| Next changeset 1:63f76b9f4ba7 (2017-09-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd |
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added:
kallisto_pseudo.xml macros.xml test-data/cached_locally/kallisto_indexes.loc test-data/cached_locally/sacCer2_chrX.kallistei test-data/felCat8_chrM.fa test-data/felCat8_chrM_F.fq test-data/felCat8_chrM_R.fq test-data/kallisto_pseudo_out1.cells test-data/kallisto_pseudo_out1.ec test-data/kallisto_pseudo_out1.tab test-data/kallisto_pseudo_out2.ec test-data/kallisto_pseudo_out2.tab test-data/kallisto_pseudo_out3.ec test-data/kallisto_pseudo_out3.tab test-data/kallisto_pseudo_out4.ec test-data/kallisto_pseudo_out4.tab test-data/kallisto_pseudo_out5.bam test-data/kallisto_pseudo_out5.ec test-data/kallisto_pseudo_out5.tab test-data/kallisto_pseudo_out6.bam test-data/kallisto_pseudo_out6.cells test-data/kallisto_pseudo_out6.ec test-data/kallisto_pseudo_out6.tab test-data/kallisto_quant_out1.tab test-data/kallisto_quant_out2.tab test-data/kallisto_quant_out3.tab test-data/kallisto_quant_out4.bam test-data/kallisto_quant_out4.tab test-data/kallisto_quant_out5.bam test-data/kallisto_quant_out5.tab test-data/mm10_chrM-1.f.fq test-data/mm10_chrM-1.r.fq test-data/mm10_chrM.fa test-data/mm10_chrM.umi test-data/sacCer2_chrM.umi test-data/sacCer2_chrM_F.fq.gz test-data/sacCer2_chrM_R.fq test-data/sacCer2_chrM_R.fq.gz tool-data/kallisto_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 2953303df011 kallisto_pseudo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kallisto_pseudo.xml Tue Aug 22 04:16:08 2017 -0400 |
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| b'@@ -0,0 +1,224 @@\n+<?xml version="1.0"?>\n+<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0">\n+ <description>- run pseudoalignment on RNA-Seq transcripts</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ #if $reference_genome.reference_genome_source == "history":\n+ ln -s \'$reference_genome.reference\' reference.fa &&\n+ kallisto index reference.fa -i reference.kallisto &&\n+ #set index_path = \'reference.kallisto\'\n+ #else:\n+ #set index_path = $reference_genome.index.fields.path\n+ #end if\n+ kallisto pseudo -i \'$index_path\'\n+ #if $pseudobam:\n+ $pseudobam -o .\n+ #else:\n+ --threads \\${GALAXY_SLOTS:-1}\n+ -o .\n+ #end if\n+\n+\n+ #if str($single_paired.single_paired_selector) == \'single\':\n+ --single --fragment-length $single_paired.fragment_length\n+ --sd $single_paired.sd \'$single_paired.reads\'\n+ #else:\n+ #if str($single_paired.collection.collection_selector) == \'collection\':\n+ \'$single_paired.collection.reads.forward\'\n+ \'$single_paired.collection.reads.reverse\'\n+ #else:\n+ #if str($single_paired.collection.fastq_umi.umi) == \'yes\':\n+ --batch \'$batch\' --umi\n+ #else:\n+ \'$single_paired.collection.fastq_umi.forward\'\n+ \'$single_paired.collection.fastq_umi.reverse\'\n+ #end if\n+ #end if\n+ #end if\n+ #if $pseudobam:\n+ | samtools sort -O bam -@ \\${GALAXY_SLOTS:-1} -o \'$pseudobam_output\' -\n+ #end if\n+ && if [ -f run_info.json ] ; then cat run_info.json ; fi &&\n+ mkdir outputs &&\n+ if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&\n+ if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi &&\n+ if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi &&\n+ if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&\n+ if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="batch">\n+<![CDATA[\n+#if str($single_paired.single_paired_selector) == \'single\':\n+cell1\t$single_paired.reads\n+#else:\n+#if str($single_paired.collection.collection_selector) == \'collection\':\n+cell1\t$single_paired.collection.reads.forward $single_paired.collection.reads.reverse\n+#else:\n+cell1\t$single_paired.collection.fastq_umi.forward $single_paired.collection.fastq_umi.reverse\n+#end if\n+#end if\n+]]>\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="reference_genome">\n+ <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment">\n+ <option value="indexed" selected="true">Use a built-in genome</option>\n+ <option value="history">Use a genome from history</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator">\n+ <options from_data_table="kallisto_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No genomes are available for the selected input dataset" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="reference" type="data" format="fasta'..b'taset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" />\n+ <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="reference_genome_source" value="history" />\n+ <param name="reference" ftype="fasta" value="mm10_chrM.fa" />\n+ <param name="single_paired_selector" value="single" />\n+ <param name="collection_selector" value="collection" />\n+ <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />\n+ <output name="sample">\n+ <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />\n+ <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="reference_genome_source" value="history" />\n+ <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />\n+ <param name="single_paired_selector" value="paired" />\n+ <param name="collection_selector" value="datasets" />\n+ <param name="umi" value="no" />\n+ <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />\n+ <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />\n+ <output name="sample">\n+ <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" />\n+ <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="reference_genome_source" value="cached" />\n+ <param name="single_paired_selector" value="paired" />\n+ <param name="collection_selector" value="datasets" />\n+ <param name="pseudobam" value="true" />\n+ <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />\n+ <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />\n+ <output name="sample">\n+ <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" />\n+ <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />\n+ </output>\n+ <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />\n+ </test>\n+ <test>\n+ <param name="reference_genome_source" value="cached" />\n+ <param name="single_paired_selector" value="paired" />\n+ <param name="collection_selector" value="datasets" />\n+ <param name="umi" value="yes" />\n+ <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />\n+ <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />\n+ <output name="sample">\n+ <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />\n+ <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />\n+ <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+ `kallisto <https://pachterlab.github.io/kallisto/manual>`__ is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 2953303df011 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 22 04:16:08 2017 -0400 |
