| Next changeset 1:a8d69aee190e (2018-09-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4 |
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added:
macros.xml samtools_fastx.xml test-data/samtools_fastx-in1.bam test-data/samtools_fastx-in2.bam test-data/samtools_fastx-in3.sam test-data/samtools_fastx-out1-1.fasta test-data/samtools_fastx-out1-2.fasta test-data/samtools_fastx-out1-3.fasta test-data/samtools_fastx-out2-1.fastq test-data/samtools_fastx-out2-2.fastq test-data/samtools_fastx-out2-3.fastq test-data/samtools_fastx-out3-1.fasta test-data/samtools_fastx-out3-2.fasta test-data/samtools_fastx-out3-3.fasta |
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| diff -r 000000000000 -r a0d039fa9771 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 12 12:53:10 2018 -0400 |
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| @@ -0,0 +1,84 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.3.1">samtools</requirement> + <yield/> + </requirements> + </xml> + <token name="@TOOL_VERSION@">1.3.1</token> + <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <xml name="filter_options"> + <option value="1">Read is paired</option> + <option value="2">Read is mapped in a proper pair</option> + <option value="4">The read is unmapped</option> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate strand</option> + <option value="48">Read is the first in a pair</option> + <option value="64">Read is the second in a pair</option> + <option value="256">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="768">The read is a PCR or optical duplicate</option> + <option value="1024">Supplementary alignment</option> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + </token> +</macros> |
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| diff -r 000000000000 -r a0d039fa9771 samtools_fastx.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_fastx.xml Mon Mar 12 12:53:10 2018 -0400 |
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| @@ -0,0 +1,104 @@ +<?xml version="1.0"?> +<tool id="samtools_fastx" name="Samtools extract" version="@TOOL_VERSION@"> + <description>FASTA or FASTQ from a SAM file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"> + <![CDATA[ + samtools $output.output_format + #if $output.output_format == 'fastq': + -v $output.default_quality $output.output_quality + #end if + #if $reference: + --reference '$reference' + #end if + $copy_flags $omit_read_number + -0 '$nonspecific' + -1 '$forward' + -2 '$reverse' + #if str($inclusive_filter) != 'None': + #set $filter = $inclusive_filter + @FLAGS@ + -f $flags + #end if + #if str($exclusive_filter) != 'None': + #set $filter = $exclusive_filter + @FLAGS@ + -F $flags + #end if + '$input' + ]]> + </command> + <inputs> + <param name="input" type="data" format="bam,sam" label="BAM or SAM file to convert" /> + <param argument="--reference" type="data" format="fasta" optional="True" label="Reference FASTA" /> + <param name="copy_flags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT flags to output header" /> + <param name="omit_read_number" argument="-n" type="boolean" truevalue="-n" falsevalue="" label="Do not append /1 and /2 to read names" /> + <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags be set"> + <expand macro="filter_options" /> + </param> + <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with the following flags set"> + <expand macro="filter_options" /> + </param> + <conditional name="output"> + <param name="output_format" type="select" label="Output format"> + <option value="fasta">FASTA</option> + <option value="fastq">FASTQ</option> + </param> + <when value="fastq"> + <param name="default_quality" argument="-v" type="integer" value="1" label="Default quality if none is given" /> + <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" label="Output quality in the OQ tag if available" /> + </when> + <when value="fasta" /> + </conditional> + </inputs> + <outputs> + <data name="nonspecific" format="fasta" label="${on_string} converted to ${output.output_format} (Neither or both)"> + <change_format> + <when input="output_format" value="fastq" format="fastq" /> + </change_format> + </data> + <data name="forward" format="fasta" label="${on_string} converted to ${output.output_format} (READ1)"> + <change_format> + <when input="output_format" value="fastq" format="fastq" /> + </change_format> + </data> + <data name="reverse" format="fasta" label="${on_string} converted to ${output.output_format} (READ2)"> + <change_format> + <when input="output_format" value="fastq" format="fastq" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> + <param name="output_format" value="fasta" /> + <output name="nonspecific" file="samtools_fastx-out1-1.fasta" /> + <output name="forward" file="samtools_fastx-out1-2.fasta" /> + <output name="reverse" file="samtools_fastx-out1-3.fasta" /> + </test> + <test> + <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> + <param name="output_format" value="fastq" /> + <output name="nonspecific" file="samtools_fastx-out2-1.fastq" /> + <output name="forward" file="samtools_fastx-out2-2.fastq" /> + <output name="reverse" file="samtools_fastx-out2-3.fastq" /> + </test> + <test> + <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> + <param name="output_format" value="fasta" /> + <output name="nonspecific" file="samtools_fastx-out3-1.fasta" /> + <output name="forward" file="samtools_fastx-out3-2.fasta" /> + <output name="reverse" file="samtools_fastx-out3-3.fasta" /> + </test> + </tests> + <help> + <![CDATA[ + This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a SAM or BAM file in FASTA or FASTQ format. + ]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r a0d039fa9771 test-data/samtools_fastx-in1.bam |
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| Binary file test-data/samtools_fastx-in1.bam has changed |
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| diff -r 000000000000 -r a0d039fa9771 test-data/samtools_fastx-in2.bam |
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| Binary file test-data/samtools_fastx-in2.bam has changed |
