+>chrM_14728_15189_1:2:0_2:0:0_7a/2\n+TAATAAATGGGTGTTCTCCTGGTTGGCCCCCAATTCAGGTTAAGATAAGTAGGTTGGCTACTAGGAATCA\n+>chrM_14768_15298_0:1:0_1:1:0_ac/1\n+CTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATAAGTCCTGAGCTTGGTATAAGAATTAAGA\n+>chrM_14768_15298_0:1:0_1:1:0_ac/2\n+AACAGGATTATACTCAGATGCAGATAAAATTCCATTTCACCCCTACTATACAATCAAAGATATCCTAGGT\n+>chrM_14794_15314_1:0:0_1:0:0_c0/1\n+AAATTCCATTTCACCCCTACTATACAATCAAAGATATCCTAGGTATCCTAATCATATTCTTAATTCTGAT\n+>chrM_14794_15314_1:0:0_1:0:0_c0/2\n+CAGAGTAATGTTTATACTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATACTTCCTGAGATT\n+>chrM_14820_15346_1:0:0_0:0:0_5a/1\n+AAGAGAAGATCTTCATTTCAGGTTTACAAGACCAGAGTAATGTTTATACTATCAAGACATGGATATAATT\n+>chrM_14820_15346_1:0:0_0:0:0_5a/2\n+ATCAAAGATATCCTAGGTATCCTAATCATATTCTTAATTCTCCTAACCCTAGTATTATTTTTCCCAGACA\n+>chrM_14858_15398_0:0:0_3:0:0_b3/1\n+CAGCTTTGGGTGCTGGAGGTGGGTAGTAGCTCCTTCTTCTTGATGTCTTGAGAAGAGCAGATCTTCATTT\n+>chrM_14858_15398_0:0:0_3:0:0_b3/2\n+TCTCATAACCCTAGTATTATTTTTCCCAGACATACTAGGAGACCCAGACAACTACATACCAGCTAATCCA\n+>chrM_14885_15311_3:1:0_1:0:0_3/1\n+AGTAATGTTTATACTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATAATTCCAGAGATTGGT\n+>chrM_14885_15311_3:1:0_1:0:0_3/2\n+AGACATACTAGGAGAGGCCGACAACTACCTACCAGCTAATCCACTAAACACCCCACCCCATATTAAACCC\n+>chrM_14975_15480_1:0:1_0:1:0_4e/1\n+ATACGCCATTCTACGCTCCACTCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAAT\n+>chrM_14975_15480_1:0:1_0:1:0_4e/2\n+AATAGTTTAATGTACGATATACATGAATGTACTGTTGTACTATGTAAATTTATGTACTCAAGAAGTAGTT\n+>chrM_14988_15504_0:0:0_1:1:0_38/1\n+GTATTAGCTTATATGCTTGGGGAAAATAGTTTAATGTACGATATACCTAAATGTACTGTTGTACTATGTA\n+>chrM_14988_15504_0:0:0_1:1:0_38/2\n+CGCTCAATCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAATTTTAGCCCTAATAC\n+>chrM_15171_15615_1:0:0_0:1:0_c3/1\n+TAACACAGATATGTCCTTATAACATTAGTTTAATGTGTTTAAGATAATATTCATGGTATATATATTGGTT\n+>chrM_15171_15615_1:0:0_0:1:0_c3/2\n+GTAGAACACCCATTTATTATCATTGGCCAACTAGCCTCCATCACATACTTCTCAATCATCTTAATTCTTA\n+>chrM_15196_15749_1:1:1_2:1:0_c4/1\n+GCTAACTAGCCCCATCTCATACTTCTCAATCATCTTAATTCTTATACCAATGTCAGGAATTATCGAAGAC\n+>chrM_15196_15749_1:1:1_2:1:0_c4/2\n+TGGCCCGGAGCGAGAAGAGGGGCATTGGTGGGCGGGTTGTAGGTTTCACGGAGGATGGAAGATTAATAGA\n+>chrM_15361_15805_1:0:0_2:0:0_81/1\n+TGAAGTAAGAACCAGATGTCTTATAAAGTTTCAGTTTAGCTACCCGCAAGTTTAATGGGCCCGGAGCGAG\n+>chrM_15361_15805_1:0:0_2:0:0_81/2\n+AAGAAGGAGCTACTCCCCACCACCAGCACCCAAAGCTGGTATTCTAATTAAACTACTTCTTGAGAACATA\n+>chrM_15417_15889_0:0:0_2:0:0_50/1\n+TTCTTGAGTACATAAATTTACATAGTACAACAGTACATTTATGTATATCGTACATTAAACTATTTTCCCC\n+>chrM_15417_15889_0:0:0_2:0:0_50/2\n+GTTGGTCATGGGCTGATTAGACCCGAAACCATCGAGATGTCTTATTTAAGGGGCACGTATGGGCGATAAC\n+>chrM_15462_15945_2:1:0_0:0:0_0/1\n+TATCGTACATTAAACAATTTTCCCCAAGCATATAAGGTAATACATTAAATCAATGGTTCAGGTCATAAAA\n+>chrM_15462_15945_2:1:0_0:0:0_0/2\n+TGTTGATGAAAGTAGGCCAAAATAAAAAGATACCAAATGCATGACACCACAGTTATGTTGGTCATGGGCT\n+>chrM_15481_15968_1:2:0_2:0:0_6d/1\n+GTCCTTACATGCCTTGACGGCTATGTTGATGAAAGTAGGCCAAAATAAAAAGATCCCAAATGCATGACAC\n+>chrM_15481_15968_1:2:0_2:0:0_6d/2\n+TTCCCCAAGCATATAAGCTAATACATTAAATCCATGGTTCAGGTCATAAAATAATCATCAACATAAACCA\n+>chrM_15523_16020_2:1:0_1:1:0_31/1\n+GGGTTTTGCGGACTAATGATTCTTCACCTAAGGTGCGTCTAGACTGTGTGCTGTCCTTTCATGCCTTGAC\n+>chrM_15523_16020_2:1:0_1:1:0_31/2\n+GTCATAAAATACTCAACAACATAAACCAATATATATACCATGAATATTATCTTAAACACATTAAACTAAT\n+>chrM_15549_16044_0:1:0_1:1:0_59/1\n+ATGAATAATTAGCCTTAGGTGATTGGGTTTTGCGGACTAATTATTCTTCACCGAAGGTGCGTCTAGACTG\n+>chrM_15549_16044_0:1:0_1:1:0_59/2\n+CAATATATATACCATGAATATTATCTTAAACACATTAAACTAATGTTATAAGGACATATCTGTGTTATCC\n+>chrM_15642_16224_2:1:0_0:0:0_a5/1\n+AGTACTAAAATATAAGTCATATTTTGGGAACTACTAGAATTGATCAGGACATAGGGTTTGATAGTTAATA\n+>chrM_15642_16224_2:1:0_0:0:0_a5/2\n+CTCTTCTCTTCCATCTGACTATCCCCTTCCCCATTTTGTCTATTAATCTTCCATCCTCCGTGAAACCAAC\n+>chrM_15720_16131_0:1:0_2:1:0_58/1\n+TGTTTATGGGGTTTGGCATTAAGAGGACGGGGTGGGGGGTTTTGAGAGTTAAAATTTGGTATTGAGTAGC\n+>chrM_15720_16131_0:1:0_2:1:0_58/2\n+CACCAATGCCCCTCCTCTCGCTCCGGGCCCATTAAACTTGGGGGTAGCTAAACTGAAACTTTATCAGACA\n+>chrM_15820_16268_3:1:0_1:0:2_7f/1\n+TTAGAGTTTTGGTTCACGGAACATGATTTTGTAAAATTTTTACAAGTACTAAAATAAGTCATATTTTGGG\n+>chrM_15820_16268_3:1:0_1:0:2_7f/2\n+GTTATCGCCCATACGTTTCCCTTAACTCAGACATCTCGATGGTATCGGGTCTAATCAGCCCCTGACCAAC\n' |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out1.fasta.gz |
| b |
| Binary file test-data/samtools_fastx-out1.fasta.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out2-1.fastq.gz |
| b |