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| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">0.43.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">kallisto</requirement> + <requirement type="package" version="1.5">samtools</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">doi:10.1038/nbt.3519</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 2953303df011 test-data/cached_locally/kallisto_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/kallisto_indexes.loc Tue Aug 22 04:16:08 2017 -0400 |
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| @@ -0,0 +1,1 @@ +sacCer2_chrX sacCer2 S. cerevisiae Chromosome X (sacCer2_chrX) ${__HERE__}/sacCer2_chrX.kallistei |
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| diff -r 000000000000 -r 2953303df011 test-data/cached_locally/sacCer2_chrX.kallistei |
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| Binary file test-data/cached_locally/sacCer2_chrX.kallistei has changed |
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| diff -r 000000000000 -r 2953303df011 test-data/felCat8_chrM.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/felCat8_chrM.fa Tue Aug 22 04:16:08 2017 -0400 |
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| b'@@ -0,0 +1,342 @@\n+>chrM\n+GGACTAATGACTAATCAGCCCATGATCACACATAACTGTGGTGTCATGCA\n+TTTGGTATTTTTTATTTTTAGGGGGTCGAACTTGCTATGACTCAGCTATG\n+ACCTAAAGGTCCTGACTCAGTCAAATATATTGTTGCTGGGCTTATTCTCT\n+ATGCGGGGTCTCCACACGCACAGACAGTCAGGGTGCTATTCAGTCAATGG\n+TCACAGGACATATACTTAAATTCCTATTGTTCCACAGGACACGGGATGCG\n+CGCACCCACGTTTGCGTGCACACGTGTACACGTACACACGTACACACGTA\n+CACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACA\n+CACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACA\n+CGTACACACGTACACACGTGTACACGTACACACGTACACACGTGTACACG\n+TACACACGTACACACGTACACACGTGTACACGTACACACGTACACACGTA\n+CACACGTACACACGTACACACGTGTACACGTACACACGTACACACGTACA\n+CACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGC\n+TTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTATAATAATACGTG\n+CCTATTTATGTCTTGCCAAACCCCACAAACAAGACTAGACCGTACCTAAA\n+TATAAGGCCTAAGAAAACGCTTATAAGCTTACCAATCCCCTATTATTACT\n+AGCTACTAATACTAAATCATAACTCTGTTCGCAGTTATCTATAGATATAC\n+CGACCTGACTCTAATTCGTCCCTATCGAACAACATTTTACATGTCTACGT\n+TAGCCCCACATCCCAGTTAATGTAGCTTAAACATATAAAGCAAGGCACTG\n+AAAATGCCTAGATGAGTCGCCAGACTCCATAAACACAAAGGTTTGGTCCT\n+GGCCTTTCCATTAGTTATTAATAAGATTACACATGCAAGCCTCCGCATCC\n+CGGTGAAAATGCCCTCTAAGTCACCCAGTGACCTAAAGGAGCTGGTATCA\n+AGCACACAACCACAGTAGCTCATAACACCTTGCTCAGCCACACCCCCACG\n+GGATACAGCAGTGATAAAAATTAAGCCATGAATGAAAGTTCGACTAAGCT\n+ATATTAAACAAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGCCATACGA\n+TTAACCCAAACTAATAGACCCACGGCGTAAAGCGTGTTACAGAGAAAAAA\n+ATATACTAAAGTTAAATTTTAACTAGGCCGTAGAAAGCTACAGTTAACAT\n+AAAAATACAGCACGAAAGTAACTTTAACACCTCCGACTACACGACAGCTA\n+AGACCCAAACTGGGATTAGATACCCTACTATGCTTAGCCCTAAACTTAGA\n+TAGTTACCCTAAACAAAACTATCCGCCAGAGAACTACTAGCAATAGCTTA\n+AAACTCAAAGGACTTGGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTC\n+TATAATCGATAAACCCCGATATACCTCACCATCTCTTGCTAATTCAGCCT\n+ATATACCGCCATCTTCAGCAAACCCTAAAAAGGAAGAAAAGTAAGCACAA\n+GTATCTTAACATAAAAAAGTTAGGTCAAGGTGTAGCTCATGAGATGGGAA\n+GCAATGGGCTACATTTTCTAAAATTAGAACACCCACGAAGATCCTTACGA\n+AACTAAGTATTAAAGGAGGATTTAGTAGTAAATTTGAGAATAGAGAGCTC\n+AATTGAATCGGGCCATGAAGCACGCACACACCGCCCGTCACCCTCCTCAA\n+GTGGTAACTCCCAAAAAAACCTATTTAAATTATCACACCCACAAGAGGAG\n+ATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGATAACAAGA\n+TGTAGCTTAAACAAAGCATCTGGCTTACACCCAGAAGATTTCATATTAAA\n+CTGACCATCTTGAGCTAAAGCTAGCCCAAACATCTACAAACACAACTAAC\n+ACTAGAAAATAAAACAAAACATTTAGTCACCTTATAAAAGTATAGGAGAT\n+AGAAATTTAACTTGGCGCTATAGAGAAAGTACCGCAAGGGAAAGATGAAA\n+GATAAAATTAAAAGCACCACACAGCAAAGATTACCCCTTGTACCTTTTGC\n+ATAATGAGTTAGCTAGAACAACCTAACAAAGAGAACTTCAGCTAGGCCCC\n+CCGAAACCAGACGAGCTACCCATGAACAATCTATTACAGGATGAACTCGT\n+CTATGTTGCAAAATAGTGAGAAGATTTGTGGGTAGAGGTGAAAAGCCTAA\n+CGAGCCTGGTGATAGCTGGTTGCCCAGAACAGAATCTTAGTTCAACTTTA\n+AACTTACCTCAAAAACCTAAAATTCCAATGTAAGTTTAAAATATAGTCTA\n+AAAAGGTACAGCTTTTTAGACCTAGGATACAGCCTTTATTAGAGAGTAAG\n+CATAAATATAAACCATAGTTGGCCTAAAAGCAGCCATCAATTAAGAAAGC\n+GTTCAAGCTCAACAATCAAAGCATCTTAATGTCAAAAATAATGCAACCAA\n+CTCCTAACCTAAAACTGGGCTAATCTATTTAATAATAGAAGCAATAATGC\n+TAATATGAGTAACAAGAAATATTTCTCCCTGCATAAGCTTATATCAGAAC\n+GGATAACCACTGATAGTTAACAACAAGATATATATAACCTAACCATAAAC\n+AAAATATCAAATTAATTGTTAACCCAACACAGGTATGCAAATTAGGGAAA\n+GATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAGCCCCGCCTGTTTAC\n+CAAAAACATCACCTCTAGCATTTCCAGTATGAGAGGCACTGCCTGCCCGG\n+TGACGCTAGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAA\n+TCATTTGTTCCCTAAATAGGGACTTGTATGAACGGCCACACGAGGGCTTT\n+ACTGTCTCTTACTTCCAATCCGTGAAATTGACCTTCCCGTGAAGAGGCGG\n+GAATATAATAATAAGACGAGAAGACCCTATGGAGCTTTAATTAACCGACC\n+CAAAGAGACCATATGAACCAACCGACAGGAACAACAAACCTCTATATGGG\n+CCGGCAATTTAGGTTGGGGTGACCTCGGAGAATAAAACAACCTCCGAGTG\n+ATTTAAATCTAGACTAACCAGTCGAAAGTACTACATCACTTATTGATCCA\n+AAAACCTTGATCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT\n+ATTTCAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGATCA\n+GGACATCCCGATGGTGCAGCAGCTATCAAAGGTTCGTTTGTTCAACGATT\n+AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT\n+ATCTATTTAATAACTTCTCCCAGTACGAAAGGACAAGAGAAGTGAGGCCC\n+ACTTCACCAAAGCGCCTTTAACCAAATAGATGATATAATCTTAATCTAGA\n+CAGTTTATCCAAACACACTACCCGAGAGCTCGGGTTTGTTAGGGTGGCAG\n+AGCCCGGTAACTGCATAAAACTTAAGCTTTTATTATCAGAGGTTCAATTC\n+CTCTCCTTAACAACATGTTTATAATTAATGTACTCTCACTAATTATTCCT\n+ATTCTCCTAGCTGTAGCCTTCCTAACCCTAGTCGAACGAAAAGTGCTAGG\n+CTATATGCAACTCCGCAAAGGACCAAATGTCGTAGGACCATACGGCCTAC\n+TTCAACCTATCGCAGATGCTGTAAAACTCTTTACCAAAGAGCCTCTCCGA\n+CCCCTTACATCCTCCATATTA'..b'GAGACGTAGGCTTCATCATAGCCATAGCATGATTT\n+CTCACCAACTCAAACGCATGGGACTTCCAACAAATCTTTATCACCCAACA\n+CGAGAACCTAAATATTCCATTACTAGGGCTTCTATTAGCAGCCACAGGTA\n+AATCCGCCCAATTCGGCCTACATCCGTGACTGCCATCAGCCATAGAAGGC\n+CCAACTCCTGTCTCCGCCCTACTCCACTCAAGTACAATAGTCGTAGCAGG\n+GGTCTTCTTACTTATCCGGTTTTACCCGCTCATAGAACAAAACAAAACTA\n+TACAAACTCTCACCCTATGTTTAGGAGCTATTACAACCTTGTTCACAGCT\n+ATTTGTGCTCTCACACAAAATGATATCAAAAAAGTTGTTGCCTTTTCAAC\n+CTCAAGCCAACTGGGCCTAATAATTGTAACCATTGGGATTAACCAACCTT\n+ACCTCGCATTTCTACACATTTGCACACACGCATTCTTCAAAGCCATGCTA\n+TTCATATGTTCAGGATCAATTATCCACAGTCTGAACGACGAACAAGACAT\n+TCGAAAAATAGGCGGATTATACAAACCAATGCCCTTCACCACTACCTCCC\n+TAATCATTGGAAGCCTCGCACTCACAGGTATACCTTTCCTAACAGGTTTT\n+TATTCCAAAGACCTAATCATCGAGACAGCCAACACGTCGTATACCAACGC\n+CTGAGCCCTACTAATTACTCTCATTGCCACATCCCTTACAGCTGCCTACA\n+GTACTCGAATTATATTCTTTGTGCTACTAGGACAACCACGATTCAATACC\n+TTGAATCTAATCAATGAAAATAATACCCACCTCATCAACTCCATTAAACG\n+TCTCTTAATCGGAAGTATCTTTGCAGGATATCTAATTTCTTACAACATCC\n+CCCCAACAACTATCCCACAAATAACTATACCCTACTATCTAAAACTAACT\n+GCTCTTGCCGTGACTATCGCAGGCTTCATCCTAGCATTAGAACTTAATCT\n+CGCGGCTAAAAACTTAAAATTTATATACCCTTCAAACCTCTTTAAGTTTT\n+CCAACCTCTTAGGGTACTTTCCAATTGTAATACACCGCCTCCCATCAAAA\n+ATGAGCCTAACTATGAGCCAAAAGTCCGCATCGATACTATTAGACATAAT\n+TTGACTAGAAAATGTATTACCCAAATCCATCTCCTTATTCCAAATAAAAA\n+TGTCAACTACTGTATCTAATCAGAAAGGACTAGTTAAACTCTACTTTTTA\n+TCTTTCATAATCACCCTAGCCCTCAGCCTAATCTTACTTAATTCCCACGA\n+GTAACTTCCATAATCACCAACACACCAATAAGCAAAGATCAGCCGGTGAC\n+AACCACTAATCAAGTTCCATAACTATATAGCGCCGCAATTCCCATGGCCT\n+CCTCACTAAAGAACCCTGAGTCACCTGTATCATAAATCACCCAATCACCT\n+GCACCATTAAACTTAAATACGACTTCTACCTCATCTTCCTTTAAAATATA\n+ACAAGCAGTTAATAATTCTGCTAACACCCCCGTAATAAACATTGCTAATA\n+CAGCCTTATTAGACGTCCACGCCTCAGGATAAGGCTCAGTAGCCATAGCC\n+GTAGTATATCCAAACACTACGAGTATACCCCCTAAATAAATTAAGAAAAC\n+CATTAAACCTAAAAATGATCCCCCAAAATTCAACACAATACCACAACCAG\n+TACCACCAGCCACAATTAAACCAAACCCACCATAAATTGGAGAAGGCTTT\n+GAAGAAAAACTTACAAAGCTCACTACAAAAACTGTACTTAAAATAAATAC\n+AATGTATGTTATCATTATTCTCACATGGAATTTAACCATGACTAATGATA\n+TGAAAAACCATCGTTGTATTTCAACTATAAGAACTTAATGACCAACATTC\n+GAAAATCACACCCCCTTATCAAAATTATTAATCACTCATTCATCGATCTA\n+CCCGCCCCATCTAACATCTCAGCATGATGAAACTTCGGCTCCCTTCTAGG\n+AGTCTGCCTAACCTTACAAATCCTCACCGGCCTCTTTTTGGCCATACACT\n+ACACATCAGACACAATAACCGCCTTTTCATCAGTTACCCACATCTGTCGC\n+GACGTTAATTATGGCTGAATCATCCGATATTTACACGCCAACGGAGCTTC\n+TATATTCTTTATCTGCCTGTACATACATGTAGGACGGGGAATATACTACG\n+GCTCCTACACCTTCTCAGAGACATGAAACATTGGAATCATACTATTATTT\n+ACAGTCATAGCCACAGCTTTTATGGGATACGTCCTACCATGAGGCCAAAT\n+GTCCTTCTGAGGAGCAACCGTAATCACTAACCTCCTGTCAGCAATTCCAT\n+ACATCGGGACTGAACTAGTAGAATGAATCTGAGGGGGGTTCTCAGTAGAC\n+AAAGCCACCCTAACACGATTCTTTGGCTTCCACTTCATTCTTCCATTCAT\n+TATCTCAGCCTTAGCAGGAGTACACCTCTTATTCCTTCATGAAACAGGAT\n+CTAACAACCCCTCAGGAATTACATCCGATTCAGACAAAATCCCATTCCAC\n+CCATACTATACAATCAAAGACATCCTAGGTCTTCTAGTACTAGTTTTAAC\n+ACTCATACTACTCGTCCTATTTTCACCAGACCTGCTAGGAGACCCAGACA\n+ACTACATCCCAGCCAACCCTTTAAATACCCCTCCCCATATTAAACCTGAA\n+TGATACTTCCTATTCGCATACGCAATTCTCCGATCCATCCCTAACAAACT\n+AGGGGGAGTCCTAGCCCTAGTACTCTCCATCCTAGTACTAGCAATCATTC\n+CAATCCTCCACACCTCCAAACAACGAGGAATAATGTTTCGACCACTAAGC\n+CAATGTCTATTCTGACTCCTAGTAGCGGATCTCCTAACCCTAACATGAAT\n+CGGTGGCCAACCTGTAGAACATCCGTTCATCACCATCGGGCAACTAGCCT\n+CCATCCTATATTTCTCAACCCTCCTAATCCTAATACCCATCTCAGGCATT\n+ATTGAAAACCGTCTACTCAAATGAAGAGTCTTTGTAGTATATAAAATACT\n+TTGGTCTTGTAAACCAAAAAAGGAGAACATATGCCCTCCCTAAGACTTCA\n+AGGAAGAAGCAACAGCCCCACTATCAGCACCCAAAGCTGAAATTCTTTCT\n+TAAACTATTCCTTGGCAATACCAGAAAGCAACCCCATAACTTTCATAATT\n+CATATATTGCATATACCCATACTGTGCTTGGCCAGTATGTCCTTATTTCC\n+CACAAAAAAACCAAGTAAAAACCCCCAAACACCACAACCCAAAACACACA\n+ATGTAAAATCACTCTATTAACCACCAACTCACCCCAGGGGGTATTATACA\n+CCCATATACATAAGACATACTATGTACATCGTGCATTAATTGCTAGTCCC\n+CATGAATATTAAGCATGTACAGGAGTTTATATATATTACATAAGACATAC\n+TATGTATATCGTGCATTAATTGCTAGTCCCCATGAATATTAAGCATGTAC\n+AGTAGTTTATATATATTACATAAGACATACTATGTATATCGTGCATTAAT\n+TGCTAGTCCCCATGAATATTAAGCATGTACAGTAGTTTATATATATTACA\n+TAAGACATAATAGTGCTTAATCGTGCATTCACCTTAATTCTAGGACAGTC\n+TTCTATGGACCTCAACTATTCCAAAGAGCTTAATCACCTGGCCTCGAGAA\n+ACCAGCAATCCTTGCTCGAACGTGTACCTCTTCTCGCTCCGGGCCCATTT\n+CAACGTGGGGGTTTCTATAACGGAACTATACCTGGCATCTGGTTCTTACT\n+TCAGGGCCATAAAATCCTTGAAACCAATCCTTCAGTTCTCTCAAATGGGA\n+CATCTCGAT\n' 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| diff -r 000000000000 -r 2953303df011 test-data/felCat8_chrM_F.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/felCat8_chrM_F.fq Tue Aug 22 04:16:08 2017 -0400 |
| b |
| b'@@ -0,0 +1,800 @@\n+@chrM_15514_16085_4:1:0_0:0:1_0/1\n+TGGTGATGAACGGATGTTCTACAGGTTGGCCACCGATTCATGTTAGGGTTAGGAGATCCGCTACTAGGAGTGTCAGAATAGACATTGGCTTAGTGGTCGAAACATTATTCCTCGTTGTTTGGAGGTGTGGAGGATTGGAATGATTGCTAGTACTAGGATGGAGAGTACTAGGGCTAGGACTCCCCCTAGTTTGTTAGGGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15542_16042_0:2:0_4:0:1_1/1\n+TCAGTAGACAAAGCCACCCTAACACGATTCTTTGGCTTCCACTTCATTCTTTCATTCATTATCTCAGCCTTAGCAGGAGTACACCTCTTATTCCTTCATGAAACAGGATCTAACAACCCCTCAGGAATTACATCCGATTCAGACAAAATCCCATTCCACCCATACTATACAATCAAAGAAATCCTAGGTCTTCTAGTACT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11314_11771_5:1:0_3:0:0_2/1\n+TAGTTTTAGTACTACGGCGGCAAGTACTATTGAACCAGCGATGGGAGCTTCAACATGTGCTTTTGGCAATCATAGGTGGAGTCCAAATAGAGGTATTTTTACTATAAATGCTATCATGCATGCTAGTCAGAGGAAAATATTGGACCAGGTGGTTGAGATGGGCTTGGCTCAGTATTGGATGATCAGGAAATTTAAAGTTG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12782_13288_5:1:0_6:0:0_3/1\n+CTAATCGAAGCCCTAGTAATGGAATATTTAGGTTCTCGTGTTGGGTGATAAAGATTTGTTGGAAGTCCCATGCGTTTGAGTTGGTTAGAAATCCTGCTATGGCTATGATTAAGCCTACGTCTCCAATTCGGTTGTAGAGGATTGCTTGTAGGGCGGCAGTGTTTGCATCTGCTCGGCCATATCATCATCCGATAAGTCGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10423_10968_7:0:0_3:1:0_4/1\n+ACGCCAACTAAACATCTATGCAGCAAAAGCAATCCCGTATGAGTGCGGATTTGATCCTATAGGGTCCGCCCGCCTACCCTTGTCCATAAAATTCTTCCTGGTAGCCATTACATTCTTGCTATTTGATCTAGAAATTGCACTACTACTCCCCCTTCCCTGAGCGTCACAAACAGACAAACTACCAACCATAGTCACTATAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1035_1495_4:3:0_1:1:0_5/1\n+AAAGGAGCTGGTATCAAGCACACAGCCACAGTAGCTCATAACACCTTGTTCAGCCACACCCCGACGGGATACAGCAGTGATAACAAATAAGCCATGAATGAAAGTTCGACTAAGCTATATAAAACAAGGGTTGGTAAATTTCGTGCCCGCCACCGCGGCCATACGATTAACCCAAACTAATAGACCCACGGCGTAAAGCG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_991_1476_6:4:0_5:1:0_6/1\n+GTCCGCATCCCGGTGAACATGCCCTCTAAGACACCCAGTGACCTAAAGGAGCTGGTATCAAGCACACAGCCACAGTAGCTCATAACACCTTGTTCAGCCACACCCCGACGGGATACAGCAGTGATAAAAATTAATCCATGAATGAAAGTTCTACTAAGCTATATTAAACAAGGGATGGTAAATTTCGTTCCAGCCACCGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4260_4730_5:2:0_4:0:1_7/1\n+GCAGCAGGCCCCTTCGCCCTATTCTTCCTAGCAGAAAATGCCAACAACATCATAATAAATATCCTCACAACAATCCTATTCTTCGGAGCATTCCACAGGCCTTATATACCAGAGCTATATACCATTAACTTAACAGTAAAGGCCCTACTCCTAACAACTACTTTGTTATGGATCCGAGCATCCTACCCACGATTCCGATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12869_13312_1:1:0_2:0:0_8/1\n+GCTTTAAAATAGATTATTTCTCAACCATCTTTATCCCTGTAGCGCTTTTCGTCACATGGTCCATCATAGCATTCTCAATGTGGTACATGCACTCAGACCCATACATCAACCGATTCTTTAAATATATCCTCATATTCCTAATCACTATGATAATTCTAGTTACCGCTAACAATCTATTTCAACTATTCATCGGCTGAGAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_163'..b'22222222222222222222222\n+@chrM_14202_14601_2:0:0_4:3:0_bf/1\n+CAACCTCTTAGGGTACTTTCCAATTGTAATACACCGCCTCCCATCAAAAATGAGCCTAACTATGAGCCAAAAGTCCGCATCGATACTATTAGACATAATTTGACTAGAAAATGTATTACCCAAATCCATCTCCTTATTCCCAATAAAAATGTCAACTACTGTATCTAATCAGAAAGGACTAGATAAACTCTACTTTTTAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2463_2979_3:2:0_4:0:5_c0/1\n+AATTTCACGGATTGGAAGTAAGAGACAGTAAAGCCCTCGTGTGGCCGTTCATACAAGTCCCTTAGGGCACAAATTTATGCTAGCTTTGCACGGTCAGGATACCGCGGCCGTTTAACTAGCGTCACCGGGCAGGCAGTGCCTCTCATACTGGAAATTCTAGAGGTGATGTTTTTGGTAAACAGGCGGGGCTTGTTTTTGCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12878_13401_5:1:0_5:0:0_c1/1\n+TAGATTATTTCTCAACCATCTTTATCCCTGTAGCGCTTTTCGTCACATGGTCCATCATAGAATTCTCAATGTGGTACATGCACTCAGACCCATACATCACCCGATTCTTTACATATATCGTCATATTCCTAATCACTATGATAATTCTAGTTACCGCTACCAATGTATTTCAACTATTCATCGGCTGAGAGGGAGTAGGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10289_10727_2:1:0_1:0:0_c2/1\n+TTAGTATTAATAAGTACAGTTGACTTCCAATCAACCAGTTTCGGTATAACCCGAAAAGGAATAATAAATGTAATACTTGCCTTACTTACCAATACACTCCTGTCCACACTACGTGTACTCATCGCATTCAGATTACCCCAACTAAACATCTATGCAGAAAAAGCAAGCCCCTATGAGTGCGGATTTGATCCTATAGGTTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_111_723_3:2:0_4:1:0_c3/1\n+CCTGACTCAGTCAAATATGTGGTTGCTGGGCTTATTCTCTATGCGGGTTCTCCACACGCACAGACAGTCAGGGTGCTATTCAGTCAATGGTCACAGGACATATACTTAAATTCCTATTGTTCCACAGGACACGGGATGCGCGCACCCAGGTTTGCGTGCACACGTGTACACGTACACACGTAGACACGTACACACGTACA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4757_5258_2:1:0_1:1:0_c4/1\n+AGATGGATATTGTTAGGATTAGGTTAGGGTTAATGGTGGATGAGATTTGGTAGAGGATTGATAGTGGTGCAATTTTTTGTCATGTTAGTAGAATTAAGCCTGATGATATAGAAATTCCTTGTGTAACTTCGGGTACTCAGAAGTGGAATGGGGCTAGTCCAAGTTTTATTGCTAGAGCGGTTGTGATTATGATTGATGCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2201_2719_6:1:0_8:2:0_c5/1\n+CCGAAACCAGACGAGCTACCCATGGACAATCTATTCCAGGATGAACTCGTCTATGTTGCAAAATCTTGAGAAGATTTGTGGGTAGAGGTGAAAAGCCTAAGGAGCCTGGTGATAGCTGGTTGCCCAGAACAGAATCTTAGTTCAACTTTAAACTTACCTCAACAACCTAAAATTCGAATGTAAGTTTAAAATATAGTCTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_13287_13773_8:1:1_5:1:0_c6/1\n+AGCAGCCACAGGTAAATCCGCCCAATTCGGCCAACATCCGTGACTGCCATCAGCCATAGAAGGCCCAACTCCTGTCTCCGGCCTACTCCACTCAAGTACAATAGTCGTAGCATGGGTCTTCTTACTTATCCGGTTTTACCCGCCACATAGAACAAAACAAAACTATACAACCTCTCACCCTATGATTCGGAGCTATTACA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5317_5806_3:0:0_4:0:1_c7/1\n+TATTGGTGCGAGTGGAAGTAGTATGGTTGATATTACCAACTAGAGGGGGTAGGAAGGTTATTATTTTTGTGCATTGAAATCGTCATTTTATTTTTATACTGTTGTTTGAGGGGAACATGGTTAGTGCGGTGGTGAATGTTAGTCGTATGTAGAAGTATAGGTTGAGTAGTGCTGTTATGGGTAGTAATGTTGGCATTATG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/felCat8_chrM_R.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/felCat8_chrM_R.fq Tue Aug 22 04:16:08 2017 -0400 |
| b |
| b'@@ -0,0 +1,800 @@\n+@chrM_15514_16085_4:1:0_0:0:1_0/2\n+ACTAGTAGAATGAATCTGAGGGGGGTTCTCAGTAGACAAATCCACCCTAACACGATTCATTGGCTTCCACTTCATTCTTTCATTCATTATCTCAGCCTTAGCAGGAGTACACCTGTTATTCCTTCATGAAACAGGATCTAACAACCCCTCAGGAATTCCATCCGATTCAGACAAAATCCCATTCCACCCATACTATACAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_15542_16042_0:2:0_4:0:1_1/2\n+TAGGGTTAGGAGATCCGCTACTAGTAGTTTCAGAATAGACATTGGCTTAGTGGTCGAAACATTATTCCTCGTTGTTTGGAGGTGTGGAGGATTGGAATGATTGCTAGTACTAGGATGGAGAGTACTAGGGCTCGGACTCCCCCAAGTTTGTTAGGGATGGATCGGAGAATTGCGTATGCGAATAGGAAGTATCATTCAGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11314_11771_5:1:0_3:0:0_2/2\n+AAGAAACTCCTAGTCGAAAAAAAGTATACATCAGAATACTCACTCTCCTGCAGCTTCATTTGCTTATAACATTTACCGCTACAGAACTAATTATATTTTACATTTTATTTGAAGCCACATTAATCCCCACCTTAATCATCATTACCCGATGGGGTGAGCAGACAGAGCGATTAAACGGCGGCCTATACTTTCTATTTTAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12782_13288_5:1:0_6:0:0_3/2\n+CAACTATAATATTTATCTCCTCAGGAGAACAAGCAATTATCTCAAACTGACACTGACTATCAATCCAAACTCTCAAGCTATCACTAAGCTTTAAAATAGATTAATTCTCAACCATCATTATCCGTGTAGCGCTTTTCGTCACATGGTCCATCATAGAATTCTCAATGTGGTACATGCACTCCGACCCATACATCAACCGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10423_10968_7:0:0_3:1:0_4/2\n+TGCAAATACTAATAGGATAATGGGGGTTGTGCTGGCTAGTGTGAGATGGTTGTTTAGGATGGCTACGGCTATTCTAATGAATAGGGATAATATCATGCCTTCTAGACATAGGAGGGAAGACATTAAGTGGGCTCGATATATTAGTAGTCCTATGAGCGACATGATGAAAGCCAGGAAAATATTAATGTATACTATGGACA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1035_1495_4:3:0_1:1:0_5/2\n+GGCTCCTCTAGAGGGATGTAAAGCACCGCCAAGTCCTTAGAGTTTTAAGCTATTGCTAGTAGTTCTCTGGCGGATAGTTTTGTTTAGGGTAACTATCTAAGTTTAGGCCTAAGCATAGTAGGGTATCTAATCCCAGTTTGGGTCTTAGCTGTCGTGTAGTCGGAGGTGTTAAAGTTACTTTCGTGCTGTATTTTTATGTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_991_1476_6:4:0_5:1:0_6/2\n+AAAGCACCGCCAAGTCCTTTGAGTTTTAAGCTATTGCAAGTAGTTCTCTGGCGGATAGTTTTGTTTAGGGTAACTATCTAAGTTTAGGCCTAAGCATAGTAGGGTATCTAATCCCAGTTTGGGTCTTAGCTGTGGTGTAGTCGGAGGTGTTAAAGTTACTTACGTGCAGTATTTTTATGTTAACTGTAGCTTTGTACGGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4260_4730_5:2:0_4:0:1_7/2\n+TTATTTAGCTGACCTTACTTTAGAAAATGGTGTAATAATGGTAGCACGAAGATTTTTGGATTCTTAGGATTAGGTTGGATTCCTGTTATTCTAGAAATAAGAGGGTTTAAACCTCTATGTTTTACTCTATCAAAGTAACACTTTTGTCAGACATATTTCTTATGTTTGAGGTGGTATGCTTGCTGTGATATAGGTAGGGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12869_13312_1:1:0_2:0:0_8/2\n+ATTGGGCGGATTTACCTGTGGCTGCTAATAGAAGCCCTAGTAATGGAATATTTAGGTTCTCGTGTTGGGTGATAAAGATTTGTTGGAAGTCCCATGCGTTTGAGTTGGTGAGAAATCATTCTATGGCTATGATGAAGCCTACGTCTCCAATGCGGTTGTAGAGGATTGCTTGTAGGGCTGCAGTGTTTGCATCTGCTCGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_163'..b'22222222222222222222222\n+@chrM_14202_14601_2:0:0_4:3:0_bf/2\n+CAGGTGATTGGGTGGTTTATGATACAGGAGACTCAGGGTTCTTTAGGTAGGAGGCCATGGGAATTGCGGCGCTATATAGTTATGGAACTTGATTATTGGTTGTCACCGGGTGATCTTTGCTTATTGGTATGTTGGTGATTATGGAAGTTACTCGTGGGAATTAAGTAAGATTAGGCTGAGGGCTAGGGTGATTATGAAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2463_2979_3:2:0_4:0:5_c0/2\n+CCATAGTTGGCCTAACAGCAGCCATCAATTAAGAAAGCTTTCAAGCTCAACAATCAAAGCATCTTAATGTCAAAAATAATGCAACCAACTCCTAACCTAAAACTGGGCTAATCTATTTAATAATAGAAGCAATAATGCTAATATGAGTAACAAGAAAGATTTCTCCCTGCATAAGCTAAAATCAGAACGGATAACCACTG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12878_13401_5:1:0_5:0:0_c1/2\n+CCCTGCTACGACTATTGTACTTGAGTGGAGTAGGGCGGAGACAGGAGTTGGGCCTTCTATGGCTGATGTCAGTCACGGATGTAGGCCGAATTGGGCGGATTTACCTTTGGCTGCTAATAGCAGCCCTAGTAATGGAATATTTAGGTACTCGTGTTGGTTGATAAAGATTTGTTGGAAGTCCCATGCGTTTGAGTTGGTGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10289_10727_2:1:0_1:0:0_c2/2\n+TCATTTGTTTTGGTTTAAACTAATTATCATATTCAGTTCATTCTAGTCCTTTTTGGGTTCATTCGTAGGCTAGGCTTGCGGCTAGTAATGAGATTAGTAGAAGGGCTATAGTGAGTAAGGTTGGTAGTTTGTCTGTTTGTGAGGCTCAGGGAAGGGGGAGTAGTAGTGCAATTTCTAGATCAAATAGCAAGAATGTAATG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_111_723_3:2:0_4:1:0_c3/2\n+TAAGCGTTATCTTAGGCCTAATATTTAGGTACGGTCTAGTCTTGTTTGTGGGGTTTGGCAAGACATAAATAGGCACGTATTATTATAAATAAGGTTAACGGGGGGTAAGGGGGGTTTGATTAAGCTAGTTATTTACTTAAAATAAAGCGTTCGGGTGTATAAGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4757_5258_2:1:0_1:1:0_c4/2\n+TTGGTTTATACCCGTCCCATACTAAACAACCCCCCTATCTTTATTATTATTATATTAACCGTTATCTCAGGAACTATAATTGTAGTGACAACCTCCCACTGACTTCTAGTCTGAATTGGCTTTGAAAAGAACCTATTAGCCATCATCCCCATCCTCATGAAAAAATACAACCCACGAGCCATAGAAGCAGCCACAAAATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2201_2719_6:1:0_8:2:0_c5/2\n+AGAATTAATTTGATATTTTGTTTATGGTAAGGTTATATAAATGTTGTTGTTAACTATCAGTGGTTATCCGTTCTGATATTAGCTTATGCAGGGAGAAAACTTTCTTGTTACTCATATTAGCATTATTGCTTCTATTATTAAATAGATTAGCCCCGTTTTAGGTTAGGAGTTGGTTGCATTATTTTTGACCTTAAGATGCA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_13287_13773_8:1:1_5:1:0_c6/2\n+GAGTGCGAGGCATCCAATGATTAGGGAGGTAGTGGTGAAGGGCATTGGTTTGTATAATCCGCCTATTTTACGAATGTCTTGTTCGTCGTTCAGACTGTGGAAAATTGATCCTGAACATATGCATAGCATGTCTTTGAAGAATGCGTGTGTGCAAATGTGTAGAAATGCGAGGTACGGTTGGTTAATCCCAATGGTTACAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5317_5806_3:0:0_4:0:1_c7/2\n+AGCATACTCCTCAATCGCCCATATAGGCTGAATTACAGCTATCATAATGTACAGCCCCACAATAATAATCTTAAACCTAACTATCTATATCATTATAACACTAACCACCTTCATACTATTTATACACAACTCCACCACAACAACAGCATCCCTATCACAAAGATGAAATAAAACCCCTCTCATCACCTCACTCATCCTAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out1.cells --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out1.cells Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +cell1 +cell1 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out1.ec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out1.ec Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 0 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out1.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +0 0 100 +0 1 100 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out2.ec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out2.ec Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 0 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out2.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 100 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out3.ec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out3.ec Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 0 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out3.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 100 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out4.ec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out4.ec Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 0 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out4.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out4.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 200 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out5.bam |
| b |
| Binary file test-data/kallisto_pseudo_out5.bam has changed |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out5.ec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out5.ec Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 0 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out5.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out5.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 19 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out6.bam |
| b |
| Binary file test-data/kallisto_pseudo_out6.bam has changed |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out6.cells --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out6.cells Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +cell1 +cell1 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out6.ec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out6.ec Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +0 0 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_pseudo_out6.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_pseudo_out6.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +0 0 18 +0 1 18 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_quant_out1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_quant_out1.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +target_id length eff_length est_counts tpm +chrM 16299 15800.9 100 1e+06 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_quant_out2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_quant_out2.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +target_id length eff_length est_counts tpm +chrM 16299 15800.9 100 1e+06 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_quant_out3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_quant_out3.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +target_id length eff_length est_counts tpm +chrM 16299 16100 100 1e+06 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_quant_out4.bam |