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| diff -r 000000000000 -r a0d039fa9771 test-data/samtools_fastx-in3.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-in3.sam Mon Mar 12 12:53:10 2018 -0400 |
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| b'@@ -0,0 +1,435 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@SQ\tSN:2micron\tLN:6318\n+@SQ\tSN:chrI\tLN:230208\n+@SQ\tSN:chrII\tLN:813178\n+@SQ\tSN:chrIII\tLN:316617\n+@SQ\tSN:chrIV\tLN:1531919\n+@SQ\tSN:chrIX\tLN:439885\n+@SQ\tSN:chrM\tLN:85779\n+@SQ\tSN:chrV\tLN:576869\n+@SQ\tSN:chrVI\tLN:270148\n+@SQ\tSN:chrVII\tLN:1090947\n+@SQ\tSN:chrVIII\tLN:562643\n+@SQ\tSN:chrX\tLN:745742\n+@SQ\tSN:chrXI\tLN:666454\n+@SQ\tSN:chrXII\tLN:1078175\n+@SQ\tSN:chrXIII\tLN:924429\n+@SQ\tSN:chrXIV\tLN:784333\n+@SQ\tSN:chrXV\tLN:1091289\n+@SQ\tSN:chrXVI\tLN:948062\n+@PG\tID:kallisto\tPN:kallisto\tVN:0.43.1\n+chrI_25874_26397_2:0:0_7:1:0_2\t83\tchrI\t25658\t255\t200M\t=\t25739\t-119\tGCTGTAGTGGCTGTTGTTGGTGTTCTGATGTCAATGATGGTTTCATCAGTTGGCAAACCGTTCGAACCGGTGACGGTGGTCATTTCAGTGGATGTAGAGGTAAAAGTGTCGTTCCATGGCTGAGTTGTAGTCATGGCAGTAGGGGCTGTTGTTGGTGTTCTGATGACAATGATGCTATCATCAGTTCGCAAACCATTGGT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrI_25874_26397_2:0:0_7:1:0_2\t163\tchrI\t25739\t255\t200M\t=\t25658\t119\tATTTCAGTGGATGTAGAGGTAAAAGTGTCGTTCCATGGCTGAGTTGTAGTCATGGCAGTAGTGTCTGTTGTTGGTGTTCTGATGACAATGATGGTTTCATCAGTTGGCAAACCGTTGGTACCGGTGACGGTGGTCCTTTCAGTGGATGTAGAGGTAAAAGTGTCGTTCCATGGCTGAGTTGTAGTTATGGCAGTAGTGGC\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrI_93599_94144_3:1:0_9:0:0_1\t163\tchrI\t93599\t255\t200M\t=\t93945\t546\tTGTTATATCTAAGCCTTCCAAGCGACCCACACACCATTCGCATTCATCAGACGGGAGTTCTAGCACGCAGACAGATATATCGTTACAGAGCTTGCTTTACCATGATCTTGAAAGCTCACCAAAGAAACATGTTTCGCCGTCAAGACCGCCCTCTGTAGCTTCCGAATCCTCTCCTGCCGTTGCTCATCCCATTGGGCTTT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrI_93599_94144_3:1:0_9:0:0_1\t83\tchrI\t93945\t255\t200M\t=\t93599\t-546\tGCCAATCTTTCGCTAAATTCACATGAATTAGACTACTATCAGCCTCATATCGGATTCCAGTTACAGCTGACAGAAGCTTTACTAAACCACAGTTTGAAAGATGAGGTTCTGAAAGATGAAAATGACCTTGTTAAAAACATTGCAAATTTGGACAAGATCGTTAAAGAGCTATGGGACTTAAGATCCAGGACCATTGGATG\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrI_139586_140147_6:0:0_3:0:0_3\t163\tchrI\t139586\t255\t200M\t=\t139948\t562\tTGCAGCGCCACCTGGAGCACCACCAGCTTTGTACAACTTAGAGATGATTGGGTTGGCAATGTCTTGCAAGTCCTTCAACTTGTCATCGAATTCTTGCTTGCTGGCAGTGGTGTTGCTGTCTAACCAAGAAATAGTCTCTTCAGGCTTCTTGGTGCCGGTGTCCTTGTCAGCTTGTTCCAATTTGTCACCAGCTTCAGAAA\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrI_139586_140147_6:0:0_3:0:0_3\t83\tchrI\t139948\t255\t200M\t=\t139586\t-562\tTAGACTTACCAGTACCCTTTTCGACGGCGGAAACATTCAAAATACCGTTAGAGTCGACATCGAAAGTGACTTCAATTTGTGGGACACCTCTTGGAGCTGGTGGAATACCACTCAATTCGAACTTACCCAACAAGTTGTTGTCCTTAGTCTTGGATCTTTCACCTTCAAAGACTTGAATCAACACACCTGGTTGGTTTTCA\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrI_176449_177020_5:0:1_5:0:0_0\t99\tchrI\t176449\t255\t200M\t=\t176821\t572\tTAGGCCGTTATTTCCGTAAAGGATGGTATAATAATAAGAAATTTATCATATTAATAATACCTATATCCAAAAATTTATATTTATATACATGCGCCTAACTATTCATACTATTAATTTCATATTATTAAGCTTTTTTTTTTTCATTTATCATTTTTTTTCGTAACCCTCTCCTACCTGTACAGGTTTCATTCGTAAAGCAG\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrI_176449_177020_5:0:1_5:0:0_0\t147\tchrI\t176821\t255\t200M\t=\t176449\t-572\tTTCAACTGGATAAGTTTCAGTTGGGTGAGCAGCTTAGAAAGAGTAGTATTCAG'..b'2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_866925_867424_2:1:0_4:0:0_e\t99\tchrXVI\t866925\t255\t200M\t=\t867225\t500\tACGTTCTTGACGTCCTTTTTCAACCATAGTTTGATAGTATTGTCGATAGAAAAAGTACTTTGACCTGTTCCCACATTTGTAGTAGGAGCCACGGTGGTAATTCTGGAGTTGATAGCTTTAATCATCTTTTCATACTCTGCATAAGCTAAATTAAAATTAAAATATGCGTCTTTCGCCCTTAAGGCAACCCTAGCGGCTGA\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_866925_867424_2:1:0_4:0:0_e\t147\tchrXVI\t867225\t255\t200M\t=\t866925\t-500\tTTTATGGCAGTGCACAGTGAACCAAAATTTTTGGATGTCGCTACTAATGGAATTATGCTATTTTTCAATGTAGGTAATGACCTAAAGGTTTCGAAATTCATCCTAATATGTCTAGTCAAATTAGATCGAGGGTCGGATAGTTCTTTTTCCAACGTTTCATTCCATTGGGAAACCCAGGGGGAGATTTCAGAGCGAACTGT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_889501_889988_11:0:0_5:0:0_0\t99\tchrXVI\t889501\t255\t200M\t=\t889789\t488\tCAACAAAGATTCTCATACAATCCGCACAAAATGCAATTTATTTACGTCCCCAATACAAAGCCGAATGGGCTAGGAGGCAATGCGGGTTTTCTAGCAGATATAGAGGACAAAGTTCAAATGTTCTTGACACGATATTACCTCACGAACGACAGAGTCAAGAGAAATGAAAACTACCAAAACAGTGACATGTATACTCCATA\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_889501_889988_11:0:0_5:0:0_0\t147\tchrXVI\t889789\t255\t200M\t=\t889501\t-488\tCTACTAGGTAGGGATGCTCAAAACTTTCTACTATTGGGGCTCTTAAATAAGAACTTTAAGGGCAATTGGTCACTGGAAGATCCGTCTGGATCTGTCGAAATTGACATTTCCCAAACTATCCCTACACAACGACATTACTACGTCCCAGGTTGCATGGTTCTTGTGGAAGGAATATACTATTCTGGACGAAATAAATTCCA\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_908795_909263_5:0:0_2:0:0_a\t99\tchrXVI\t908795\t255\t200M\t=\t909064\t469\tAGAGGCAGATCAGATTGGCACTCACCCTTGCCATCAATATCCCCTTCGATGCATTATGGATCGTTGAACTCGAGAATGTCTCAAGGCGCCAATGCAAGCCATTTGATTGCAAGAGGCGGTGGGAATTCATCTACTAGTGCCTTGAATAGTAGAAGGAATTCTTTAGATAAGAGCTCAAACAAGCAGGGTATGTCATGCTT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_908795_909263_5:0:0_2:0:0_a\t147\tchrXVI\t909064\t255\t200M\t=\t908795\t-469\tAGGAGTAGAAGAAGATGATGATGACGAGAATGACCGTTTGCTCAACCAAATGGGAAACAGTCCTACAAAATTCAAAAGTTCAATATCTCCAAGATCAATTGATAGCATTTCAAGTTCTTTCATAAAAAGTAGGATACCTATCAGACAACCATACCATTACTCTAAACCAACTACTGCGCCCTTTCAAGCTCAGGCGAAAT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_912895_913350_7:0:0_5:0:0_9\t163\tchrXVI\t912895\t255\t200M\t=\t913151\t456\tATAACCATTTAGCGTGGAAAGGACTTTTTCTCTTATTTAGAACCACTGAGGTTGTCCCAGACATACTTTCGTATGATGAATATTTTGACCTGTGTGGCCAATATGCAGACGCACTTTAAAAGCCGGAACAGTCTCAAGTAGAACTAATAAATGACAAAAAATTACTACAGCAAACGCATCCATATTGTCAAAAAGCCTTT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n+chrXVI_912895_913350_7:0:0_5:0:0_9\t83\tchrXVI\t913151\t255\t200M\t=\t912895\t-456\tTACACCCCAGGACGCGTTATGAAATCTTATAAAGATACGGTCTAATATTGAAACAACGGAAATAGGTAAGACCCTTAGTCAGAACAGGTTAAAACTAAAACCTAGTGATCCTCATTATCAAATTAAACTAAATTCATTCTCCTGGGAAATAATTAAAAATTCAGAAATTGATCAGTTATACAACCAGTTGGTAAATATTC\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tNH:i:1\n' 