| Binary file test-data/samtools_fastx-out2-1.fastq.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out2-2.fastq --- a/test-data/samtools_fastx-out2-2.fastq Mon Mar 12 12:53:10 2018 -0400 +++ b/test-data/samtools_fastx-out2-2.fastq Fri Sep 28 04:39:19 2018 -0400 |
| b |
| b'@@ -10,30 +10,14 @@\n GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAGCCCAAACTAATTATCTTCGGCGTAAAACG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_655_1179_0:1:0_1:2:0_60\n-CACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAAACCTAAAAAGGTATTAAAGTAAGC\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_709_1253_2:0:0_2:1:0_23\n-AGGTATTAAAGTCAGCAACAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAG\n+@chrM_361_902_2:3:0_1:1:0_8e\n+GTGCGTACTTCATTGCTCAATTCACTTAAGATCTCTATTCTTAATTTACTACTAAATCCTCCTTAGTCCT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_364_806_2:3:0_0:0:0_54\n TTCTTTTATAAGAAAATGTAGCCCATTTCTTCCCATTTCATTGGCTACACCTTGACCTAACGTTTTTATG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_748_1226_0:0:0_3:2:0_a\n-TCTTTCCCTTGCGGTACTAGTTCTATATGACCTAGATGTACGAATTTCTCTCTCCAATACTTTTATTAGG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_820_1322_1:2:0_1:1:0_32\n-TTAATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGATCTTAATTGGATTGAGCA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_361_902_2:3:0_1:1:0_8e\n-GTGCGTACTTCATTGCTCAATTCACTTAAGATCTCTATTCTTAATTTACTACTAAATCCTCCTTAGTCCT\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_406_958_3:0:0_1:1:0_c3\n TCTAGAAATTAATTATGTTAAGTTTAATTTAATTTGAGGAGGGTGAGTGGCGGTGTGTGCGTACTTCATT\n +\n@@ -42,18 +26,30 @@\n CATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_1023_1543_3:0:0_1:0:0_30\n-ATCATAGTGTAGGTTCCTATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTG\n+@chrM_655_1179_0:1:0_1:2:0_60\n+CACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAAACCTAAAAAGGTATTAAAGTAAGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_709_1253_2:0:0_2:1:0_23\n+AGGTATTAAAGTCAGCAACAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_713_1102_2:0:0_0:0:1_50\n AGGTGATTAGTTCAGAGTGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_748_1226_0:0:0_3:2:0_a\n+TCTTTCCCTTGCGGTACTAGTTCTATATGACCTAGATGTACGAATTTCTCTCTCCAATACTTTTATTAGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_787_1256_2:0:0_1:1:0_5a\n TGCTTGTTCTTACTTTTAATTAGTCTTTCATGTTTCCCTTGCGGTACTAGTTCTATATCTCCTAGATGTA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_820_1322_1:2:0_1:1:0_32\n+TTAATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGATCTTAATTGGATTGAGCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_835_1289_4:2:0_0:1:0_44\n GTTCATTATGCAAAAGGTACAAGGTTTAATCTATGCTTGTTCTTACTTTTAATTAGTCTTTCATCTTTCC\n +\n@@ -62,58 +58,50 @@\n ATTTAGTAGTAAATTAAGACTAGAGATCTTACTTGAATTGAGCAATGAAGTACGCACACACCGCCAGACA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_1370_1912_0:0:0_1:1:1_79\n-TCAACTCGTCTATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTG\n+@chrM_961_1470_3:2:0_1:0:0_2c\n+ACTTAAATTCATTTTTTGGGTAACCAGCTATCACCCAGCTCGTTAGGCTTTTCACCTCTACCTAAAAATC\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_961_1470_3:2:0_1:0:0_2c\n-ACTTAAATTCATTTTTTGGGTAACCAGCTATCACCCAGCTCGTTAGGCTTTTCACCTCTACCTAAAAATC\n+@chrM_1023_1543_3:0:0_1:0:0_30\n+ATCATAGTGTAGGTTCCTATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_1053_1571_0:1:1_4:0:0_bb\n CTATAAAAGGTTTTTTCGGTTCCAGAAGAGCTGTCCCTCTTTTGGCTATACTCTAAACTTAGTTTTTGAT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_1550_2018_2:0:0_0:1:0_e\n-GAACGGAAAAAACCTTTAATATTGAATAATTAACAAAACAGCTTTTAACCATTGTAGGCCTAAAAGCCGC\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_1762_2310_0:1:0_3:1:1'..b'AAGCGAAGCATCGGGTCAAGGTGGCTTTGTCTACTGATAAGCCCCCTCAAATTCATTCGACTAGG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_14660_15119_2:0:0_3:0:0_b3\n AGCCACCTTGACCCGATTCTTCGCATTCCACTTCATCTTACCATTTATTATCGGGGCCCTAGCAATCGTT\n +\n@@ -726,34 +750,34 @@\n TTCGCTTTCCACTTCATCTTACCATTTATTATCGCGGCCCTAGCAATCGTTCACCTCTTCTTCGTCCACG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14379_14856_2:1:0_0:2:0_41\n-TTACGAATATGATTAGGATACCTAGGATATCTTTGATTGTATAGTAGGGGTGACATGGAATTTTATCTGC\n+@chrM_14698_15195_1:2:0_0:0:0_c6\n+CAATGATAATAAATGGGTGTTCTACTGGTTGGCCCCCAATTCAGGTTAAGATAAGTAGGTTGGCTACTAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14703_15218_4:2:0_3:0:1_a0\n+TTTATTATCGCGGCCCTAGCAATCGTTCACCACTTCTTCCACCACGTAACAGGAAGAAACAACCCAACAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14792_15274_1:2:0_4:0:0_94\n+AGAATTTTGTCTTCGATACTTCCTGAGCTTGGTAAAAGAATTAAGATGATTGAGAAGTATGAGATGGAGG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_14825_15378_0:3:0_2:1:0_7d\n