| b |
| Binary file test-data/kallisto_quant_out4.bam has changed |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_quant_out4.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_quant_out4.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +target_id length eff_length est_counts tpm +chrM 17009 16510 200 1e+06 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_quant_out5.bam |
| b |
| Binary file test-data/kallisto_quant_out5.bam has changed |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/kallisto_quant_out5.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_quant_out5.tab Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +target_id length eff_length est_counts tpm +chrX 745742 745258 19 1e+06 |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/mm10_chrM-1.f.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm10_chrM-1.f.fq Tue Aug 22 04:16:08 2017 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+@chrM_5240_5736_3:1:2_4:0:0_0/1\n+GAATATCACCTTAAGACCTCTGGTAAAAAGAGGATTTAAACCTCTGTGTTTAGATTTACAGTCTAATGCTTCCTCAGCCATTTTACCTATGATCATTAATCGTTGATTATTCTCAACCAATCAAAAAGATATCGGAACCCTCTATCTACTATTCAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTAATTTAATTCGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_8038_8553_4:0:0_5:0:1_1/1\n+AATTAATGCTACTGCAAATACTAGAATTGTGAGTAGAAGTAAAATAATAAATGTAATGGTAGCTGTTGGTGGGCTAATATTATTAATACTAGAGTAGCTCCTCCGATTAGGTGTATTAATAAGTGTCCTGCATTACTGTTAGCTGTACGCCGGACTGCTAATGCCATTGGTTGAATAAATAGTCTAATTGTTTCAATAAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2612_3121_4:0:0_3:0:0_2/1\n+ATTGAGGCTCATCCTGATCATAGAATGGAGTAAACTGATAGGCTAGATGTTGCTAAAATAAATAAAATCCCTAGGTTTAAATTAATTAATGGGTGTGGTATTGGTAGGGGAACTGATAGACTTAATGCTAGTGTGAGTGATAGGGAAGGTGCAATAATAAATAAGGATATAGAGGTTGTTAAAGGGCGTATTGGTTCTTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1564_1964_7:0:2_6:0:0_3/1\n+TTTAATAGTGAATAATTAACAAAACAGCTTTTAACCATTTTAGGCCTAAAAGCAGCCACCAATAAAGAAAGCTTTCAAGCACAACATAAAATTTCAATTAATTCCATTTTACACCAACTTCCTAAACTTAACATTGGGTAAATCTATAACTTTATAGATGCAACACTGTTAGTATGAGTAACAATAATTGCAATTCTCCA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5567_6002_1:0:0_1:0:0_4/1\n+CTGACTTGTCCCACTAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAAGCAGGAGCAGGAACAGGATGAACAGTCTACCCACCTCTAGCCGGAAATCTAGCCCATGCAGGAGCATCAGTAGACGTAACAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11896_12384_1:0:0_4:0:0_5/1\n+TAATATTTTTCCACAATAATATATAATATATAATTACAACCTGGCACTGAGTCACCATAAATTCAATAGAACTTAAAATAAGCTTCAAAACTGACTTTTTCTCTATCCTGTTTACATCTGTAGCCCTTTTTGTCACATGATCAATTATACAATTCTCTTCATGATATATACACTCAGACCCAAACATCAATCGATTCATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4051_4557_7:0:0_4:0:0_6/1\n+ATAGGGGCTGTAAGCATAAAATAGCTTATGAGGTTGAGTAGAGTGAGGGATGGGTTGTAAGGAAGAATAGCTAATATTCATCCTATGTGGGCAATTGATGAATAGGCTATAATTTTTCGTATTTGTGTTTGGTTAAGTCCTCCTCATGCCCCTATGAAAATAGAAGTAATTGCTAGTATTAAAATGATAGTAGAGTTGAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12048_12447_5:0:0_6:0:0_7/1\n+CTGATGGTAGTCATGGGTGGAGTCCAAATTGTGCTGATTTTCCTGTAGCTGCGATTAATAGGCCTATAAGTGGAATTCGATTGTCGTTGTTGTTGGAGAATATAATCTGTTGAAGTTCTCATGAGTTTATTTTTATGGAAAATCAAACTATAGCTAACATGAATCCGAAGTCTCCGATGCGGTTATAGAGGATTGCTTGT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10715_11230_1:0:0_5:1:0_8/1\n+ACACACCTTAGACGCTTCATGATCTAACAACTTACTATGGTTTGCATGCATAATAGCATTTCTTATTAAAATACCATTATATGGAGTTCACCTATGACTACCAAAAGCCCATGTTGAAGCTCCAATTGCTGGGTCAATAATTCTAGCAGCTATTCTTCTAAAATTAGGTAGTTACGGAATAATTCGCATCTCCATTATTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6545_708'..b'22222222222222222222222\n+@chrM_2076_2571_6:0:0_1:0:0_5b/1\n+TTTCGTACTGGGAGAAATCGTAAATAGATAGAAACCGACCTGGATTGCTCCGGTCTGAACTCAGATCACGTAGGACTTTAATCGTAGAACAAACGAACCATTAATAGCTTCTACACCATTGGGATGTCCTGATCCAACATCGAGGTCGTAAACCCTAATTGTCGATATGAACTCTTAAATAGGATTGCGCTGTTATCCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12874_13353_6:0:0_4:0:0_5c/1\n+GTGTAATGCGGTGAATAATAGATGGGAAAAACCCCAGTAAAGTTGAGAAGGATGAATATGGATTTGCTTTATTTATTGATAGATTTATTGTTAGGTTGTTTAGTTCTAGTGCGATTAGGAATCCTAATACTGCAATAATTAGGGCTGTGGTTTTTAAAAATCATGGTATTGTGAGGACTGGAATGCTGGTTGGTTGAATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5469_5973_2:0:0_5:0:0_5d/1\n+TTAGGTTGCGGTCTGTTAGTAGTATAGTAAAGCCTGCGGGTAGCACTGGTAGTGATAATAGGAGCAGTACGGCTGTAATACGTACGGATGAGACAAATAGTGGAGTTTGATACTGTGTTATGGCTGGGGGTTTCATGTTGATAATAGTGGTAATAAAATTAATTGCACCTAAAATAGATGACACTCCAGCTAAAAGAAGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_8345_8858_5:0:0_2:0:0_5e/1\n+AATTATACCATATCGTAGTCCTTTTTGTACAATAGGAGTGTGGTGGCCTTGGTAGGTTCCTTCACGAATTACGTCTCGTCATCATTGCTATATTGTGAGGATATTGGTGAGTAGGCCAAGGGTTAATAGTGTAATTGAATTATAGTGAAATCATATTCCTAGACCTGATGTTAGAAGGAGGGCTGAAAAGGCTCCAGTTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10736_11195_1:0:0_6:1:0_5f/1\n+CTCTAACAACTTACTATGGTTGGCATGCATAATAGCATTTCTTATTAAAATACCATTATATGGAGTTCACCTATGACTACCAAAAGCCCATGTTGAAGCTCCAATTGCTGGGTCAATAATTCTAGCAGCTATTCTTCTAAAATTAGGTAGTTACGGAATAATTCGCATCTCCATTATTCTAGACCCACTAACAAAATATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_8411_8855_3:0:0_3:0:0_60/1\n+TATACCATATCGTAGTCCTTTTTGTACAATAGGAGTGTGGTGGCCTTGGTAGTTTCCTTCACTAATTACGTCTCGTCATCATTGATATATTGTGAGGATATTGGTGAGTAGGCCAAGGGTTAATAGTGTAATTGAATTATAGTGAAATCATATTACTAGACCTGATGTTAGAAGGAGGGCTGAAAAGGCTCCAGTTCATG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12619_13196_3:0:0_2:0:0_61/1\n+AAATCATGGTATTGTGAGGACTGGAATGCTGGTTGGTGGAATATTATATGAGATGACAAATCCTGCAAAGATGCTTCCGAATGCTAGGCGTTTGATTGGGTTTATGAGGTCTGGGTCATTTTCGTTAATGGAGATTAGGGGGGGAAAACGCGGTATTGTTATTGTTACGAAGTAAATGATTCGAATGCTGTACATAGCTG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4804_5319_5:1:0_4:1:0_62/1\n+TGGCTGAGTAAGCATTAGACTGTAAATCTAAACACAGAGGTTTAAATCCTCTTTTTACCAGAGGTCTTAAGGTGATATTGGTGTCGAATTGCAAATTGGAAGGTGTAGAGAAATCTCTACTAAGACTTCTACCGCCATTTTTATTTTTCGGCGTTAGAAGTAGATTGAAGCCAGTAATAGGGTATTTAGCTGTTAACTAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2861_3359_2:0:0_3:0:0_63/1\n+TCCTTCTGTCAGGTCGAAGGGGGCCCGGTTTGTTTCTGCTAGGGTTGAGATAAATCATATTATGGCTATGGGTCAGGCTGGGAGAAGTAATCATATGTGTTCTAGGGTTGTAATAAGTGTTTGTAGAGAGTAGGATCCATTTATTAAAAGAACTGATAAAAGGATAATAGCTATGGTTACTTCATATGAAATTGTTTGGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/mm10_chrM-1.r.