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| diff -r 000000000000 -r a0d039fa9771 test-data/samtools_fastx-out1-2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-out1-2.fasta Mon Mar 12 12:53:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+>chrM_101_581_3:0:0_1:0:0_45\n+GAGGTAAAATTACACATGCAAACCTCCATAGACCGGAGAAAAATCCCTTAAAGATTTACTTAAAATTTAA\n+>chrM_317_794_1:3:0_0:1:0_18\n+CTCGGTCATACGATTAACCCAAACTAAATATTTTCGGCGTAAAACGTGTCATCTATAAATAAATAAATAG\n+>chrM_424_929_1:0:1_1:1:0_4a\n+GGACCTAAACCGTCAATAACGAAAGTAATTCTAGTCATTTATAATCCACGACAGCTAAGACCCAAACTGG\n+>chrM_296_703_3:1:0_0:1:0_b\n+GGGTTTGCTGAAGATGGCGGTATATAGGCTGAATTAGCAAGTGATGGTGAGGTAGAGCGGGGTTTATCGA\n+>chrM_271_788_1:2:0_0:1:0_73\n+TAGCCCATTTCTTCCCATTGCATTGGCTACACCTTGACCTAACGTTTTTATGTTTGATTCTTTTGCTTAC\n+>chrM_1166_1638_1:0:0_3:1:0_54\n+AGAATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGAACTAGTACCGCAAGGGAAAGATGAAAGACT\n+>chrM_1187_1670_2:0:0_1:1:0_5\n+TACATCTAGGAGCTATAGAACTAGAACCGCAAGGGAAAGATGAAAGCCTAATTAAAAGTAAGAACAAGCA\n+>chrM_826_1305_2:0:0_0:0:0_63\n+AGAAGTTTTCTAGTTAGTTCATTATGCAAAAGGTACAAGGTTTAATCTTTGCTTGTTCTTACTTTTAATT\n+>chrM_769_1311_4:2:0_1:0:0_9b\n+CAAAGGGAAGACATGGGGTACATTTTCTTATAACAGAACATTACTATCCCCTTTATGAAACTAAAGGACT\n+>chrM_946_1374_2:0:1_1:0:0_b7\n+GTTGATTCATAAAATTGTTTTTAGGTAGGTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTA\n+>chrM_1461_2059_1:2:0_0:0:0_8f\n+GAATTTAAGTTCAATTATAAACTTGCTGAAAAAAGAACAAAATCAAAAAGTAAGTTTAGATTATAGCCAA\n+>chrM_1366_1837_1:0:0_0:0:0_24\n+ATTTATAGTGTGATTATTGCCTATAGTCTGATTAACTAACAATGGTTATCCGAGTTGTTATACGCGTATG\n+>chrM_1396_1891_4:1:0_3:0:0_55\n+GAGAAGATTTTTAGGTAGAGGTGAAACGCCTACCGAGCTTGTTGATAGCTTGTTACCCAAAAAGTGAATT\n+>chrM_1654_2097_0:1:0_1:0:0_a8\n+AGAGACAGTTGGACCCTCGTTTAGCCGTTCATGCTAGTCCCTAATTAAGGACCAAGTGATTATGCTACCT\n+>chrM_2195_2667_1:0:0_2:0:0_95\n+TTTAATTTATTAAACCTAATGGCCCAAAAACTATAGTCTAAGTTTGAAATTTCGGTTGGGGTGACCTCGG\n+>chrM_1772_2275_1:0:0_1:0:0_3f\n+ATTTTTATTCTCCGAGGTCACCCCAACCGAAATTTCAAACTTATACTATAGTTTTTGGGCCATTAGGTTT\n+>chrM_2021_2595_3:0:0_2:0:0_22\n+AAGGTGGCTCTATTTCTCTTGACCTTTCGTACTGGGAGAAATCGTAAATAGATAGAAACCGACCAGGATT\n+>chrM_2706_3137_0:1:0_1:0:1_af\n+AGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGTTCTTTATTATTATCCTAACAC\n+>chrM_2789_3314_1:0:0_0:1:0_f\n+TCTAATCGCCATAGCCTTCCTCACATTAGTAGAACGCAAAATCTTAGGGTACATACAACTACGAAAAGGC\n+>chrM_2674_3159_3:1:0_1:1:1_e\n+CTACGGCTCGTAAAGCTCCGATTAGTGAGAATTTGGAGTTTGAGGCTCATCCTGATCAAGAATGGAGTAA\n+>chrM_3103_3621_2:1:0_1:0:0_71\n+GATCAGGATGATCCTCAAACTCCAAATCCTCACTAATCGGAGCTTTACGAGCCGTAGCCCAAACAATTTC\n+>chrM_3169_3659_1:2:0_2:0:0_68\n+TTTCATATGATGTAACCATAGCTATTATCCTTTTAACAGTTCTATTAATAAATGGATTCTACTCTCTACA\n+>chrM_2740_3253_1:1:0_1:1:0_6c\n+GTTGTAATAAGTGTTTTTAGAGAGTAGAATCCATTTATTAATAGAACTGATAAAAGGATAATAGCTATGG\n+>chrM_3187_3702_2:1:0_1:1:0_8d\n+TAGCTATTCTCCTTTTATCAGTTCTATTAATAAATGGATTCTACTCTCTACAAACACTTATTACAACCGA\n+>chrM_3204_3728_0:1:0_2:2:0_4b\n+TCAGTTCTATTAATAAATGGATTCTACTCTCTACAAACACTTATTACAACCCAAGAACACATATGATTAC\n+>chrM_2945_3338_1:0:0_1:1:0_19\n+GGCCCGGTTTGTTTCTGCTAGGGTTGAGATATATCATATTATGGCTATGGGTCAGGCTGGCAGACGTAAT\n+>chrM_3289_3819_1:1:0_4:1:0_3c\n+CCAAAGCCATAATATGATATATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGG\n+>chrM_3504_4052_0:0:0_0:2:0_b9\n+CCAGAACTCTACTCAACTAACTTCATAATAGAAGCTCTACTACTATCATCAACATTCCTATGGATCCGAG\n+>chrM_3542_4113_1:0:0_0:0:0_65\n+ACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCGACGCTTCCGTTACGATCAACTTATACAT\n+>chrM_3560_4153_2:0:0_1:0:0_4f\n+CCTATGGATCCGAGCATCTTATGCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACATT\n+>chrM_3562_4117_0:0:0_3:0:0_51\n+TATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACTTTCT\n+>chrM_3135_3669_1:2:0_1:0:0_2c\n+AAGAAATATGTCACATACATAATGCTAGAGTTAGGGGTAGAAAGTTTTTTCATAGAAGATGTATAAGTTG\n+>chrM_3422_3872_1:0:0_2:1:0_3b\n+CCCTATAGCTTAATTAGCTGACCTTAGTATTAGGATAAGGTGTTTAGGTAGCAAGGAGAATTTTGAATTC\n+>chrM_3587_4003_0:0:0_1:1:0_a7\n+TCATATCAGTATTAGGTTGGTGCTGGATATTGTGATTACAGGACCTAATAAGATTGTGAAGTAGATGATG\n+>chrM_3998_4489_2:1:0_1:1:0_be\n+ATATGAGAAGGCCTGGAATTCCGCCAACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGAT\n+>chrM_4007_4449_2:0:0_3:1:0_17\n+GTCCTGGAATTCAGCCTACTAGCACTTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAG\n+>chrM_4139_4621_1:0:0_4:0:0_7e\n+CTCAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACTGTCTTATCCTTAACATAACAT\n+>chrM_4200_4733_4:0:0_0:1:0_6f\n+ACATCAGATTAATAGCCCTAACCATAAAACTAGGCCTCGCCCCATTCCACTACTGATTACCAGAAGTAAC\n+>chrM_3799_4278_3:2:0_1:0:0_1d\n+TTAAGAATTCAAA'..b':1:0_0:1:0_1f\n+TCAGTTAGATCCCCAAGTCTCTGGATATTCCTCAGTAGCTATAGCAGTTGTATATCCAAACACAACCAAC\n+>chrM_13482_13976_0:0:0_1:2:0_c1\n+TAATTGTTACTGGGTTTGTTGGTCGTTTAATGGTTTTAGGGTTTGGTTGATCGTTTTTAGGTTTAATAGT\n+>chrM_13910_14543_2:1:0_1:1:0_30\n+ATTAAACCTAAAAACGATCCACCAAACCCTAAAACCATTAAACGAGCAACAAACCGACTAACAATTAAAC\n+>chrM_13936_14395_2:2:0_1:1:1_76\n+CCCTAAAACCATTAAACGACCAACAAACCCAGTAACCATTAAACCTAAACCTCCATAAATAGGTGAATGC\n+>chrM_13940_14475_1:1:0_3:2:0_27\n+AAAACCATTAAACGACCAACAAACCCACTAACAATTAACCCTAAACCTCCATAAATAGGTGAAGGCTTTA\n+>chrM_14052_14489_0:0:0_3:4:0_4c\n+CAAAAATATAATTATTCATTATTTCTACACAGCATTCAACTGCGACCAATGACATGAAAAATCATCGTTG\n+>chrM_14105_14613_0:0:0_2:0:0_48\n+ATGAAAAATCATCGTTGTAATTCAACTACAGAAACACCTAATGACAAACATACGAAAAACACACCCATTA\n+>chrM_14128_14614_0:1:0_1:1:0_97\n+AACTACAGAAACACCGAATGACAAACATACGAAAAACACACCCATTATTTAAAATTATTAACCACTCATT\n+>chrM_14131_14628_2:1:0_2:1:0_36\n+TACAGAAACACCGAATGACAAACATACGACAAACACACCCATTATTTAAAATTATAAACCACTCATTCAT\n+>chrM_13791_14330_0:0:0_3:0:0_29\n+GGCTGTTATTGTAACTGATGTGTAGTGAATGGCTAAGAAAAGACCTGTAATGATTTGGACTATAAGGCAG\n+>chrM_13944_14351_1:1:0_0:0:0_44\n+AATGTGTGTTACTGATGAAAAGGCTGTTATTGTATCTGATGTGTAGTGTATGGCTAAGAAAAGACCTGTA\n+>chrM_13992_14451_1:1:0_1:3:0_52\n+ATAAGCCTCGTCGGAGCTGAAGGAACAAGCAAATAAAAAATATTGAGGCTCCGTTTGCGTGTATATATCG\n+>chrM_14442_15026_1:2:0_3:0:0_60\n+CGAGGCTTATATTATGGATCAGATACATTTATAGAAACCTGAAACATTGGAGTACTTCTTCAGTTCGCAG\n+>chrM_14576_14894_2:0:0_0:0:0_5f\n+AGTTATTCCAAACCTCCTATGAGCCATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGC\n+>chrM_14707_15163_1:1:0_1:2:0_9\n+TTATCGGGGCCCTAGCAATCGTTCACCTCATCTTCCTCCACGAAACAGGATCAAACAACCCAACAGGATT\n+>chrM_14728_15189_1:2:0_2:0:0_7a\n+TTCACCTCATCTTCCTCCACGAAACAGGATCAAACCACCCAACAGGATTATACTCAGATGCAGATAAAAT\n+>chrM_14794_15314_1:0:0_1:0:0_c0\n+AAATTCCATTTCACCCCTACTATACAATCAAAGATATCCTAGGTATCCTAATCATATTCTTAATTCTGAT\n+>chrM_14975_15480_1:0:1_0:1:0_4e\n+ATACGCCATTCTACGCTCCACTCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAAT\n+>chrM_15196_15749_1:1:1_2:1:0_c4\n+GCTAACTAGCCCCATCTCATACTTCTCAATCATCTTAATTCTTATACCAATGTCAGGAATTATCGAAGAC\n+>chrM_14768_15298_0:1:0_1:1:0_ac\n+CTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATAAGTCCTGAGCTTGGTATAAGAATTAAGA\n+>chrM_14885_15311_3:1:0_1:0:0_3\n+AGTAATGTTTATACTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATAATTCCAGAGATTGGT\n+>chrM_14820_15346_1:0:0_0:0:0_5a\n+AAGAGAAGATCTTCATTTCAGGTTTACAAGACCAGAGTAATGTTTATACTATCAAGACATGGATATAATT\n+>chrM_14858_15398_0:0:0_3:0:0_b3\n+CAGCTTTGGGTGCTGGAGGTGGGTAGTAGCTCCTTCTTCTTGATGTCTTGAGAAGAGCAGATCTTCATTT\n+>chrM_15417_15889_0:0:0_2:0:0_50\n+TTCTTGAGTACATAAATTTACATAGTACAACAGTACATTTATGTATATCGTACATTAAACTATTTTCCCC\n+>chrM_14988_15504_0:0:0_1:1:0_38\n+GTATTAGCTTATATGCTTGGGGAAAATAGTTTAATGTACGATATACCTAAATGTACTGTTGTACTATGTA\n+>chrM_15462_15945_2:1:0_0:0:0_0\n+TATCGTACATTAAACAATTTTCCCCAAGCATATAAGGTAATACATTAAATCAATGGTTCAGGTCATAAAA\n+>chrM_15171_15615_1:0:0_0:1:0_c3\n+TAACACAGATATGTCCTTATAACATTAGTTTAATGTGTTTAAGATAATATTCATGGTATATATATTGGTT\n+>chrM_15361_15805_1:0:0_2:0:0_81\n+TGAAGTAAGAACCAGATGTCTTATAAAGTTTCAGTTTAGCTACCCGCAAGTTTAATGGGCCCGGAGCGAG\n+>chrM_15481_15968_1:2:0_2:0:0_6d\n+GTCCTTACATGCCTTGACGGCTATGTTGATGAAAGTAGGCCAAAATAAAAAGATCCCAAATGCATGACAC\n+>chrM_15523_16020_2:1:0_1:1:0_31\n+GGGTTTTGCGGACTAATGATTCTTCACCTAAGGTGCGTCTAGACTGTGTGCTGTCCTTTCATGCCTTGAC\n+>chrM_15549_16044_0:1:0_1:1:0_59\n+ATGAATAATTAGCCTTAGGTGATTGGGTTTTGCGGACTAATTATTCTTCACCGAAGGTGCGTCTAGACTG\n+>chrM_15720_16131_0:1:0_2:1:0_58\n+TGTTTATGGGGTTTGGCATTAAGAGGACGGGGTGGGGGGTTTTGAGAGTTAAAATTTGGTATTGAGTAGC\n+>chrM_15642_16224_2:1:0_0:0:0_a5\n+AGTACTAAAATATAAGTCATATTTTGGGAACTACTAGAATTGATCAGGACATAGGGTTTGATAGTTAATA\n+>chrM_15820_16268_3:1:0_1:0:2_7f\n+TTAGAGTTTTGGTTCACGGAACATGATTTTGTAAAATTTTTACAAGTACTAAAATAAGTCATATTTTGGG\n+>chrM_13991_14484_3:1:0_3:4:0_20\n+TAAATAGGTGAAGGCTTTAATGCTAACCCCAGACAACCAACCCAAAATAATGATCTTAAAACCAAAATAT\n+>chrM_8781_9305_4:1:0_3:0:1_3e\n+TAAGTGATGTTTTGATGTGCAGTGAAATTTTAGTTTTCTAGTAGGCAAACAATAAGGAATGTTGATCCAA\n+>chrM_14312_14826_2:1:1_4:1:0_a4\n+CTTTGATTTTATAGTAGGGGTGAAATGGACATTTATCTGCATCTGAGAATAATCCTGTTGGGTTGTTTGA\n+>chrM_408_812_0:2:1_4:2:0_ad\n+TGAAAAATCATTGTTAGGACCTAAACCGTCAATAACGAAAGTAATTCTACTCATTTATAATACACGACAG\n' |
| b |
| diff -r 000000000000 -r a0d039fa9771 test-data/samtools_fastx-out1-3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-out1-3.fasta Mon Mar 12 12:53:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+>chrM_271_788_1:2:0_0:1:0_73\n+TGACTAAGTTATACCTCTTAGGGTTGGCAAATTTCGTGCCAGCCACCTCGTTCATACGATTAACCCAAAC\n+>chrM_296_703_3:1:0_0:1:0_b\n+TTTAAATTTCGTGCCAGCCACCTGGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGT\n+>chrM_101_581_3:0:0_1:0:0_45\n+TTTTAAGCTATGGCTAGTAGTTCTCTGGCAAATATTTTTGTTAAATTTAATTATTTAGGTTTATGGCTAA\n+>chrM_317_794_1:3:0_0:1:0_18\n+AAAATGTAGCCCATTTCTTCCCATTGCATTGGCTACACCTTGACCTAACGTTTTTATGTTTGATTCTTTT\n+>chrM_826_1305_2:0:0_0:0:0_63\n+AAACTAAAGGACTAAGGAGGATTTAGTAGTAACTTAAGAATAGAGAGCTTAATTGAATTGAGGAATGAAG\n+>chrM_424_929_1:0:1_1:1:0_4a\n+TAATTTGAGGAGGGTGACTGGCGGTGTGTGCGTACTTCATTGCTCAATTCAATTAAGCTCCCTATTCTTA\n+>chrM_946_1374_2:0:1_1:0:0_b7\n+CTTATTTCTAGACATCCGTTTCTGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTT\n+>chrM_769_1311_4:2:0_1:0:0_9b\n+TTAGTTAGAAGTTTTCTAGTTAGTTCATTATGCAAAAGGAACAAGGTTTAATCTTTGCTTGTTCTTACTT\n+>chrM_1366_1837_1:0:0_0:0:0_24\n+TGAATCAACTCGTCTATGTGGCAAAATAGTGAGACGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTT\n+>chrM_1166_1638_1:0:0_3:1:0_54\n+ATCGCATTCTTTATTGGTGGCTGCTTATAGGCCTCCAATGGTTAAAAGCTGTTTTGTTAATTATTCACTA\n+>chrM_1187_1670_2:0:0_1:1:0_5\n+ATGGAATTAATTGAAATTTTATTTTGAGCTTGATCGCTTTCTTTATTGGTGGCTGCTTTTAGGCCTACAA\n+>chrM_1654_2097_0:1:0_1:0:0_a8\n+ATTTCAATTAATTCCATAATCTACACCAACTTCCTAAACTTAAAATTGGGTTAATCTATAACTTTATAGA\n+>chrM_1772_2275_1:0:0_1:0:0_3f\n+CGCGTATAACAACTCGGATAACCATTGTTAGTTAATCAGACTATAGGCAATAATCACACTATACATAATC\n+>chrM_1396_1891_4:1:0_3:0:0_55\n+ATCTTTCCTATAGGCATTCCGGATTTGGGTTAACAGAGAAGTTATAGGTGGATTATTTATAGTGTGATTA\n+>chrM_1461_2059_1:2:0_0:0:0_8f\n+CCCTAATTAAGGAACAAGTGATTATGCTACCTTTGCACGGTCAGGATACCGCGGCCGTTAAACTTTAGTC\n+>chrM_2021_2595_3:0:0_2:0:0_22\n+CGTGCAACGGTAGCATAATCACTTGTTCCTTAATTAGGGACTAGCATGAACGGCTCAACGAGGGTCCACC\n+>chrM_2195_2667_1:0:0_2:0:0_95\n+GTAGGTTAGAGGGTGTACGTATATATTTTATTTAGATTTTATTCATAAATTAAGTTGAGAGCGCTTATAT\n+>chrM_2740_3253_1:1:0_1:1:0_6c\n+TCTCCCTAAAAGTGTTCTTTATTATTATCCTAACACTCCTCGTCCCCATTCTAATCGCCATAGCCTTCCT\n+>chrM_2945_3338_1:0:0_1:1:0_19\n+AACCTCTATATCCTTATTTATTATAGCACCTACCCTATCACTCACACTAGCATTAAGTCTATGAGTTCCC\n+>chrM_2706_3137_0:1:0_1:0:1_af\n+TAGTGAGTATTTGGAGTTTGAGGCTCATCCTGATCAAGAATGGAGTAAACTGCTAGGCTAGATGTTGCTA\n+>chrM_2674_3159_3:1:0_1:1:1_e\n+TTATTGGGGTGGCAGAGCCATGAAATTGCGTAAGACTAAAAACCTTGTTCCCAGAGGTTCAAATGCTCTC\n+>chrM_3135_3669_1:2:0_1:0:0_2c\n+GTAATCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGATGTAACCATAGCTATTATCCTTTTAT\n+>chrM_3204_3728_0:1:0_2:2:0_4b\n+ATTCTTTTATCAGACATATTTCTATATGTCTGGTGGCACTCCCGCTTTAAAAATTGGTAAAGCAATATGT\n+>chrM_2789_3314_1:0:0_0:1:0_f\n+TGAGATATATCATATTATGGCTATGGGTCAGGCTGGCAGAAGTAATCATATGTGTTCTTGGGTTGTAATA\n+>chrM_3422_3872_1:0:0_2:1:0_3b\n+TATAGCAGAGTACACTAACATTATTCTAATAAACGCCCTAACAACTATAATCTTCCTAGGACCCCTATAC\n+>chrM_3103_3621_2:1:0_1:0:0_71\n+TTCATAGAAGATGTATAAGTTGATCGTAACGGAAGCGTGGCTAAGATGCTCGGATCCATAGGAATGTTGA\n+>chrM_3587_4003_0:0:0_1:1:0_a7\n+CTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACTTTCTACCCCTAACACTAGCATTATGTATG\n+>chrM_3169_3659_1:2:0_2:0:0_68\n+TCACATACATCATTCTAGTGTTAGGGGTAGAAAGTTTTTTCATAGAAGATGTATAAGTTGATCGTAACGG\n+>chrM_3187_3702_2:1:0_1:1:0_8d\n+TGTATGGTGGCACTCCGGCTGTAAAAATTGGTAAAGAAATATGTCACATACATAATGCTAGTGTTAGGGG\n+>chrM_3289_3819_1:1:0_4:1:0_3c\n+AGGAGAATTTTGAAATCTTAATTGTAGGTTCAATTCCTAATGTCCTAGAAATAAGCGGGCTTGAACCTCT\n+>chrM_3889_4361_3:0:0_3:0:0_33