AGATATCCTAGGTATCCTAATCATATTCGTAATTCTCATAACCCTAGTATTAAATTTCCCAGACATACTA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14473_14928_1:3:0_1:2:0_1\n-GTGGATTAGCTGGTATGTAGTTGTCTGGGTCTCCTAGTATGTCTGGGAAATTTAATCCTAGGGTTATGAG\n+@chrM_14851_15357_4:2:0_3:1:0_5d\n+GATGTCTTGAGAAGAGAAGCTCTTCATTTGAGGTTTACAAAACCAGAGTAATGTTTATACTATCAAGAGA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14464_14944_1:1:0_0:1:0_b7\n-TGGGGTGGGGTGTTTAGTGGATTAGCTGGTATGTAGTTGTCTGGGTCTCCTAGTATGTCTGGGAAAATTA\n+@chrM_15077_15578_4:0:0_2:0:0_10\n+GCAACGAAGCCTACTATTCCGCCCAATCACACAAATTTTGTACTGAATCCTATAAGCCAACCAACTTATC\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_15119_15633_0:0:0_2:1:0_13\n CTGAATCCTAGTAGCCAACCTACTTATCTTAACCTGAATTGGGGGCCAACCAGTAGAACACCCATTTATT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14698_15195_1:2:0_0:0:0_c6\n-CAATGATAATAAATGGGTGTTCTACTGGTTGGCCCCCAATTCAGGTTAAGATAAGTAGGTTGGCTACTAG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14792_15274_1:2:0_4:0:0_94\n-AGAATTTTGTCTTCGATACTTCCTGAGCTTGGTAAAAGAATTAAGATGATTGAGAAGTATGAGATGGAGG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_15261_15717_1:0:0_0:2:0_29\n GAAGACAAAATACTAAAATTATATCCCTGTCTTGATAGTATAAACATTACTCTGGTCTTGTAAACCTGAA\n +\n@@ -762,14 +786,6 @@\n GAAGACAAAATACTAAAATTATATCCATGTCTTGATAGTATAAACATTACTCTGGTCTTGTAAACCTGAA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14851_15357_4:2:0_3:1:0_5d\n-GATGTCTTGAGAAGAGAAGCTCTTCATTTGAGGTTTACAAAACCAGAGTAATGTTTATACTATCAAGAGA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_15077_15578_4:0:0_2:0:0_10\n-GCAACGAAGCCTACTATTCCGCCCAATCACACAAATTTTGTACTGAATCCTATAAGCCAACCAACTTATC\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_15343_15804_3:2:1_2:1:0_11\n TCTTCTCAAGACATCAAGAAGAAGGAGCTACACCCCACCAACCAGAACCCTAATCTGGTATTCTAATTCA\n +\n@@ -782,19 +798,3 @@\n AGGACATAGGGTTTGATAGTTACTATTATATGTCTTTCAAGTTCTTAGTGTATTTGGGGTTTGGCATTAA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_4389_4907_2:1:4_2:1:0_43\n-TTACTTGTATTTTCATAGGGGCAAGAGGAGGACTTTAACCAAACACAAATACGAAAAATTGCCTATTCAG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_4740_5317_2:2:0_2:3:0_46\n-GCTGAGTAAGCATTAGACTGTAAATCTAAAGACCCAGGTTTAAGTCCTTTTTTTACCAGAGGTCTTAAGG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_8286_8815_1:2:0_4:0:0_4f\n-TGGCCTTGGTAGGTTCCTTCCCGAATTACGTCTCTTCATCATTGATATATTTTGAGGATATTTGTGAGTA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14703_15218_4:2:0_3:0:1_a0\n-TTTATTATCGCGGCCCTAGCAATCGTTCACCACTTCTTCCACCACGTAACAGGAAGAAACAACCCAACAG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out2-2.fastq.gz |
| b |
| Binary file test-data/samtools_fastx-out2-2.fastq.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out2-3.fastq --- a/test-data/samtools_fastx-out2-3.fastq Mon Mar 12 12:53:10 2018 -0400 +++ b/test-data/samtools_fastx-out2-3.fastq Fri Sep 28 04:39:19 2018 -0400 |
| b |
| b'@@ -1,11 +1,3 @@\n-@chrM_406_958_3:0:0_1:1:0_c3\n-TGTGAAAATTCATTGTTAGGACCAAAACTCAATCACGAAAGTAATTCTAGTCATTTATAATCCACGACAG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_600_1083_1:1:0_0:0:0_77\n-ACATTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_235_738_2:1:0_0:0:0_ab\n TGTTTGATTCTTTTGCTTACTTTAATACCTTTTTAGGGTTTGCTGAAGATGGCGGTATATAGGCTGAATT\n +\n@@ -14,28 +6,24 @@\n TTTCTTCCCATTACATTGGCTACACCTTGACCTAACGTTTTTATGTTTGATTCTTTTGCTTACTTTAATA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_713_1102_2:0:0_0:0:1_50\n-ATTAAAGTAAGCACAAGAATCAAACATAAAAACGATAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAAT\n+@chrM_293_831_0:1:0_1:0:0_b\n+TAGTTTCATAAAGGGTATAGTAATGTTCTTTTATAAGAAAATGTAGCCCAATTCTTCCCATTTCATTGGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_361_902_2:3:0_1:1:0_8e\n+CGTGTCAACAATAAATAAATAAATAGAATTAAAATCCAGCTTATATGTGAAAATTTATTGTTATGACCTA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_364_806_2:3:0_0:0:0_54\n GTCAACAATAAATAAATAAATAGAATTAAAATCCACCTTATATGTGAAAATTTATTGATAGGACCTCAAC\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_748_1226_0:0:0_3:2:0_a\n-TAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATAC\n+@chrM_406_958_3:0:0_1:1:0_c3\n+TGTGAAAATTCATTGTTAGGACCAAAACTCAATCACGAAAGTAATTCTAGTCATTTATAATCCACGACAG\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_293_831_0:1:0_1:0:0_b\n-TAGTTTCATAAAGGGTATAGTAATGTTCTTTTATAAGAAAATGTAGCCCAATTCTTCCCATTTCATTGGC\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_787_1256_2:0:0_1:1:0_5a\n-TACATTTTCTTCTAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGAA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_361_902_2:3:0_1:1:0_8e\n-CGTGTCAACAATAAATAAATAAATAGAATTAAAATCCAGCTTATATGTGAAAATTTATTGTTATGACCTA\n+@chrM_600_1083_1:1:0_0:0:0_77\n+ACATTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_655_1179_0:1:0_1:2:0_60\n@@ -46,14 +34,26 @@\n TTGTTCTTACTTTTAATTAGTCTTTGATCTTTCCCTTGCGGTACTAGTTCTATATCTCCAAGATGTACGA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_835_1289_4:2:0_0:1:0_44\n-GACTAAGGATGATTTAGTAGTAAATTACGAATAGAGATGTTAATTGGATTGAGCAATGAAGTACGCACAG\n+@chrM_713_1102_2:0:0_0:0:1_50\n+ATTAAAGTAAGCACAAGAATCAAACATAAAAACGATAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_748_1226_0:0:0_3:2:0_a\n+TAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATAC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_787_1256_2:0:0_1:1:0_5a\n+TACATTTTCTTCTAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGAA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_820_1322_1:2:0_1:1:0_32\n CTGTAATTCTTTTAGTTAGAAGTTTTCTAGTTAGTTCATAATGCAAAAGGTACAAGGTTTAATCTATGCT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_835_1289_4:2:0_0:1:0_44\n+GACTAAGGATGATTTAGTAGTAAATTACGAATAGAGATGTTAATTGGATTGAGCAATGAAGTACGCACAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_846_1403_2:3:0_2:2:0_85\n ATCTTCTCACTCTTTTGCCACATAGACGAGTTGATGCATAACATTGTTTTGAGGTAGCTCGTTTGGTTTC\n +\n@@ -62,10 +62,6 @@\n TCCGATTATGAGAGGACATAAGTCGTAACATGTTAAGGATACTGGAAAGTGTGCTTGGAATAATCATAGT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_1415_1865_4:0:0_1:2:0_5e\n-GGTGAAAAGCCTCACGAGCATGGTGATAGGTGGTTACCCAAAAAATGAATTTAAGTTCCATTTTAAACTT\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_1023_1543_3:0:0_1:0:0_30\n AGCTGTCCCTCTTTTGGCTATAATCTAAACTTACATTTTGATTTTGTTGTTTTTTTAGCAAGTTTAAAAT\n +\n@@ -74,6 +70,18 @@\n GGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAA'..b'CTACGTGCT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14070_14563_1:1:0_0:1:0_bd\n-AATGATATTTGTCCTCATGGAAGGACGTAGCCTATAAATGCTGTGGATATGACTGCGAACAGTAGAAGTA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14107_14610_1:2:0_0:2:0_8c\n-TATATGGGATGGCTGATAGGAGGTTTGTAATAACTATGGTACCTCAGAATGATATTTGTCCTCATGGAAG\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14698_15195_1:2:0_0:0:0_c6\n-TACCATTTATTATCGCGGCCCTAGCAATCGTTCACCTCTTCTTCCTCCACGTAACAGGATCAAACCACCC\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14792_15274_1:2:0_4:0:0_94\n-TAAAATTCCATGTCACCCCTACTATACAATCAAATATATCCTAGGTATCCTAATCATATTCGTAATTCTC\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14458_14976_1:3:0_3:1:0_61\n-ATGCAAATAGGACATATTATTCGGGTTTAATATGGGGTGGGTAGTTTAGTGGATTAGCTGGTATGTAGTT\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_14592_15040_1:0:0_0:1:0_39\n AGGATTGATAAGATTAAGGCTAGGACACCTCCTAGTTTATTGGGGATTGAGCGTAGAATGGCGTATGCAA\n +\n@@ -746,22 +750,30 @@\n ATTGAGAAGTATGAGATTGAGGCTAGTTGGCCAATGATAATACATGGGTGTTCTACTGGTTGGCCCCCAA\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14851_15357_4:2:0_3:1:0_5d\n-TCGTAATTCTCATAACCCTAGTATTAATTTTCCCAGACAAACTAGGAGAGCCAGACAACTCGATACCAGC\n+@chrM_14698_15195_1:2:0_0:0:0_c6\n+TACCATTTATTATCGCGGCCCTAGCAATCGTTCACCTCTTCTTCCTCCACGTAACAGGATCAAACCACCC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14703_15218_4:2:0_3:0:1_a0\n+GTATGAGATGAGGCTAGTTGTCCAATGATAATAAAAGGGTGTTCTACTGTTTGGCCCCCAATTCAGGTTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14792_15274_1:2:0_4:0:0_94\n+TAAAATTCCATGTCACCCCTACTATACAATCAAATATATCCTAGGTATCCTAATCATATTCGTAATTCTC\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_14825_15378_0:3:0_2:1:0_7d\n GGGGAGTAGCTCCTACTTCTTGCTGTCTTGAGCAGAGAAGATCTTCATTTCAGGTTTACAAGACCAGAGT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14851_15357_4:2:0_3:1:0_5d\n+TCGTAATTCTCATAACCCTAGTATTAATTTTCCCAGACAAACTAGGAGAGCCAGACAACTCGATACCAGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_15077_15578_4:0:0_2:0:0_10\n TTTAAGATAATATTCATGGTATATATATTGATTTATGTTGATGATTATTTTATTACCTTAACCATTGATT\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_15560_16128_1:1:0_1:1:0_38\n-CCATGAATATTATCTTAACCACATTAAACTAATGTTATAAGGCCATATCTGTGTTATCTGACATACACCA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_15119_15633_0:0:0_2:1:0_13\n TGTATGGTGTATGTCAGATAACACAGAAAAGTCCTTATAACATTAGTTTAATGTGGTTAAGATAATATTC\n +\n@@ -778,23 +790,11 @@\n GCAGTAAGAACCAGATGTCTGATAAAGTTTCAGTTTAGCTACCCCCAAGTTTAATGGGCCCGGAGCGATC\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15560_16128_1:1:0_1:1:0_38\n+CCATGAATATTATCTTAACCACATTAAACTAATGTTATAAGGCCATATCTGTGTTATCTGACATACACCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n @chrM_15744_16179_0:1:0_0:2:0_4c\n