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm10_chrM-1.r.fq Tue Aug 22 04:16:08 2017 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+@chrM_5240_5736_3:1:2_4:0:0_0/2\n+CTAGATTTCCGGCTAGAGGTGGGTAGACTGTTCATCCTGTTCCTGCTCCTGCTTCTACTATTGATGATGCTAGGCGAAGGAGAAATGATGGTGGTAGGAGTCAAAAACTTATATTATTTATTCGTGGGAATGCTATATCTGGGGCTCCGAATATTAGTTGGACACGTCAGTTTCCAAAGCCTCCAATTATTATTGGTATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_8038_8553_4:0:0_5:0:1_1/2\n+ATCAACAACCGTCTCCATTCTATCCAACACTGACTAGTTAAACTTATTATCAAACAAATAATGCTAATCCACACACCAAAAGGACGAACATGAACCCTAATAATTGTTTCCCTAATCATATTTATTGGATCAACAAATCTCCTAGGCCTTTTACCACATACATTTACACCAACTACGCAACTAACCATAAATCTAAGTAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2612_3121_4:0:0_3:0:0_2/2\n+AACTAAATTTATGAATAAAATCTAAATAAAATATATACGTACACCCTCTAACCTAGAGAAGGTTATAAGGGTGGGAGAGCCAGGAAATTGCGTAAGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGTTCTTAATTAATATCCTAACACTCCTCGTCCCCATTCTAATCGCCATAGCCTTCCTAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1564_1964_7:0:2_6:0:0_3/2\n+TTGTAATGCTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTTCTTGTATGCCGAGTTCCTTTTATCTTTTTGGATCTTTCCTTTAGGCATTCCGGTGTTGGGTTAACAGAGAAGTTAAAGGTGGATTATAAATAGTGTGATTATTGCCTATAGTCTGATTACCTAACAATGTTTATCCGAGTTGTTATACGCGTATGCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5567_6002_1:0:0_1:0:0_4/2\n+TCCTCCAGCGGGATCAAAGAAAGTTGTGTTTAGGTTGCGGTCTGTTAGTAGTATAGTAATGCCTGCGGCTAGCACTGGTAGTGATAATAGGAGCAGTACGGCTGTAATAAGTACGGATCAGACAAATAGTGGAGTTTGATACTGTGTTATGGCTGGGGGTTTCATGTTGATAATAGTGGAAATAAAATTAATTGCACCTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11896_12384_1:0:0_4:0:0_5/2\n+CTCTAAGTGGAATTAGATTGTCGTTGTTGTTGTAGAATATACTCTGTTGAAGTTCTCATGAGTTTATGTTTAGGGAAAATCAAACTATAGCTAAAATGAATCCGATGTCTCCGATGCGGATATAGAGGATTGCTTGTAGGGCTGCAGTATTTGCGTCTGTTCGTCCGTACCATCATCCAATTAGTAGGAAAGATATAATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4051_4557_7:0:0_4:0:0_6/2\n+CCAAAAAAACCCACGATCAACTGAAGCAGCAACAAAATACTTCTTCACACAAGCAACAGCCTCAATACTTATCCTCCTGGCCATCGTACTCAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACGGTCTTAACCTTAAGATAACATTAATAGCCCTATCCCTAAAACTAGGCCTCGCCCCATTCCCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12048_12447_5:0:0_6:0:0_7/2\n+TTGTCTTCATGATATATACACTCAGACGCAAACATCAATCGATTCATTAAATATCTTACACTATTCCTGATTACCATGCTTATCCTCACCTCAGCCAACAACATAATTCAACTTTTCATTGGCTGAGAAGGGGTGTGAATTATATCTTTCCTACTAATTTGATGATGGTACGGACGAACAGACGCAAATACTGCAGCCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10715_11230_1:0:0_5:1:0_8/2\n+ATAAGTGGGAAGACCATTTGAAGTCCTCGGGCCATGATTATAGTACGGCTGTGGATGCGTTCGTAGTAGGAGTTTGCTAGGCAGAATAGGAGTGATGATGTGAGGCCATGTGCGATTATAAGTATAGTTGCTCCTATGAAGCTTCATGGAGTTTGGATAATGATTGATGCAATAACCAGTGCTATGTGGCTAACTGAGGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6545_708'..b'22222222222222222222222\n+@chrM_2076_2571_6:0:0_1:0:0_5b/2\n+AAACGAGGGTCCAACTGTCTCTTATCTTTAATCAGTGAAATTGACCTTTCAGTGAAGAGTCTGAAATATAATAATAAGACGAGAAGACCCTATGGAGCTTAAATTATATAACTTATCTATTTAATTTATTAAACCTAATGGCCCAAAAACTATAGTAACAGATTGAAATTTCGGTTGGTGTGACCTCGGAGAATCAAAAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12874_13353_6:0:0_4:0:0_5c/2\n+TCGCCCTCCCAGGAATACCAATCCTAACAGGGTTCTACTCAAAAGACCTAATTATTGAAGCAATTAATACCTGCAACACCAACGCCTGAGCCCTACTAATTACACTAATCGCCACATCTATAACATCTATGTACAGCATACTAATCATTTACTACGTAACAATAACAAAACCGCGTTTTCCCCCCCTAATCTCCATTAAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5469_5973_2:0:0_5:0:0_5d/2\n+TTAGGCGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTTGTTATAATTTTCTTCATAGTAATACCAATAATAATTGGAGGCTTTGGAAACTGACTTGTCCCACTAATAATCGGAGCCCCAGATATAGCATTCCCACGACTAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_8345_8858_5:0:0_2:0:0_5e/2\n+TACTTATTATTATTGAAACAATTAGCCTCTTTATTCAACCACTGGCATTATCAGTCCGGCTTACAGCTAACATTACTGCAGGACACTTATTAATCCACCTAATCGGAGGAGCTCCTCTAGTATTAATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_10736_11195_1:0:0_6:1:0_5f/2\n+GATTATAGTACGGCTGTGGATCCGTTCGTAGTTGGAGTTTGCTAGGCAGAATAGGAGTGATGCTGTGAGGCCATGTGCGATTATAAGTATTGTTGCTCCTCAGAAGCTTCATGGAGTTTGGATTATGATTGATGCAATAACAAGTGCTATGTGGCTAAGTGAGGAGTATGCGATTAGTGATATTAAATCTGTTTGGCGTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_8411_8855_3:0:0_3:0:0_60/2\n+CTAACATTACTGCAGGACACTTATTACTACACCTAATCGGAGGAGCTACTCTAGTATTAATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCAATAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATGTACATGATAATACATAATGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_12619_13196_3:0:0_2:0:0_61/2\n+TCACCCAAAACGACATCAAAAAAATCATTGCCTTCTCTACATCAAGCCAACTAGGCCTGATAATAGTGACGCTAGGAATAAACCAACCACCCCTAGCATTCCTACACATCTGTACCCACGCATTCTTCAAAGCTATACTCTTTATATGCTCTGGCTCAATCATTCATAGCCTGGCAGACGAAGAAGAGATCCGAAAAATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4804_5319_5:1:0_4:1:0_62/2\n+TTATTCCACTTCACTAACAATCTTCCCAACCAACAATAACTCAAAAATAATAACTCACCAAACAAAAACTAACCCCAACCTAATATTTTCCACCCTAGCTATCATAAGCACAATAACCCTACGGCTAGCCCCCCAACTAATTACCTAGAAGTTTAGGATATACTAGTCCGCGAGCCTTCAAAGCCGTAAGAAAACACACA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2861_3359_2:0:0_3:0:0_63/2\n+TAACATTGTTGGTCCATACGGCATTTTACAACCATTTGCAGACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTTTAACAACCTCTATATCCTTATTTATTATTGCACCTACCCTATCCCTCACACTAGCATTAAGTCTATGAGTTCCCCTACCAATACCACACGCATTAATTAATTTAAACCTAGGGATTTTAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/mm10_chrM.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm10_chrM.fa Tue Aug 22 04:16:08 2017 -0400 |