\n+TTTTGTATAAATCCTTCCCGTACTAATAAATCCTATCACCCTTGCCATCATCTACTTCACAATCTTCTTA\n+>chrM_3912_4414_3:0:0_2:1:0_91\n+TAATAAATCCTATCACCCTTGCCAACATCTAGTTCACAATCTTCTTAGGTCCTGTAATCACAAAATCCAG\n+>chrM_3945_4422_1:2:0_0:1:0_64\n+TCACAATCTTCTTAGGTCCTGTAATCACAATATCCAGGACCAACCTAATACTGATATGAGTATGCCTGGA\n+>chrM_3504_4052_0:0:0_0:2:0_b9\n+TGTTGATTAGTATGGGGATAATTGCTAGTAGGCTGAATTCCAGGCATACTCATATCAGTATTAGGTTGGT\n+>chrM_3542_4113_1:0:0_0:0:0_65\n+GAGGCTGTTGCTTGTGTGACGAAGTATTTTGTTGCTGCTTCAGTTGATCGTGGGTTTTTTTTGTTGATTA\n+>chrM_3562_4117_0:0:0_3:0:0_51\n+TCTTGAGGCTGATGCTTGTGTGACGAAGTATTTTGTTGCTTCTTCAGTTGATCGTGGGTTTTTTTTGTTG\n+>chrM_4079_4594_1:0:0_3:0:0_28\n+GCAACAAAATACTTCGTCACACAAGCAACAGCCTGAATAATTATCCTCCTGGCCATCGTACTCAACTATA\n+>chrM_3560_4153_2:0:0_1:0:0_4f\n+TTGTTTATAGTTGAGTACGATGGCCAGGAGGATACTTATTGAGGCTGTTGCTTGTGTGACGAAGTATTTT\n+>chrM_4140_4598_2:0:0_2:0:0_12\n+TCAACTATAAACA'..b':1:0_3:2:0_27\n+CTATAAATGTATCTGATCCATAATATAATCGTCGTCCGACAAGAAGGAACAAGCAAATAAAAAATATTGA\n+>chrM_13944_14351_1:1:0_0:0:0_44\n+CCATTAAACGACCAACAAACCCACTAACAATTAAACCTAAACGTCCATAAATAGGTGAAGGCTTTAATGC\n+>chrM_13494_14044_3:1:0_1:1:0_7d\n+TTCATTATTTTCGGTTGGTTGTCTTGGGTTCGCATTAAAGCCTTCACCTATTTATGGAGGTTTAGGTTTA\n+>chrM_13992_14451_1:1:0_1:3:0_52\n+AAATAGGTGAAGGCTTTAATTCTAACCCAAGACAACCAACCAAAAATAATGATCTTAAAACAAAAATATA\n+>chrM_14052_14489_0:0:0_3:4:0_4c\n+AATGTTTCAGGTAACTATAAATGTATCTGATCCATAATATAAGCCTCGTCGGACCTTAAGGAACAAGCAA\n+>chrM_13715_14154_1:0:0_1:1:0_96\n+TGTTTGTCATACGGTGTTTCTGTAGTTGAATTACAACGATGATTTTTCATGTCATTGGTCGCAGTTGAAT\n+>chrM_13813_14351_0:1:0_0:1:0_1f\n+AATGTGTGTTACTGATGAAAAGGCTGCTATTGTATCTGATGTGTAGTGTATGGCTAAGAAAAGACCTGTA\n+>chrM_13936_14395_2:2:0_1:1:1_76\n+GCGTGTATATATCGGATTAGTCACCCGTAAATTAACATCTCGACAAATGTGTGTTACTGATGAAAAGGCT\n+>chrM_13910_14543_2:1:0_1:1:0_30\n+AAGGAGGTAGCCTATAAATGCTGTGGCTATGACTGCGAACAGAAGAAGTACTCCAATGTTTCAGGTTTCT\n+>chrM_14128_14614_0:1:0_1:1:0_97\n+CCAATATCTTGGATGGCTGATAGGAGGTTTGTAATAACTGTGGCACCTCAGAATGATATTTGTCCTCATG\n+>chrM_14105_14613_0:0:0_2:0:0_48\n+CAATATATGGGATGGCAGATAGGAGGTTTGTAATAACTGTGGCACCTCAGAATGATATTTGTCCTCATTG\n+>chrM_14131_14628_2:1:0_2:1:0_36\n+CGACTAGGGTTGTTCCAATATATTGGATGGCTGATAGGAGGATTGTAATAACTGTGTCACCTCAGAATGA\n+>chrM_14768_15298_0:1:0_1:1:0_ac\n+AACAGGATTATACTCAGATGCAGATAAAATTCCATTTCACCCCTACTATACAATCAAAGATATCCTAGGT\n+>chrM_14820_15346_1:0:0_0:0:0_5a\n+ATCAAAGATATCCTAGGTATCCTAATCATATTCTTAATTCTCCTAACCCTAGTATTATTTTTCCCAGACA\n+>chrM_14576_14894_2:0:0_0:0:0_5f\n+TAGTATGTCTGGGAAAAATAATACTAGGGTTATGAGAATTAAGAATATGATTAGGATACCTAGGATATCT\n+>chrM_14858_15398_0:0:0_3:0:0_b3\n+TCTCATAACCCTAGTATTATTTTTCCCAGACATACTAGGAGACCCAGACAACTACATACCAGCTAATCCA\n+>chrM_14885_15311_3:1:0_1:0:0_3\n+AGACATACTAGGAGAGGCCGACAACTACCTACCAGCTAATCCACTAAACACCCCACCCCATATTAAACCC\n+>chrM_14442_15026_1:2:0_3:0:0_60\n+TAAGGCTATGACACCTCCTAGTTTCTTGGGGATTGAGGGTAGAATGGCGTATGCAAATAGGAAATATCAT\n+>chrM_14988_15504_0:0:0_1:1:0_38\n+CGCTCAATCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAATTTTAGCCCTAATAC\n+>chrM_14707_15163_1:1:0_1:2:0_9\n+CCCCCAATTCAGGTTACGATAAGTAGGTTGGCTACTAGGATTCAGTACAAAATTTTTCTGATTGGGCGGA\n+>chrM_14728_15189_1:2:0_2:0:0_7a\n+TAATAAATGGGTGTTCTCCTGGTTGGCCCCCAATTCAGGTTAAGATAAGTAGGTTGGCTACTAGGAATCA\n+>chrM_15171_15615_1:0:0_0:1:0_c3\n+GTAGAACACCCATTTATTATCATTGGCCAACTAGCCTCCATCACATACTTCTCAATCATCTTAATTCTTA\n+>chrM_14794_15314_1:0:0_1:0:0_c0\n+CAGAGTAATGTTTATACTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATACTTCCTGAGATT\n+>chrM_15361_15805_1:0:0_2:0:0_81\n+AAGAAGGAGCTACTCCCCACCACCAGCACCCAAAGCTGGTATTCTAATTAAACTACTTCTTGAGAACATA\n+>chrM_14975_15480_1:0:1_0:1:0_4e\n+AATAGTTTAATGTACGATATACATGAATGTACTGTTGTACTATGTAAATTTATGTACTCAAGAAGTAGTT\n+>chrM_15481_15968_1:2:0_2:0:0_6d\n+TTCCCCAAGCATATAAGCTAATACATTAAATCCATGGTTCAGGTCATAAAATAATCATCAACATAAACCA\n+>chrM_15523_16020_2:1:0_1:1:0_31\n+GTCATAAAATACTCAACAACATAAACCAATATATATACCATGAATATTATCTTAAACACATTAAACTAAT\n+>chrM_15549_16044_0:1:0_1:1:0_59\n+CAATATATATACCATGAATATTATCTTAAACACATTAAACTAATGTTATAAGGACATATCTGTGTTATCC\n+>chrM_15642_16224_2:1:0_0:0:0_a5\n+CTCTTCTCTTCCATCTGACTATCCCCTTCCCCATTTTGTCTATTAATCTTCCATCCTCCGTGAAACCAAC\n+>chrM_15196_15749_1:1:1_2:1:0_c4\n+TGGCCCGGAGCGAGAAGAGGGGCATTGGTGGGCGGGTTGTAGGTTTCACGGAGGATGGAAGATTAATAGA\n+>chrM_15720_16131_0:1:0_2:1:0_58\n+CACCAATGCCCCTCCTCTCGCTCCGGGCCCATTAAACTTGGGGGTAGCTAAACTGAAACTTTATCAGACA\n+>chrM_15417_15889_0:0:0_2:0:0_50\n+GTTGGTCATGGGCTGATTAGACCCGAAACCATCGAGATGTCTTATTTAAGGGGCACGTATGGGCGATAAC\n+>chrM_15462_15945_2:1:0_0:0:0_0\n+TGTTGATGAAAGTAGGCCAAAATAAAAAGATACCAAATGCATGACACCACAGTTATGTTGGTCATGGGCT\n+>chrM_15820_16268_3:1:0_1:0:2_7f\n+GTTATCGCCCATACGTTTCCCTTAACTCAGACATCTCGATGGTATCGGGTCTAATCAGCCCCTGACCAAC\n+>chrM_13991_14484_3:1:0_3:4:0_20\n+AAGAGGTTTCTATAAATGTATCTGATCCATAATATAAGCCTCGTCGGACCTGAAGGAACAAGCAAATAAA\n+>chrM_8781_9305_4:1:0_3:0:1_3e\n+CGATACGTAATTCGTGAAGTAACCTAACAATGCCACCACACTCCTATAGTACAAAAAGGACTACGATATG\n+>chrM_14312_14826_2:1:1_4:1:0_a4\n+ATCAGATAGAATAACAGCCTTTTCATCAGTAACACACATTTGTCGATATGTAAATTTACGGGTGACTAAT\n+>chrM_408_812_0:2:1_4:2:0_ad\n+GAAATGTTCTGTTATAAGAAAATGACGCCCATTTCTTCCCATTGCATTGGCTCCACCTTGACCTAACGTT\n' |
| b |
| diff -r 000000000000 -r a0d039fa9771 test-data/samtools_fastx-out2-2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-out2-2.fastq Mon Mar 12 12:53:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,800 @@\n+@chrM_235_738_2:1:0_0:0:0_ab\n+TCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGCCTAAGTTGTACCTCTTCGGGTTGGTAAATTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_292_781_1:1:0_1:0:0_bf\n+GGTTGGTAACTTTCGTGCCAGCCACCGCGGTCATACGATTAGCCCAAACTAATTATCTTCGGCGTAAAAC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_293_831_0:1:0_1:0:0_b\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++\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+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_600_1083_1:1:0_0:0:0_77\n+CATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1023_1543_3:0:0_1:0:0_30\n+ATCATAGTGTAGGTTCCTATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_713_1102_2:0:0_0:0:1_50\n+AGGTGATTAGTTCAGAGTGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_787_1256_2:0:0_1:1:0_5a\n+TGCTTGTTCTTACTTTTAATTAGTCTTTCATGTTTCCCTTGCGGTACTAGTTCTATATCTCCTAGATGTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_835_1289_4:2:0_0:1:0_44\n+GTTCATTATGCAAAAGGTACAAGGTTTAATCTATGCTTGTTCTTACTTTTAATTAGTCTTTCATCTTTCC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_846_1403_2:3:0_2:2:0_85\n+ATTTAGTAGTAAATTAAGACTAGAGATCTTACTTGAATTGAGCAATGAAGTACGCACACACCGCCAGACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1370_1912_0:0:0_1:1:1_79\n+TCAACTCGTCTATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_961_1470_3:2:0_1:0:0_2c\n+ACTTAAATTCATTTTTTGGGTAACCAGCTATCACCCAGCTCGTTAGGCTTTTCACCTCTACCTAAAAATC\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_d\n+TGCCTTGTAAGTCTAGGTGTATAATCCTTCGGAGGATTTTTTATTCTCCGAGGCCACCCCAAGCGAAATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1415_1865_4:0:0_1:2:0_5e\n+GCGTTAACAGAGAAGTTAAAGGTGCATTATTTATAGTGTGATTATTGCCTATAGTCTGATTAACTAACAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1881_2335_1:1:1_1:1:2_34\n+TCAATAAGATATGTTGATTTTACATTGACTTGTAAG'..b'22222222222222222222222\n+@chrM_14592_15040_1:0:0_0:1:0_39\n+CTATCAGCCATCCCATATATTGGAACAACCCTAGTCGAATGAATTAGAGGGGGCTTCTCAGTAGACAAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14168_14690_2:0:0_2:0:0_2f\n+GTGGAAAGCGAAGCATCGGGTCAAGGTGGCTTTGTCTACTGATAAGCCCCCTCAAATTCATTCGACTAGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14660_15119_2:0:0_3:0:0_b3\n+AGCCACCTTGACCCGATTCTTCGCATTCCACTTCATCTTACCATTTATTATCGGGGCCCTAGCAATCGTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14679_15226_1:1:0_2:0:0_3d\n+TTCGCTTTCCACTTCATCTTACCATTTATTATCGCGGCCCTAGCAATCGTTCACCTCTTCTTCGTCCACG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14379_14856_2:1:0_0:2:0_41\n+TTACGAATATGATTAGGATACCTAGGATATCTTTGATTGTATAGTAGGGGTGACATGGAATTTTATCTGC\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++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14464_14944_1:1:0_0:1:0_b7\n+TGGGGTGGGGTGTTTAGTGGATTAGCTGGTATGTAGTTGTCTGGGTCTCCTAGTATGTCTGGGAAAATTA\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+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15261_15721_0:0:0_1:2:0_5f\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+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15560_16128_1:1:0_1:1:0_38\n+TTTTGGGGTTTGGCATTAAGAGGAGGGGGTGGGGGGTTTGGAGAGTTAGAATTTGGTCTTGAGTAGCATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15744_16179_0:1:0_0:2:0_4c\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 000000000000 -r a0d039fa9771 test-data/samtools_fastx-out2-3.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-out2-3.fastq Mon Mar 12 12:53:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,800 @@\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+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_292_781_1:1:0_1:0:0_bf\n+TTTCTTCCCATTACATTGGCTACACCTTGACCTAACGTTTTTATGTTTGATTCTTTTGCTTACTTTAATA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_713_1102_2:0:0_0:0:1_50\n+ATTAAAGTAAGCACAAGAATCAAACATAAAAACGATAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAAT\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++\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++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_655_1179_0:1:0_1:2:0_60\n+CTCTCTCCAATACTTTTAGTAGGATAAATGATTTGATTTATATAATAGTATAATTATATTTGTCTAGGGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_709_1253_2:0:0_2:1:0_23\n+TTGTTCTTACTTTTAATTAGTCTTTGATCTTTCCCTTGCGGTACTAGTTCTATATCTCCAAGATGTACGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_835_1289_4:2:0_0:1:0_44\n+GACTAAGGATGATTTAGTAGTAAATTACGAATAGAGATGTTAATTGGATTGAGCAATGAAGTACGCACAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_820_1322_1:2:0_1:1:0_32\n+CTGTAATTCTTTTAGTTAGAAGTTTTCTAGTTAGTTCATAATGCAAAAGGTACAAGGTTTAATCTATGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_846_1403_2:3:0_2:2:0_85\n+ATCTTCTCACTCTTTTGCCACATAGACGAGTTGATGCATAACATTGTTTTGAGGTAGCTCGTTTGGTTTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_961_1470_3:2:0_1:0:0_2c\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+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1053_1571_0:1:1_4:0:0_bb\n+GGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTAATCACCTAGCCCTAGCCCTAGACAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1614_2107_1:1:0_2:0:0_2e\n+AGCAGCGACCAATAAAGAAAGCGTTCAAGCTCAACATAAAATTTAAATTAATTCCATAATTTACACCAAC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1736_2168_2:2:0_0:1:0_a2\n+CGTATGAGTGACAAGAATTCCAATTCTCCAGGCATACGCGTATAACAACTCGGATACCCGTTGTTAGTTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1762_2310_0:1:0_3:1:1_d\n+TCCAGGCATACGCGTATAACAACTCGGATAACCGTTGTTAGTTAATCAGACTATAGGCAATAATCACACT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1370_1912_0:0:0_1:1:1_79\n+GAGTACCTTTTATCTTTTGGATCTTTCCTTTAGGC'..b'22222222222222222222222\n+@chrM_14473_14928_1:3:0_1:2:0_1\n+TAGAAACCTGAAAAATTGGACTACTTCTACTGTTCGCAGTCATATCCACAGCATTTATAGGCTACGTGCT\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+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14660_15119_2:0:0_3:0:0_b3\n+GTACAAAATTTGTGTGATTGGGCGGAATATTAGGCTTCGATGCTTTGAGGTCTGAAGGAAAGGTATAAGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14679_15226_1:1:0_2:0:0_3d\n+ATTGAGAAGTATGAGATTGAGGCTAGTTGGCCAATGATAATACATGGGTGTTCTACTGGTTGGCCCCCAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14851_15357_4:2:0_3:1:0_5d\n+TCGTAATTCTCATAACCCTAGTATTAATTTTCCCAGACAAACTAGGAGAGCCAGACAACTCGATACCAGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_14825_15378_0:3:0_2:1:0_7d\n+GGGGAGTAGCTCCTACTTCTTGCTGTCTTGAGCAGAGAAGATCTTCATTTCAGGTTTACAAGACCAGAGT\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+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15261_15717_1:0:0_0:2:0_29\n+CGGGTTGTTGGTTTCACGGAGGATGGTAGCTTAATAGACTAAATGGGGAAGGGGATAGTCATATGGAAGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15261_15721_0:0:0_1:2:0_5f\n+TGGGCGGGTTGTTGTTTTCACGGAGGATGGTAGCTTAATAGACTAAATGGGGAAGGGGATAGTCATATGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15343_15804_3:2:1_2:1:0_11\n+GCAGTAAGAACCAGATGTCTGATAAAGTTTCAGTTTAGCTACCCCCAAGTTTAATGGGCCCGGAGCGATC\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 