GGGCCCATTAAACTTGGGGGTAGCTAAACTGAAACTTTATCAGACATCTGGTTCTTACTTCAGCGCCATC\n +\n 2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_4389_4907_2:1:4_2:1:0_43\n-TTATAGCTAGGGTGGAAAATATTCGGTTGGGTTTAGTTTTTGTTTGGTGAGTTATTATTTTGGAGTTATT\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_4740_5317_2:2:0_2:3:0_46\n-TAATAATAGCAACACTCATAGCAATAATAGCTCTACTATACCTATTCGTATATACTCGCCTAATTTATTC\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_8286_8815_1:2:0_4:0:0_4f\n-ACTAAGAAGCTCACTTGCCCACTTCCTTCCACAAGGAACTCCAAATTCACTAATTCCAATACTTACTATT\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n-@chrM_14703_15218_4:2:0_3:0:1_a0\n-GTATGAGATGAGGCTAGTTGTCCAATGATAATAAAAGGGTGTTCTACTGTTTGGCCCCCAATTCAGGTTA\n-+\n-2222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out2-3.fastq.gz |
| b |
| Binary file test-data/samtools_fastx-out2-3.fastq.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out3-1.fasta.gz |
| b |
| Binary file test-data/samtools_fastx-out3-1.fasta.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out3-2.fasta --- a/test-data/samtools_fastx-out3-2.fasta Mon Mar 12 12:53:10 2018 -0400 +++ b/test-data/samtools_fastx-out3-2.fasta Fri Sep 28 04:39:19 2018 -0400 |
| b |
| b'@@ -1,13 +1,13 @@\n->chrI_25874_26397_2:0:0_7:1:0_2\n-ACCAATGGTTTGCGAACTGATGATAGCATCATTGTCATCAGAACACCAACAACAGCCCCTACTGCCATGACTACAACTCAGCCATGGAACGACACTTTTACCTCTACATCCACTGAAATGACCACCGTCACCGGTTCGAACGGTTTGCCAACTGATGAAACCATCATTGACATCAGAACACCAACAACAGCCACTACAGC\n->chrI_93599_94144_3:1:0_9:0:0_1\n-CATCCAATGGTCCTGGATCTTAAGTCCCATAGCTCTTTAACGATCTTGTCCAAATTTGCAATGTTTTTAACAAGGTCATTTTCATCTTTCAGAACCTCATCTTTCAAACTGTGGTTTAGTAAAGCTTCTGTCAGCTGTAACTGGAATCCGATATGAGGCTGATAGTAGTCTAATTCATGTGAATTTAGCGAAAGATTGGC\n->chrI_139586_140147_6:0:0_3:0:0_3\n-TGAAAACCAACCAGGTGTGTTGATTCAAGTCTTTGAAGGTGAAAGATCCAAGACTAAGGACAACAACTTGTTGGGTAAGTTCGAATTGAGTGGTATTCCACCAGCTCCAAGAGGTGTCCCACAAATTGAAGTCACTTTCGATGTCGACTCTAACGGTATTTTGAATGTTTCCGCCGTCGAAAAGGGTACTGGTAAGTCTA\n->chrI_176449_177020_5:0:1_5:0:0_0\n-TAGGCCGTTATTTCCGTAAAGGATGGTATAATAATAAGAAATTTATCATATTAATAATACCTATATCCAAAAATTTATATTTATATACATGCGCCTAACTATTCATACTATTAATTTCATATTATTAAGCTTTTTTTTTTTCATTTATCATTTTTTTTCGTAACCCTCTCCTACCTGTACAGGTTTCATTCGTAAAGCAG\n->chrII_464058_464495_1:0:0_2:0:0_1\n-TTGTTGTTGTTGTTGTTGCTGTTGTTGTTGTTGTTGTTGTGCCTGCGCCTGTGCTTGTGCTTGTGCCTGTGCTTGTGCTTGTGCTTGCGCTTGTGCATGTGCTTGTGCTTGTGCTTGTGCCTGTGCTTGCGCCTGTGCTTGTGCTTGTGCTTGCGCTTGTGCTTGTGCTTGTGCTTGAGCTTGTGCTTGTGCTTGAGGTT\n+>chrIII_58852_59360_5:0:0_4:0:0_4\n+TCCAATTCCTTAGAAAACGCGGTCTTTCTCAACTGTACATAGTAATCTATCTGGTCCAGCCAATTGCACTTAGCACGGTCCCAGGGCGTATTCACTTGGGTCCTGGCATCCAGAAACGCCTCCACACAGCCCTCGATCTTGCCGCTTCCTGTACGGTCCTTCACTAATCCTCTGACAGAGATCGTCCCATTACTTAGTTT\n+>chrIII_65894_66394_3:0:0_8:0:0_1\n+ATTATTTTCGTTAGTGTTCGGTTTCCAAGTTAGAAATAATCTACTGGAAAACCTTTGGGATCAACCCAAGCTTACTCATTCTGATTTTCACAGCGTTTCTGTGACCGTCTAGACCCTCCTTCTTGGCAACGCACATAACAGCTCTACCGATGTTTTCTAAACCTTCAGGTGTAATGTTTTGGGCAGTGATCAACTTTTGG\n+>chrIII_80246_80792_1:0:0_3:0:0_0\n+TTTTCTCTTTTCGCCAATTCAAATTTCTCAGGCTCAAATATTTCATCAATCAGTGTAGCGACGTTGGAACTTGTTCTCTTTGCATCCTTTTCAATGTACTCCCAATCATCATCATCTATTAGGTTAGTAACGTTTGATAATGATTTTGATGTTAGTGAGGTTCTTTTTGTATTAGGCATATAAGATAATCTTTTGCTTGA\n+>chrIII_209470_209900_3:0:0_9:0:0_2\n+GGGTTCTGTGGCCAGCCATCTCCTGAATATCAGAAAAATAGTGCGTGTATAAAATCTACGTATACTAACTCTGGGTAAAGTAAACCTTTTTGTACTGTATTCTTTTTTTTTTTTTTGGTTTCCCGTCGTGATGACGTACGTGTATAGAGAATTGAAGCGAAAATAAAAAAAACGACAGAAAATATAGTTCTCCTTGGCTT\n+>chrIII_238949_239533_6:0:0_6:0:0_3\n+GTCACATATTCTTTGCTTCAATTGCTCTCTAGGAAACTGACACACTCGTAGATTGGAAGACCGAAGAAAATAGATAGACTTTCGAATAAGTTCAGCAACAACCTGTGGATGAAATCCTTGCTGCTCTGCCTGTACTCCTTAGTACTCTGCCAAGTCCACGCTGCACCTTCATCATGGAAGCAGATTACCTCCAAGGATGA\n >chrII_128532_129141_1:0:0_5:0:0_c\n ATGACTTGTTCCGTGTGGATTTCCAAACTTGATGTGGGCTGGGCATTATAGGGAGTTTGAAGGGTCTTCACTGTTGCTGATGGAATTTCTCTGGTATCTTCAAACTCATCATCGTCTGAAGAGGATGAATCGCTTTCGTCAATATGCAATTCCTGAATTGGTGGAAACTCTTCATATATTGTCTTTGCTTTTGGTTGAGC\n >chrII_178741_179333_0:0:0_5:0:0_7\n@@ -18,6 +18,8 @@\n GCAGATCGTTTTCCGTCTGGCTTGAAATGTTCTAGTCTCCTTTTTTTCTTGGCTTCGGGAAAATACGATTTGTTTGTTAATCTATATGCAGAGCCGCTGCTCTGCATGGATTTATGATCTCGAGTGCCATTGAACTTGAAGCATCTTATGTTGAAAGGATTTGTATGCCATCATACCCGAACTTTTTTAGCACGTGAAAA\n >chrII_462520_463118_3:0:0_3:0:0_b\n ACTGAAGCATCTGCACCTTCTACTGAAGAGGCGGAGCCAGCCGCTTCCAGAGATGCTGCAAAACAACAAGATGAAACCGCTGCTACAACGATAACTGTAATCAAACCTACTTTGGAAACAATGGAAACAGTGAAAGATGAGGCCAAAATGCGTGAGGAAGAGCAAACATCTCAAGAAAAATCCCCACAGGAGAACACACT\n+>chrII_464058_464495_1:0:0_2:0:0_1\n+TTGTTGTTGTTGTTGTTGCTGTTGTTGTTGTTGTTGTTGTGCCTGCGCCTGTGCTTGTGCTTGTGCCTGTGCTTGTGCTTGTGCTTGCGCTTGTGCATGTGCTTGTGCTTGTGCTTGTGCCTGTGCTTGCGCCTGTGCTTGTGCTTGTGCTTGCGCTTGTGCTTGTGCTTGTGCTTGAGCTTGTGCTTGTGCTTGAGGTT\n >chrII_482749_483235_3:0:0_1:0:0_0\n TTATATGACTATGGTCCACCAGGTTGTGCATTCCAAAACAACATCATTGACGGCTGGAGAAAGCATTTTATTTTGGAAGAAGATATGTTGGAAGTTGATTGTACTATGTTAACTCCATATGAGGTTTTGAAGACCTCAGGTCATGTTGACAAATTTTCTGATTGGATGTGTAGAGATTTGAAGACTGGTGAGATTTTCAG\n >chrII_509290_509702_4:0:0_3:0:0_4\n@@ -32,16 +34,6 @@\n TACAAACAGCAATATTTGAGGCCTCCAGTATTTAATATTGTCTTGACGTAGGCGAAGCAAATACTTTCTCACTTGATGATATATTAAACTTTGAGACACATCACCCCAAGCCTTCGGTGGTGAAAAATAATGAAAGAATAAAAATAGCAAAATCATAGCCAAAAACAAGACAGACGCTGAGATGCCATCAACTATTAACA\n >chrII_798295_798806_6:1:0_5:1:0_a\n AATGTTGTTCTTGATAGTACCCGAAACTCTTGCGGCTGCCAAGACAGCACCCAAGAACTCACAGAGACCCGGCAAAACCATGGCTTGCCAGTATTTTAGAGATCTAGA'..b'-CTTTTGACCATTTCATTGATGTTATAATCAGGTTGCACAACAAGTGATGCTGACAATTTTCTATTATCAGCCTTATGCTTTTTGATACCTTCTTTGCTCTGGATACTACGCAAGACCCAAGAGTCAACGTCTTTCGCATCGTACACAGATAAAGAACCGTTATAAAGACTGTGCCGTAACAGTGGAGACGATGAAAAGAA\n->chrXVI_866925_867424_2:1:0_4:0:0_e\n-ACGTTCTTGACGTCCTTTTTCAACCATAGTTTGATAGTATTGTCGATAGAAAAAGTACTTTGACCTGTTCCCACATTTGTAGTAGGAGCCACGGTGGTAATTCTGGAGTTGATAGCTTTAATCATCTTTTCATACTCTGCATAAGCTAAATTAAAATTAAAATATGCGTCTTTCGCCCTTAAGGCAACCCTAGCGGCTGA\n->chrXVI_889501_889988_11:0:0_5:0:0_0\n-CAACAAAGATTCTCATACAATCCGCACAAAATGCAATTTATTTACGTCCCCAATACAAAGCCGAATGGGCTAGGAGGCAATGCGGGTTTTCTAGCAGATATAGAGGACAAAGTTCAAATGTTCTTGACACGATATTACCTCACGAACGACAGAGTCAAGAGAAATGAAAACTACCAAAACAGTGACATGTATACTCCATA\n->chrXVI_908795_909263_5:0:0_2:0:0_a\n-AGAGGCAGATCAGATTGGCACTCACCCTTGCCATCAATATCCCCTTCGATGCATTATGGATCGTTGAACTCGAGAATGTCTCAAGGCGCCAATGCAAGCCATTTGATTGCAAGAGGCGGTGGGAATTCATCTACTAGTGCCTTGAATAGTAGAAGGAATTCTTTAGATAAGAGCTCAAACAAGCAGGGTATGTCATGCTT\n->chrXVI_912895_913350_7:0:0_5:0:0_9\n-GAATATTTACCAACTGGTTGTATAACTGATCAATTTCTGAATTTTTAATTATTTCCCAGGAGAATGAATTTAGTTTAATTTGATAATGAGGATCACTAGGTTTTAGTTTTAACCTGTTCTGACTAAGGGTCTTACCTATTTCCGTTGTTTCAATATTAGACCGTATCTTTATAAGATTTCATAACGCGTCCTGGGGTGTA\n+>chrX_20624_21148_5:0:0_6:0:0_6\n+TCAGCATCGTAATCTGCGGATCTTCTTTCTGGTGGCACCCATGAGGCTTATTTCCATGCTGGCACACCTTCCCGCCACATAGTATTCACCTCCTCCAGCGTCCGGCCTTTTGTTTCTGGTACACAGAAAAAGACATAAAAGTATGCAAAAACCAGACAGCCTAAGAATACATAACCGTAGTAAAAGTTGATTGCCCCGGT\n+>chrX_32511_32973_6:0:0_10:0:0_7\n+GGTGGAGGTGTGGCGTCTCCAACTGAGAAAATATCAAACAAACAATTTTGCGACGACGAAATAAAAGCACTTGTAGATGTCGCAAATAGTTAGCACACATACGTAACAGCACACGCCTACACTGCGGAAGCTATACAAAATTGTATCAAGTTAGGTGTTAATGGTAACGAACACGGAAACTTATTAGATGAACGTACCGC\n+>chrX_75095_75508_2:0:0_2:0:0_2\n+CAATCTACCGTTCAATTGAACAACAATCTTACCAGATCTGTGGTCATCGATGTATTCAAATTCACCAATGTAACCGTGCTTTTGCATAACTTGCAAAAACTTTATAATGACCTTGGAGGATGGTCTGATTAAAACTTGACGCTAACCGGTCTTTTCAGCGTTGTTAATGGCATTCAAAGCATCAGCTAAAACGGAAGATC\n+>chrX_131958_132464_9:0:0_5:0:0_0\n+GTGAGCCCTTAATAATATCAAGAAGCGGCCCGCGCGCCAATGTTGCATCCTCGGATACAAATGTAGACGAAGTGTTTTTTAATCGACATGATGAAGAAGAATCCTGGATACTGGACCCAATACAGGAAAAGTTGGCACATTTGATTCATTGGATAATGAACACTACATCTCGTAAACAAACAATGAAAAACAAAATTCAA\n+>chrX_185042_185518_4:0:0_1:0:0_b\n+ATTAACTACTTATATACTTAAATTATATGTTTTTGAAATTTTTAATATGTAAAGCAAATCTGTACGAATAAAGGCTTTTTTCATATTTTATTTGCCTCAATGAAATAAATCGTCTCTTCTCTGGTTCCATAAGGGCATTTTGTTCCTTATTTCTTGCAAACGCTCACGATCCAAATCAGCGAGAATTAGTTGTGGTCCAA\n+>chrX_204570_205015_2:0:0_10:0:0_3\n+GCACAAGCGATAGAGGAGATGTTTAAAGTGTTTAAGCTCACTTTATAGGGTGAAACACATTTTGACGACCGTAAAAGGTCATTTGATTTGGTATTGAGGTCGAGAAAATATTTTCAACTAGTGAAGGATACATTAAACACGCTCACAAAACAACATAAAAATCCGTGATAGTTTAATGGTCAGAATGGGCGCTTGTCGCG\n+>chrX_358634_359139_4:0:0_4:0:0_9\n+ACCTGCTTATACATCAAAGCGAACACCTACAGTATAAACAAGGGTTCCACGAACTATTAAGCGTCATTTATCTGCAATTATATCACGGTACATATCTCGATAATACCGATTAGCAAAACGTTGTGATTATCTTTAACAAGCTAATGAACCAAATCGAACCGATTTTTTATAACGAAGAAAATTTGATTAACTGGGATAAG\n+>chrX_382849_383384_3:0:0_5:0:0_1\n+GCACCAAGAGGTGTACCTCAAATTGAAGTCACATTTGCACTTGACGCTAATGGTATTCTGAAGGTGTCTGCCACAGATAAGGGAACTGGTAAATCCGAATCTATCACCATCACTAACGATAAAGGTAGATTAACCCAAGAAGAGATTGATAGCATGGTTGAATAGGCTGAAAAATTCGCTTCTGAAGACGGTTCTATCAA\n+>chrX_438844_439314_5:1:0_2:0:0_8\n+AGGAAAGTCGTATAATGTCAGAACTCTTTGGAGTATTGAAATGTAATGCTGGCAGAATTATTTTGAAGGACCCCTCCGCCACTTCTAAAGATGTTAAAGGATATATAGCTTCAGTTATCAATACCTGTAAGAAAGGGAGTATTACAAAGAAAGCAGAAGTGGCCGAAATCACTGTTGATGGTTTAGACGCCAATCAAGTT\n+>chrX_582991_583504_1:0:0_3:0:0_a\n+TCAACCAATTGAATTACATAAGCTGTCGATTGTCGATAAACACTCCCAAGGACAGCAGCAACAGCCGCATCAAAAACAACATGAAGTGCAGCCTGAATCAAAATCACCAATGGTTACGACACCTTTAAAGCCCAAAAGACTTGCTATACCTATATCAAGTCCGCACAGCTCTACGACAAATCAGTCACCCGTGAGCGACC\n+>chrX_610495_611012_5:0:0_2:0:0_5\n+TTTTCAGCACATTATTACTATTTACGAAAAAAGGGAGTAGGGAAAAATGGCGCGCTTATGGATCCTCAAATAAGGACAAAAAAGTCAAGTAATGAATATCAAATTGAAATGAGTATGCTTACATAGATTTATTTGGTATGTTTTCATTTTGTTTTTGTTTCTTATGTTGCTGCTTTATTTTGTGTAGGTAATAAGGAAGA\n+>chrX_743509_743937_3:0:0_2:0:0_4\n+ACAGCTCGAATCCCAAAAGATTGTTCTACCTCAAGATCTTTTCAGAAGCAGCTTTACCTGGTTTTGTTATGAAATTTACAAGTCCTTAGCGTTTCCGAACTTGATGCTATTATGGCTACCACTTAGCGTCTGGTGGAAACTTTCCAACAATTGTATTTACCCACTTATAGTTTCACTTCTGGTCCTGTTTCTGGGACCAA\n' |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out3-2.fasta.gz |