000000000000 -r a0d039fa9771 test-data/samtools_fastx-out3-2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-out3-2.fasta Mon Mar 12 12:53:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,396 @@\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+>chrII_128532_129141_1:0:0_5:0:0_c\n+ATGACTTGTTCCGTGTGGATTTCCAAACTTGATGTGGGCTGGGCATTATAGGGAGTTTGAAGGGTCTTCACTGTTGCTGATGGAATTTCTCTGGTATCTTCAAACTCATCATCGTCTGAAGAGGATGAATCGCTTTCGTCAATATGCAATTCCTGAATTGGTGGAAACTCTTCATATATTGTCTTTGCTTTTGGTTGAGC\n+>chrII_178741_179333_0:0:0_5:0:0_7\n+TTAACAGGCCATTCTTCCGATTTTCTGTAGGCGGTATGACGGACGAGGCAGAAATAAAAGGTCATAGGAGAACGTATATTGGTGCCTAACCTGGCAGAGTAGTTCAAGCATTAAAGAAGTGCCAAACTCAACATCCTTTGATTTTGATAGATGAAATCGATAAGATTGGACACGGCGGCATACACGGCGATCCGTCCGCG\n+>chrII_185770_186311_6:1:0_5:0:0_6\n+AGCCTCCCCTGTGCAGGCATGGGGAGGAATCCATGCTGAAAACATCGAAAACTTCGGCGAATCCAGGTAGAAAGTTCTGGATTTGCAAGAGATCACGGGGTGATTCAAATAATACAGAAAGATCATGTGGGTTTTATCAGTGGGTTTAAATATGAAAACGTCAGCTTATATTTTGGGAGAATAAAACACTTTCTTCTATG\n+>chrII_371362_371914_8:0:0_3:0:0_5\n+GCAGATCGTTTTCCGTCTGGCTTGAAATGTTCTAGTCTCCTTTTTTTCTTGGCTTCGGGAAAATACGATTTGTTTGTTAATCTATATGCAGAGCCGCTGCTCTGCATGGATTTATGATCTCGAGTGCCATTGAACTTGAAGCATCTTATGTTGAAAGGATTTGTATGCCATCATACCCGAACTTTTTTAGCACGTGAAAA\n+>chrII_462520_463118_3:0:0_3:0:0_b\n+ACTGAAGCATCTGCACCTTCTACTGAAGAGGCGGAGCCAGCCGCTTCCAGAGATGCTGCAAAACAACAAGATGAAACCGCTGCTACAACGATAACTGTAATCAAACCTACTTTGGAAACAATGGAAACAGTGAAAGATGAGGCCAAAATGCGTGAGGAAGAGCAAACATCTCAAGAAAAATCCCCACAGGAGAACACACT\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+CCAAACTATGGGAAAAGTTTAACTCTTTCTCCAAGACAACCATCTATCCGCTTTTATCTTCCTTGTATCTAGCGCCATCATGGAAAGAATATGTCCCGCTAAAATATCCTTCTAATAACTTCAAGGAATGATACAAAATTTGGGTGAAAAGGTTTACATTGGATTTATTGAAAACAGGTACAACAGAAAATCATCCATTA\n+>chrII_551662_552193_3:0:0_4:0:0_2\n+CTCCCCCATGAAAAAAGTTTCTCAAAAGTTTAAGTCAATAAACTCCACGGATACTGATATGCAAGAAGCGTTAAGAGATCAATTCTCAGTAAAACATAAAAAAACCAAAAATAATTCACCCAAAGGAAAAAACTCTCGAAAATCCTCTATTCCGAGGTTTGATAAGACTTCTTTGAAGCTAACGACACACAAAAAGCTAG\n+>chrII_561725_562138_6:0:0_5:0:0_9\n+TGTAGGCGAAGTTTACCTTAGAAATGCTGGTACTTTCAACAAAGGGTCTAGCCTTCTTTCACACCCATCATCCAAGTCCATGTAAATACCACCATAATGCGAAAGGATGAAATACCGTATTGCCTCCGCCCTCTCAATTGGATCTTCATAACTCCTAAAGGTGTCAAGAAACCACGGGTATTCCTGTTTAATGAAAGTAT\n+>chrII_600174_600690_0:2:0_1:0:0_3\n+GAAATGACTCCATTCCCTGAATTTTTTGTGAAACCAATATCTGAGACTCTTCCTTCATCTTATCAACGTATTGTTCAGTCAATTAAGTAAGAAGTATATTTGAGCGCAGCCTTAATCATATATAGCACCAGTTATATGTTTGGCCCTCTCTTGAGTTGAAAAACACATAATACATAGTACTGTACTTTTCTCTTTTTCAT\n+>chrII_688026_688533_5:0:0_2:0:0_8\n+TACAAACAGCAATATTTGAGGCCTCCAGTATTTAATATTGTCTTGACGTAGGCGAAGCAAATACTTTCTCACTTGATGATATATTAAACTTTGAGACACATCACCCCAAGCCTTCGGTGGTGAAAAATAATGAAAGAATAAAAATAGCAAAATCATAGCCAAAAACAAGACAGACGCTGAGATGCCATCAACTATTAACA\n+>chrII_798295_798806_6:1:0_5:1:0_a\n+AATGTTGTTCTTGATAGTACCCGAAACTCTTGCGGCTGCCAAGACAGCACCCAAGAACTCACAGAGACCCGGCAAAACCATGGCTTGCCAGTATTTTAGAGATCTAGAAGAGATCGACGACGCGAATGAGTTCGCCACGTCGAT'..b'AACGACCTTAGTGTAAACGTTATTACCGTTAGTAGCAGTAATAGTCTTAGTGGTCATTACACTCGACACAGCTGCTGGCGAGACGGCAGTCATAACTGTAGTAGCTCCGAAAATAGTTGAGAATTTCATTATTATTGTTTTGTGATGGCTTTATGATAGACTTTTTTCCAAGGAG\n+>chrXVI_47666_48026_6:0:0_6:1:0_f\n+GCACGTAACCGGAAAACTCTTGGCCTAGTGTCAAAGGCGTGGCATCTTGCAAGAGTGTTGTACCGATCATCACAATATGGTCAAATTGCTTGGAATTGGCTTCAAGGGCGTTCTTTAAATTGGTCAACTCAGGTATCAACTCGTTTTGAATTTTCAAACTGGCAGCGATATGCATGACAGTGGGGAAAGTATCATTGGAT\n+>chrXVI_174529_175059_1:1:0_2:0:0_2\n+ATCCTTGACTCCAAACATTGTCGCTCCTCACTGAATAATGAATGGCTGGAAATCAGTTGTCAAATTGAATAATTTAGGAGGCAAAAAAGCACTTCGTTTATTGTTTCCTTCTTTTTTCAAACAGGCTTTCATACTGCCATTGTTGAAAGTATATCCGTGATCGAACCGCGCGGAACTAACTACAGGGATACTCCTATGTG\n+>chrXVI_216257_216697_2:0:0_4:0:0_8\n+TTGGGTAACGCCTATTAGGGAAAGTAGGTAGTTCCATGACCAACGATTAATGGCAATGATAGTGGGTTCTATATATGTACCGGCTCCATACATCATCTCTGTCCATTCGCTTTTCCATTTTTCGAACTGCAGTTTAGTGTTTTCCCACAATGTTGTGCCCAAAAAGACTTCGTCAAAGTTTACCGTATCAGGACATTCTT\n+>chrXVI_286197_286773_3:0:0_1:0:0_3\n+TCCTTAGGTTAGTAAATGGCATTATAAATTAGCAAGCGTAGCCTCTTCAGCCTATACAACAGCTGAACCTGCACAATTAATGTCATGTGGCCGACGTAATGCATATCCATCTTTTTTACTCCCTTAAAAGAAGGTTTAGCCCCTACTGTATACTCAATGAACAGATAATGTCTATCCATAAAGTATATCATTTCAGGAAC\n+>chrXVI_289557_289973_4:0:0_3:0:0_d\n+ATTGGAGGGTTAGGTAATGTTTACCACTGGAATTTCGAACCTGTTTTTGCCATTTATAACGAGATACATGAGGACTTTCAAGGCATAATATCTGACGAATTGGAGGCCGAAAGCAAGGCATTTTATCACACTGAGGGCTGCAGAAGAGCAATAGGAGAAAATAATAAGTTTAATACCGTTGCTTATCACAAATACATTGA\n+>chrXVI_389175_389686_2:0:0_4:0:0_6\n+GCAATCTCCCGTTAATTATGCTTTCCCTAACCCATACAAAATTCAACAACTACAACAGGCTCCTATCCAATCAGGTATGCCTTTACCAAATACCAACATACCTCCCCCAGCATTAAAAGTGGAAACCACCGTTACTGCTCCTCCAATTCGGGCAAGAGGGGTCAGCAATGCCTGCGTGGGAAGTTCAGCGTCTTTTGGTG\n+>chrXVI_401813_402387_4:0:0_6:0:0_1\n+AGTTGAGAATGGCAGCTCTAAACAACGAACCAGAACGTTTGTGAAGAAGGATTGAAGCGTGTAATCTTGAAACATTGACAATGTCCAAGCAAATGCCTTTGCTCCCATTATTCTAGTGTTCACTATTACGTCCAATCCTAGCAAAGTAATATCTCCATCAATCATAGGTGCATCGATATTGATATGTTCATTATTTTTTG\n+>chrXVI_680224_680728_0:0:0_3:0:0_7\n+GGACTACCTTTGACGCATGATAAGACGGCAAGAGACCTACCACAGCTGTCATCTCAACTAAATTCTATTCCATATTACTCAGCTCCACACGACCCTTCAACGAGACATCATTACCTCAACGTCGCTCAAGCTCAACCAAGGGCTAACTCGACCCCTCAATTGCCCTTTATTTCATCCATTATCAACAACAGCAGTCAAAC\n+>chrXVI_693308_693805_2:0:0_2:0:0_c\n+GGGCAGCAACTTCGTTACCATCAGCTGGTCTCCAAACTTGAATGTTTGGTAGGGATCTGAAGTGTGCTAAAGTTTCAATAGGTTGATGTGTTGGACCATCTTCACCGACACCGATAGAGTCATGTGTAGCAACCCAAATAACTGGGTGGCCAGACAAAGCGGACAATCTAACGGCACCAGCAGCATAAGAAACGAAGTTC\n+>chrXVI_752128_752641_3:0:0_2:0:0_5\n+ATGAGAAGTCTTACCAGCACTTAAACTGGGATACATATGCATGTAGTGACTAGTAATATCCAAGCCCAGCATTAATTGGAAGAAAACGCACCATTGGGGATACTGCACACAAAGGAAACACATCAAGCCAGCGGTACTGGATCTGTCGGTAACCATGTCCAGAACGGCACCCAGACTGGAAACCTTATTGTACTTTCTTG\n+>chrXVI_763341_763881_3:0:0_5:0:0_4\n+AGACTTAATCAAATATACTAACTTTGGCAAAGTCTGGGACTGCCAACTGAAACCTTTGGGATTCACTTTTTAAAAACTCTTTAGGATCCGTGGAGTTATGAACGTAAATTGTGGTGCCACCAGACCAGCAGAACGCCAGACCCGCACCATCATCTGTAATCTTATAAGGATCATGTGAACCATTAATATTTAAGTGGATC\n+>chrXVI_766516_767017_5:0:0_7:0:0_b\n+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' |
| b |
| diff -r 000000000000 -r a0d039fa9771 test-data/samtools_fastx-out3-3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_fastx-out3-3.fasta Mon Mar 12 12:53:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,396 @@\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+>chrII_128532_129141_1:0:0_5:0:0_c\n+ATGCCAATAGAAACAACGGCACCCAGTCAGGAAATGAGACAGCAAATCCAAACTTAACTGAAACATTAAGTGATAGGTTAGATGGTTATTTGAATGAATATGGTATTCCAAGAAGTCAATCCTTGACATCGTCTGTTGCAAACAATGGTCCTCAATCCGTAAGAGATGATGTTGCGCTACCGGAAACGTTGGAAGAACGT\n+>chrII_178741_179333_0:0:0_5:0:0_7\n+GGAATCTTCAATACTCAACTTCTTTACCACTTGTAGGGCTGCTTTACGGTATATTTTCTCGATGTGTTTTTTCAAATTCCTTACACCACTTTCTCTACAGTAGTACTTCATTAACGCTGTTATTGCATCTTCTGTCATATCAACATGAGAGTTTTCTAGACCAGCGCTTTTCTTGGCACTTGGAACTAAATACTGCTCGG\n+>chrII_185770_186311_6:1:0_5:0:0_6\n+AAATGACATGGAGGCAATGGTTAAATAACGCATTGAAACGTCGTTATGGTATTTTTGGTGAAGGTGTAGAATATTCATTCCTGCATGTTGACGATAAGCTGGCTTACATCAGAGTAAATCATGCGGATAAAGATACATTTTCTTCGTCCATCAGTACATACATATGTACTGATGAACTCGTGGGTTGACCATTAACAGTT\n+>chrII_371362_371914_8:0:0_3:0:0_5\n+AATTGGCACCAGCTGGCTACTCGTTGCTCGAAAACTACTCTCTTTTATATTTAATTTACGAACGATTATCTTTCGAAGGAACGACCAAACGAGCTAAATATGGGCATCGCCAACGTTAAAAAAATTGACCCTACCGAAGACGTTATTATGCCAAGGCGCAGCGAAGATTCTTTCTCCTTGAGAAAAAATATGCATGAAAC\n+>chrII_462520_463118_3:0:0_3:0:0_b\n+ACCGTTTTAAAGCAAATAAGGGAATTTCTTGAAGAGATTGTAGATACACAATGAAGGATACGAAAATGCACCTTAAATCCCAATATTATTACATATGCTCATCGGGAAAACCTTATAAGCAATAATAGATTTTAAGTATGTAAAGATACAAATAATAATATATTTATATACGCATATATTTACATGTGCATATATGAAAA\n+>chrII_464058_464495_1:0:0_2:0:0_1\n+GCGCCAACGAATGCCTCTCCTGCCCCACCTCCTGTGATTTTACAACCTACCTTACAACCTAATGATCAAGGAAATCCTTTGAACACTAGAATTTCAGCCCAATCTGCCAATGCTACTGCTTCAATGGTAGCACAACAGCATCCTGCTCAACAAACGCCTATTAACTCTTCTGCAACAATGTACAGTAATGGAGCTTCCCC\n+>chrII_482749_483235_3:0:0_1:0:0_0\n+TTGGAGATTCTAAAGTTTCACCGGTGACTGGGTTACCGATATCGTATTTATCCATCAATTCACCTAATTCTGGGCCGGAATAACCATCTATTTTAGCCAAAATTTCTTCCTATTCTTTGACAACGTCGTCATCCAATTTGACTGCTTTAATTTGTTTAACTTTTTTCTTTCTCTTCTTCTTTTCGGCATCGTCCTTAGCA\n+>chrII_509290_509702_4:0:0_3:0:0_4\n+TTCATAGCACATTCTTAACGAATCCACTTGCAAGTTATTCATTGCTTCCAGATTGCACGTGAAAATGCAGTCAAATTCAATAATAATCCCGTTTAAAATATCAGCGTATGGAGTTCCTTTTTCTGCCTTGATCATAATGTCCAGAGAAATATAAGGTAGCAAAAAATTTGATAGTGAGCCATCATCTTCCCTAATCAAAG\n+>chrII_551662_552193_3:0:0_4:0:0_2\n+AAGGTTTGTAAGCCGATAATTTTTGGATTTACGAGACTCTGGCTTGGAGATGTCAGCAATATTCGGAGAAAGTTTTCTTAATGTTTTCTCTTTAATTTTCAAACGATGTGGCGTTTGCGACGTTGTTAAATTTTTATTTTTATTAGGGGAAATATACGCTTTTGTTGGTCTCCAATAACCTCTTACAGGGCTTTGGTAAT\n+>chrII_561725_562138_6:0:0_5:0:0_9\n+GATACTTCCAAAGATGCGCTAACAGATGAACATCTGAACCCCCCCAATGGCTTCAATTGACCATTCTATGAGTCTCCTCCTCAACTCATACCGAAAATCATTCATCAAACCTACAAAACAAACTATATCCCAGAACAGTGGGTAAACGGGAGGCAGAAGTGCATTGATTTACATCCGGATTACACTTACAATTTATGGAC\n+>chrII_600174_600690_0:2:0_1:0:0_3\n+AAAAATTGTCCCAGCTTTTTGTTGCTGTTTTGTTTCGAGTCAGAACCAGAATGTAGAGAAGAAATTTGCTCATCCTCTCTAAACATACATTTGATAACCCTCAGAGATGATCCTCGCACTTGTAGGTCAACTATGTAGCTCATATCCTTATTTTATGTCTTCAGTTTGAGATCAGAATATTTTTATGAAAATGTTGTCAC\n+>chrII_688026_688533_5:0:0_2:0:0_8\n+GGGGATGCTCGGTGCTGCTTATGTATTAGAAGCAATTGCAAATGATAACATTATTCCTGGTTTGGAGATTTTTGCTCATTCACCGTTATATTCATTGATTTTTACATGGATTCTAACACCGCTATGTTTGTTTTCAGCCGTCAATAAAAACGCCACATTTATCACAATGACATTCTTAATGACGTTTGTGGTCATGAATT\n+>chrII_798295_798806_6:1:0_5:1:0_a\n+ATCAATACTAGATGTCACAGCCACTTTGGATCCTTCTATTATGTCAATCATTAGATTAACTCAGTCAATAGCAGATTTTTTTTACAATGGCTACTGGGTGGACATCTCCAAACAATTCATGTCACTAAGCCCGGTTATCGATAT'..b'ATCCTGTATAGGATTTAAAACAATGCACCGTAAGTTCAAATGCACCCCCCCTCGGCCCGCAGCGGACCCTTGAACAGAGAACTGTTTCGAGGTTCACCCAATTGGATCACTTGTATAATTTGTAATCGAGTTCGGATAAGATGTATACGAATCTAACTGTGTGCAGTATAATTAG\n+>chrXVI_47666_48026_6:0:0_6:1:0_f\n+CTAGACGACCACATTCCATTGGTTGTTATGCAAACGGGTTCCGGTACCCAGTCTAACATGAATGGTAATGAAGTTCTTTCCAATCGTGCCATTGAGATCCTAGGAGGCAAGCTTGGATCTAAACAAGTCCATCCAAACAATCATTGCAACCAATCTCAATCATCCAATGATACTTTCCCCACTGTCATGCATATCGCTGC\n+>chrXVI_174529_175059_1:1:0_2:0:0_2\n+TCATCACTGTTGGTGCACACTTCAAGCAAGCTAACAACTTTTTGTGGCCATTCAAGTTGTCCAACCCATCTGGTGGTTGGGGTGTCCCAAGAAAGTTCAAGCATTTCCTCCAAGGTGGTTCTTTCGGTAACCGTGAAGAATTCATCAATAAATTGGTTAAGGCTATGAACTAACATTATTCCGTGTGGCAATAATCTCAA\n+>chrXVI_216257_216697_2:0:0_4:0:0_8\n+ATTCCAGTTGCGATCATTTCATCTCGAGGAGTGATGACTAGAGAACATCCGATCTACACAGTAGAAGACAAATTCGATTTCATCAAAGATAAACTAAGAGACAAAAAGAAGGGAGAGGTACTTTCTGAGATAATGCTATATCTTGTCGAAAAATCACTCGATCTCATTGACGATCCATTCATCCCATTCAGCATATCGAA\n+>chrXVI_286197_286773_3:0:0_1:0:0_3\n+AATTCTCGCAAACACGTCACAAGAAACACATTAATGCAAAATGTGGCACAGTCAAAAAACTGCGAAAATGTGTAAAAGATGAAAAGAACCGTGATCAGCACCAGCAGTGTACCAGATTTTGTGATCTGATTTATTATAGATTTACTCGATGACCTGAACTTGAATTATATTTAAATCGATGAAGGGGTTGAAACAGGTGT\n+>chrXVI_289557_289973_4:0:0_3:0:0_d\n+AACATTAAAAACAAATTTTTAGAAAAACAAAAGCTGAATTAAAGACTAAATATTACACAATTTCTTCATACATTTCCGCCCCAAAGTCAAACAGCCTAAATAATATAAAAATTAACTTTTGGCAGCTCCAACCTCTGTACTGCCATCTAAAACTTTTCCAGTAAACGGCTTATATACAGTTAACAACCCGTCACTATCAA\n+>chrXVI_389175_389686_2:0:0_4:0:0_6\n+TACCAACCGGTTGTGAGGTATATTGCACCTGATAAGATTGTTGATAGTTGGGTGCGTATCTAGAGGCGTGTTCATTCTGGTTTGGTGTATACGAACTAATAGAGCTTGTATGGCCTCTATGGGTCTTTACAAAATTGGGGGTATTTACGGCCGAAGCGGCAAGGTTTTGCACAACTGATGGATATTGCTTCTGCTGAACT\n+>chrXVI_401813_402387_4:0:0_6:0:0_1\n+TATTGACTCTACTGATAGCATTCTTATCAATAAAGGATGATTCTACTAAAAACTGGTTAAACGGCAAGGTATTCCGTCTAGTTTTTCAGAATATTTTACTGGAGCAAAACCCGGAACTATTGGAACTGTCTTTAGATGTTTATGTTGCGTTATTGGAGCATTATAAAGTTAAGCATACCTAAAAAACTTTAGATCATGTT\n+>chrXVI_680224_680728_0:0:0_3:0:0_7\n+GAGGAATGTTTTGGTTTGGTATATGAGGAATGTGATGATGCGTAGGGGTAGTTGTGGACAATCGATTGTTCCTGGTGTGAGACAGTGGTTTGACAATATAAGTTGTTCCCATCTGCTTTAGCTGCTGGTACTGATCCAGTTGAAAATCTTGCAGAGAAGGTAATAGAGGGGGAGGAAAATATTGATTTGAATTGTTGATA\n+>chrXVI_693308_693805_2:0:0_2:0:0_c\n+CTAAGTTGCCAACTTACACCGCCAAGGACTCTGCCGTGGCCACTAGAAAATTATCAGAAACTGTTCTTGAGGATGTTTACAATCAATTGCCAGAGTTGATTGGTGGTTCTGCCGATTTAACACCTTCTAACTTGACCAGATGGAAGGAAGGCCTTGACTACCAACCTCCTTCTTCCGGTTCAGGTAACTACTCTGGTAGA\n+>chrXVI_752128_752641_3:0:0_2:0:0_5\n+TCTCGAGTATTTTTCACTTTTAGTATATAAGTAAAACATAAAAAACATGAGAGGTGGTATGGTTTATTTGCCGTCACTGTGGAGCCTTCAAGTAATGTAAATAAGAGGGAAAGTGTGATAGTACAAGATGAGTTCGAATTCAACACCAGAAAATGTTACTGCAGCACACGTTCTGTGGTATATTCCCAATAAGATCGGTT\n+>chrXVI_763341_763881_3:0:0_5:0:0_4\n+AAGCTGCCAGCACCATGCGCGCTTCATACTGTTTATGTTCCTTTTGTCAGCTCTGCCCAAAGAAGCCCCTATAATTACGCCAATACAATATATGGTTTGCACATCATTCGTACAATTAATTCAGTCAAAACATATTTCAATATTAGGTCAATGGTTACATCTTCTTCATCTGCCAGAATAACATGGGGGAAATCTCTGCA\n+>chrXVI_766516_767017_5:0:0_7:0:0_b\n+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' 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