| b |
| Binary file test-data/samtools_fastx-out3-2.fasta.gz has changed |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out3-3.fasta --- a/test-data/samtools_fastx-out3-3.fasta Mon Mar 12 12:53:10 2018 -0400 +++ b/test-data/samtools_fastx-out3-3.fasta Fri Sep 28 04:39:19 2018 -0400 |
| b |
| b'@@ -1,11 +1,13 @@\n->chrI_25874_26397_2:0:0_7:1:0_2\n-ATTTCAGTGGATGTAGAGGTAAAAGTGTCGTTCCATGGCTGAGTTGTAGTCATGGCAGTAGTGTCTGTTGTTGGTGTTCTGATGACAATGATGGTTTCATCAGTTGGCAAACCGTTGGTACCGGTGACGGTGGTCCTTTCAGTGGATGTAGAGGTAAAAGTGTCGTTCCATGGCTGAGTTGTAGTTATGGCAGTAGTGGC\n->chrI_93599_94144_3:1:0_9:0:0_1\n-TGTTATATCTAAGCCTTCCAAGCGACCCACACACCATTCGCATTCATCAGACGGGAGTTCTAGCACGCAGACAGATATATCGTTACAGAGCTTGCTTTACCATGATCTTGAAAGCTCACCAAAGAAACATGTTTCGCCGTCAAGACCGCCCTCTGTAGCTTCCGAATCCTCTCCTGCCGTTGCTCATCCCATTGGGCTTT\n->chrI_139586_140147_6:0:0_3:0:0_3\n-TGCAGCGCCACCTGGAGCACCACCAGCTTTGTACAACTTAGAGATGATTGGGTTGGCAATGTCTTGCAAGTCCTTCAACTTGTCATCGAATTCTTGCTTGCTGGCAGTGGTGTTGCTGTCTAACCAAGAAATAGTCTCTTCAGGCTTCTTGGTGCCGGTGTCCTTGTCAGCTTGTTCCAATTTGTCACCAGCTTCAGAAA\n->chrI_176449_177020_5:0:1_5:0:0_0\n-TGGTCAAATTAACTTCAATCGCTGCCGGTGTCGCCGCCATTGCTGCTGTTGCCTCGGCCGCAGGAACCACTACATTAACTCAATCTGACGAAAGAGTTAATTTGGTTGAATTAGGTGTTTATGATTCCGATATCAGAGCTCATTTGGCTGAATACTACTCTTTCTAAGCTGCTCACCCAACTGAAACTTATCCAGTTGAA\n+>chrIII_58852_59360_5:0:0_4:0:0_4\n+AATTTATCATTGCGTGGGTACAACCGTGCACCATTTCTGAAAAATTTGCGATGAGCATCCCTCAAAATCCGTATTATCCGCTAGTGTTTTGAGGTTCAACAAGACAACATATAAGAAGGGAAGAAGGACAGGAGGCAATGAGAACTTGGGTCTAGCTCGAGAGTCCAGATCCACATGCAGGTTCAAAAAATGGTGCGAGA\n+>chrIII_65894_66394_3:0:0_8:0:0_1\n+ACAATCAAGCTTTACACCTGCCACGTGTGGAACTTGTTCGTACATGTATTGCTCACAGTACGATCGTTCTTTGTGACGGTTACGAAGAAGCCCATGAAATGTCCAACCAATATGCACCATAACATTTGATTCTACAAATCGCCAATGCTAACGATTATGTTAAATTGGTTGACAATGCATGGTCCTTATTTGTGGGTGCT\n+>chrIII_80246_80792_1:0:0_3:0:0_0\n+GTTTCAAACTGGACTCTGTAAGGGGATCGAATAAGAAGAACCGCAATAAGATAAAGAAAACCAAAAAAAATAAAAGATCTAGCACACTTTCGTCATCGTCATCATTATTATTGAACAACCGAAGCATACAATCTACGCCACGCAGACGTCCATCCAAGAGGCATTCCAGGGAATTCTCTTCTAGCAGGAAGAGATCGTCC\n+>chrIII_209470_209900_3:0:0_9:0:0_2\n+TCGATGAACTGTCTCCATGACCTGTTGGAATTCGACGTGAATTGTTGGAATGCTGTGGGATTTTTGAACCTCACCAAATACTCCTCTGCGTATGCGAGGTTGACCAGCAAAGAGATGAGTATGCACTGTGGCTTCCTGACGAGTGTTTTTTTGCTGTTTTTCTTGGCGGATGTTAGAGGATGTCTAGCACTTGAGTATAC\n+>chrIII_238949_239533_6:0:0_6:0:0_3\n+AAAATAGGCCATTGCGAGTCTTTCAGGCCTGTCATGTTTTAAGTAAAAGTTTTCTTCATCAAATTTGTGCCCAAAGACGGTGAAAGGACCCACATCTGGGGCAACCCCACCACCGTGGATATACTTGTTAGGGTAAACCTTGTTGATTTTGGTCTTACGGAACGAGTAAGTATGTATATCATTGGGATCTTTCCCTTCGA\n >chrII_128532_129141_1:0:0_5:0:0_c\n ATGCCAATAGAAACAACGGCACCCAGTCAGGAAATGAGACAGCAAATCCAAACTTAACTGAAACATTAAGTGATAGGTTAGATGGTTATTTGAATGAATATGGTATTCCAAGAAGTCAATCCTTGACATCGTCTGTTGCAAACAATGGTCCTCAATCCGTAAGAGATGATGTTGCGCTACCGGAAACGTTGGAAGAACGT\n >chrII_178741_179333_0:0:0_5:0:0_7\n@@ -32,16 +34,6 @@\n GGGGATGCTCGGTGCTGCTTATGTATTAGAAGCAATTGCAAATGATAACATTATTCCTGGTTTGGAGATTTTTGCTCATTCACCGTTATATTCATTGATTTTTACATGGATTCTAACACCGCTATGTTTGTTTTCAGCCGTCAATAAAAACGCCACATTTATCACAATGACATTCTTAATGACGTTTGTGGTCATGAATT\n >chrII_798295_798806_6:1:0_5:1:0_a\n ATCAATACTAGATGTCACAGCCACTTTGGATCCTTCTATTATGTCAATCATTAGATTAACTCAGTCAATAGCAGATTTTTTTTACAATGGCTACTGGGTGGACATCTCCAAACAATTCATGTCACTAAGCCCGGTTATCGATATGAAGAAAATTATATATAAACGTGCTGAAGATGATCTTTACCTTGCGGTTATTTTAC\n->chrIII_58852_59360_5:0:0_4:0:0_4\n-AATTTATCATTGCGTGGGTACAACCGTGCACCATTTCTGAAAAATTTGCGATGAGCATCCCTCAAAATCCGTATTATCCGCTAGTGTTTTGAGGTTCAACAAGACAACATATAAGAAGGGAAGAAGGACAGGAGGCAATGAGAACTTGGGTCTAGCTCGAGAGTCCAGATCCACATGCAGGTTCAAAAAATGGTGCGAGA\n->chrIII_65894_66394_3:0:0_8:0:0_1\n-ACAATCAAGCTTTACACCTGCCACGTGTGGAACTTGTTCGTACATGTATTGCTCACAGTACGATCGTTCTTTGTGACGGTTACGAAGAAGCCCATGAAATGTCCAACCAATATGCACCATAACATTTGATTCTACAAATCGCCAATGCTAACGATTATGTTAAATTGGTTGACAATGCATGGTCCTTATTTGTGGGTGCT\n->chrIII_80246_80792_1:0:0_3:0:0_0\n-GTTTCAAACTGGACTCTGTAAGGGGATCGAATAAGAAGAACCGCAATAAGATAAAGAAAACCAAAAAAAATAAAAGATCTAGCACACTTTCGTCATCGTCATCATTATTATTGAACAACCGAAGCATACAATCTACGCCACGCAGACGTCCATCCAAGAGGCATTCCAGGGAATTCTCTTCTAGCAGGAAGAGATCGTCC\n->chrIII_209470_209900_3:0:0_9:0:0_2\n-TCGATGAACTGTCTCCATGACCTGTTGGAATTCGACGTGAATTGTTGGAATGCTGTGGGATTTTTGAACCTCACCAAATACTCCTCTGCGTATGCGAGGTTGACCAGCAAAGAGATGAGTATGCACTGTGGCTTCCTGACGAGTGTTTTTTTGCTGTTTTTCTTGGCGGATGTTAGAGGATGTCTAGCACTTGAGTATAC\n->chrIII_238949_239533_6:0:0_6:0:0_3\n-AAAATAGGCCATTGCGAGTCTTTCAGGCCTGTCATGTTTTAAGTAAAAGTTTTCTTCATCAAATTTGTGCCCAAAGACGGTGAAAGGACCCACATCTGGGGCAACCCCACCACCGTGGATATACTTG'..b'-TTACTTCCTTACAATGTTTCAACCAGCAAGAAAATCCCGTTTACCCTGAATTGCTGGCCCCCTTTTATGAAAATTCATCCTATAATAAGAACGCGCCAATGGTAGAAATATTTTGGATCCTGGGGCCATCAGTTGGAGGTATTTCAGATCTGGAAGATTTGATTGTTTCTCTACATCCATTGATTTTCAAGATGGATCAC\n->chrXVI_866925_867424_2:1:0_4:0:0_e\n-ACAGTTCGCTCTGAAATCTCCCCCTGGGTTTCCCAATGGAATGAAACGTTGGAAAAAGAACTATCCGACCCTCGATCTAATTTGACTAGACATATTAGGATGAATTTCGAAACCTTTAGGTCATTACCTACATTGAAAAATAGCATAATTCCATTAGTAGCGACATCCAAAAATTTTGGTTCACTGTGCACTGCCATAAA\n->chrXVI_889501_889988_11:0:0_5:0:0_0\n-TGGAATTTATTTCGTCCAGAATAGTATATTCCTTCCACAAGAACCATGCAACCTGGGACGTAGTAATGTCGTTGTGTAGGGATAGTTTGGGAAATGTCAATTTCGACAGATCCAGACGGATCTTCCAGTGACCAATTGCCCTTAAAGTTCTTATTTAAGAGCCCCAATAGTAGAAAGTTTTGAGCATCCCTACCTAGTAG\n->chrXVI_908795_909263_5:0:0_2:0:0_a\n-ATTTCGCCTGAGCTTGAAAGGGCGCAGTAGTTGGTTTAGAGTAATGGTATGGTTGTCTGATAGGTATCCTACTTTTTATGAAAGAACTTGAAATGCTATCAATTGATCTTGGAGATATTGAACTTTTGAATTTTGTAGGACTGTTTCCCATTTGGTTGAGCAAACGGTCATTCTCGTCATCATCATCTTCTTCTACTCCT\n->chrXVI_912895_913350_7:0:0_5:0:0_9\n-ATAACCATTTAGCGTGGAAAGGACTTTTTCTCTTATTTAGAACCACTGAGGTTGTCCCAGACATACTTTCGTATGATGAATATTTTGACCTGTGTGGCCAATATGCAGACGCACTTTAAAAGCCGGAACAGTCTCAAGTAGAACTAATAAATGACAAAAAATTACTACAGCAAACGCATCCATATTGTCAAAAAGCCTTT\n+>chrX_20624_21148_5:0:0_6:0:0_6\n+CATTGAGAGGTTTGGACTCCGTACGTGTCTATTGTGGGGTGCTGCTTCTATGCTATGCTGCTTTGCTGTGTTTGCCTCCGTCGGTGTGACAAAGAAGTGGCCTCAAGGCAGCAGTCACCAAGACATTACTTCTCAGGGCGCCGGTAACTGTATGCTTGTGTTTACTATGTTCTTCATTTTTTCGTTCGCCACCACTTGGG\n+>chrX_32511_32973_6:0:0_10:0:0_7\n+TCTCATGTGTCGTTTGAACTTTCCCTCTAATACGAAACTCTTGCGATTGATAACCATATATAGGACCCACTACATCTGAACCAAAACACATTTTAACTTTTATTTTGTGGGCAATTTTCATTGCATCAATTCCTTTGTAAAGCACCTCTGTATTTTTTCTACTATTTTCAGGTCCCAAGCAAGCACTAAATTGATCAGAA\n+>chrX_75095_75508_2:0:0_2:0:0_2\n+AAAAACTCAAATATTTAGGACGCGCGATTACCAGCGGCATGTTTACTCGCTGGAAGATGTGAAATAATTCTTGAATATGGGTTTGCAGTTAGACAATTTCAATCTAAATAATCTTAATCGACTATTCAATTCTTAAATTGTAAGGTTTTTTAATGGCCTTTCAGTTCTAGTATTTTTTATAAAACAAGACCAACATACAT\n+>chrX_131958_132464_9:0:0_5:0:0_0\n+GAATGGCACATTGTAAATTCAGTTTCAGAAACAGATCTGTGCCTGAGATGTTGCAAGAATTAAAGCTATCATTGATACACCGAGAAACAAATTTAAACATTTGCTTTAAAAGATTGGAATAATGGGAAAGTAACGTCATGTTATCGGGTCTTTTTTTCAAAATGTACTCTTGTATCATACTGCAATTCCTCATCAGTTTC\n+>chrX_185042_185518_4:0:0_1:0:0_b\n+CGATCAATGGGGGCTGAAATCTTATGTTTTCCCAGTGCGTTCACTATTAAAACAGGGGAAGCACATTGGTAGTTACTAGGCAGCGCACGCGCGGTTGACACTCAATGCTATGTGCTCATGCCAGGGCAGGTTGGAATGCACGATCTCAGTGATCCAGAGTGGGAGAAACAATCACATATGAGCGCTCTCGAAAAAAGCTC\n+>chrX_204570_205015_2:0:0_10:0:0_3\n+AACTCATAGCTTCAAAATTTAATAAAAGATAATAGGATTACGTAGATGAGCCAAAAAAAATAAAAAAACGGACGTACTGCAGCCTGTTCAAGGACGGCTTGGTCGATTGTTTTTCTGTGTCGTAGAACTAGACTGAATATATATCATCGGTATCTTATACCCTCCTACAAGGTGGAAATAGTACGAGAACAGTCATCAAG\n+>chrX_358634_359139_4:0:0_4:0:0_9\n+TTCACCTTGGCTCACTAGTTCGTGAAGCTCATCGTAAATGGATAACCAAAGGGTGATGATAGTGCATGCAATGAAAATATCCAAGGGATAATTGCACGTCAGGACGTGGTCCCAAACGATTAGCACATATTTTAAGGGTAATTCTCTTAAAAATAACAACCATGTCCATCGGATGAGCCAGATTAGGTTGGAGTGAATCA\n+>chrX_382849_383384_3:0:0_5:0:0_1\n+TTTCACTATTTTATCTACAATACGTCGTGTTCGCAATAATCACCATCGTCATCTTCATCTTCGTCGTCATAATCAGCGGCACCAGAACCATCATCACCTCCGTACAACTTAGAAGTAATTTGATAAGCGACCTTGGACAAAGATTCGAACTTTTCATCAAAGTCTTCAGCAATGGCGGTTTCAAAGTTATCATCTAACCA\n+>chrX_438844_439314_5:1:0_2:0:0_8\n+TGGTTTTTTCGTCATCCATACTAGGTTCTTCATCGTTCTCGGAAAGACTATCATTACTCTGCTCCTCAATCTCAGAAACATCAGCAGAGAGCATCTGCTTTTCTTTAAAAACACTTTCTGCCTCCTCTAGTTCACTTTCTTCCCCGGATGATGAGTTCAGGGTGCTACCATCAGAGAGATTGTGAGAAGGCGTGAGCACA\n+>chrX_582991_583504_1:0:0_3:0:0_a\n+GTTGCTATTAACATTATTATTGGGCTTACTCAAAAAATCGTTTATACTCTTTTTTCCCTTGAGCATATTTGGTGAATTATTTACGTCCACAAATGTCTGTTGAATTCTTTTGGTAAAAGTAGAGAGGTATTCACTTGGGTTCTGGTTACCTAATTTCTGTTGTCCATTTCGGGGCAGTGTATCTTTGAACTGTAACTCTA\n+>chrX_610495_611012_5:0:0_2:0:0_5\n+AAGGATAAGTCCATCTCATTGGAAAAACAGTCCGGTATGAAGAAAAACATAAGCATTGGTGCTCAACTACTGAAAGAAGAAGGTTTTAGAGCTTTGTACAAGGGTATTACGCGAAGAGTGATGAGGGTGGCTCCAGGTCAGTCTGTCACCTTTACCGTTTATGAATATGTAAGGGAGCATTTAGAAAATTTGGGTATATT\n+>chrX_743509_743937_3:0:0_2:0:0_4\n+TCGAGAAGGGTTGTTCTGAACGCTTCTTGGCAGCCCATGGCATTGAAGAAAAAGTACCTAGTATTCCAAGCCTTATTTTCATCTAAGTACGAATTTAGATTTGCTGCCACAACTTCCCAATCATGAGGATCAGAACATGGTGTGTTTTCAGTAACCTCTTTGCAAAACTGAATGAGTTGTTTCGATAAGGAACGCTTACG\n' |
| b |
| diff -r a0d039fa9771 -r a8d69aee190e test-data/samtools_fastx-out3-3.fasta.gz |
| b |
| Binary file test-data/samtools_fastx-out3-3.fasta.gz has changed |