| b |
| b'@@ -0,0 +1,327 @@\n+>chrM\n+GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGAT\n+AATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTA\n+GAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTA\n+AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCT\n+TAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATA\n+TTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAA\n+ATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTT\n+CGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAAC\n+TTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAAT\n+TCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATA\n+CCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTAT\n+TTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTA\n+CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCT\n+ACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAA\n+CCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAG\n+GTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATA\n+AAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTA\n+GTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGC\n+ACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAA\n+TTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCAT\n+ACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCAT\n+CTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTAATC\n+CTAGCCCTAGCCCTACACAAATATAATTATACTATTATATAAATCAAAAC\n+ATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCT\n+ATAGAACTAGTACCGCAAGGGAAAGATGAAAGACTAATTAAAAGTAAGAA\n+CAAGCAAAGATTAAACCTTGTACCTTTTGCATAATGAACTAACTAGAAAA\n+CTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAACGAGCTAC\n+CTAAAAACAATTTTATGAATCAACTCGTCTATGTGGCAAAATAGTGAGAA\n+GATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGATAGCTGGTTA\n+CCCAAAAAATGAATTTAAGTTCAATTTTAAACTTGCTAAAAAAACAACAA\n+AATCAAAAAGTAAGTTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGG\n+AACGGAAAAAACCTTTAATAGTGAATAATTAACAAAACAGCTTTTAACCA\n+TTGTAGGCCTAAAAGCAGCCACCAATAAAGAAAGCGTTCAAGCTCAACAT\n+AAAATTTCAATTAATTCCATAATTTACACCAACTTCCTAAACTTAAAATT\n+GGGTTAATCTATAACTTTATAGATGCAACACTGTTAGTATGAGTAACAAG\n+AATTCCAATTCTCCAGGCATACGCGTATAACAACTCGGATAACCATTGTT\n+AGTTAATCAGACTATAGGCAATAATCACACTATAAATAATCCACCTATAA\n+CTTCTCTGTTAACCCAACACCGGAATGCCTAAAGGAAAGATCCAAAAAGA\n+TAAAAGGAACTCGGCAAACAAGAACCCCGCCTGTTTACCAAAAACATCAC\n+CTCTAGCATTACAAGTATTAGAGGCACTGCCTGCCCAGTGACTAAAGTTT\n+aacggccgcggtatcctgaccgtgcaaaggtagcataatcacttgttcct\n+taattagggactagcatgaacggctaaacgagggtccaactgtctcttat\n+ctttaatcagtgaaattgacctttcagtgaagaggctgaaatataataat\n+aagacgagaagaccctatggagcttaaATTATATAACTTATCTATTTAAT\n+TTATTAAACCTAATGGCCCAAAAACTATAGTATAAGTTTGAAATTTCGGT\n+TGGGGTGACCTCGGAGAATAAAAAATCCTCCGAATGATTATAACCTAGAC\n+TTACAAGTCAAAGTAAAATCAACATATCTTATTGACCCAGATATATTTTG\n+ATCAACGGACCAAGTTACCCTAGGGATAACAGCGCAATCCTATTTAAGAG\n+TTCATATCGACAATTAGGGTTTACGACCTCGATGTTGGATCAGGACATCC\n+CAATGGTGTAGAAGCTATTAATGGTTCGTTTGTTCAACGATTAAAGTCCT\n+ACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTTTCTATCTATTT\n+ACGATTTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCCACCTTACAAA\n+TAAGCGCTCTCAACTTAATTTATGAATAAAATCTAAATAAAATATATACG\n+TACACCCTCTAACCTAGAGAAGGTTAttagggtggcagagccaggaaatt\n+gcgtaagacttaaaaccttgttcccagaggttcaaatcctctccctaata\n+GTGTTCTTTATTAATATCCTAACACTCCTCGTCCCCATTCTAATCGCCAT\n+AGCCTTCCTAACATTAGTAGAACGCAAAATCTTAGGGTACATACAACTAC\n+GAAAAGGCCCTAACATTGTTGGTCCATACGGCATTTTACAACCATTTGCA\n+GACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTTTAACAACCTC\n+TATATCCTTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAA\n+GTCTATGAGTTCCCCTACCAATACCACACCCATTAATTAATTTAAACCTA\n+GGGATTTTATTTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCT\n+ATGATCAGGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTAC\n+GAGCCGTAGCCCAAACAATTTCATATGAAGTAACCATAGCTATTATCCTT\n+TTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAACACTTATTAC\n+AACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAA\n+TATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTG\n+ACAGAAGGAGAATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGC\n+CGGCCCATTCGCGTTATTCTTTATAGCAGAGTACACTAACATTATTCTAA\n+TAAACGCCCTAACAACTATTATCTTCCTAGGACCCCTATACTATATCAAT\n+TTACCAGAACTCTACTCAACTAACTTCATAATAGAAGCTCTACTACTATC\n+ATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATC\n+AACTTATACATCTTCTATGAAAAAACTTTCTACCCCTAACACTAGCATTA\n+TGTATGTGACATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATA\n+CATATAGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATTATA\n+GAGGTTCAAGCCCTCTTATTTctaggacaataggaattgaacctacactt\n+aagaattcaaaattctccgtg'..b'AAGGCCCTACACCAGTTTCAGCACTACTACACTCAAGTACAATAGTA\n+GTTGCAGGAATTTTCCTACTGGTCCGATTCCACCCCCTCACGACTAATAA\n+TAACTTTATTTTAACAACTATACTTTGCCTCGGAGCCCTAACCACATTAT\n+TTACAGCTATTTGTGCTCTCACCCAAAACGACATCAAAAAAATCATTGCC\n+TTCTCTACATCAAGCCAACTAGGCCTGATAATAGTGACGCTAGGAATAAA\n+CCAACCACACCTAGCATTCCTACACATCTGTACCCACGCATTCTTCAAAG\n+CTATACTCTTTATATGCTCTGGCTCAATCATTCATAGCCTGGCAGACGAA\n+CAAGACATCCGAAAAATAGGAAACATCACAAAAATCATACCATTCACATC\n+ATCATGCCTAGTAATCGGAAGCCTCGCCCTCACAGGAATACCATTCCTAA\n+CAGGGTTCTACTCAAAAGACCTAATTATTGAAGCAATTAATACCTGCAAC\n+ACCAACGCCTGAGCCCTACTAATTACACTAATCGCCACTTCTATAACAGC\n+TATGTACAGCATACGAATCATTTACTTCGTAACAATAACAAAACCGCGTT\n+TTCCCCCCCTAATCTCCATTAACGAAAATGACCCAGACCTCATAAACCCA\n+ATCAAACGCCTAGCATTCGGAAGCATCTTTGCAGGATTTGTCATCTCATA\n+TAATATTCCACCAACCAGCATTCCAGTCCTCACAATACCATGATTTTTAA\n+AAACCACAGCCCTAATTATTTCAGTATTAGGATTCCTAATCGCACTAGAA\n+CTAAACAACCTAACCATAAAACTATCAATAAATAAAGCAAATCCATATTC\n+ATCCTTCTCAACTTTACTGGGGTTTTTCCCATCTATTATTCACCGCATTA\n+CACCCATAAAATCTCTCAACCTAAGCCTAAAAACATCCCTAACTCTCCTA\n+GACTTGATCTGGTTAGAAAAAACCATCCCAAAATCCACCTCAACTCTTCA\n+CACAAACATAACCACTTTAACAACCAACCAAAAAGGCTTAATTAAATTGT\n+ACTTTATATCATTCCTAATTAACATCATCTTAATTATTATCTTATACTCA\n+ATTAATCTCGAGTAATCTCGATAATAATAAAAATACCCGCAAACAAAGAT\n+CACCCAGCTACTACCATCATTCAAGTAGCACAACTATATATTGCCGCTAC\n+CCCAATCCCTCCTTCCAACATAACTCCAACATCATCAACCTCATACATCA\n+ACCAATCTCCCAAACCATCAAGATTAATTACTCCAACTTCATCATAATAA\n+TTAAGCACACAAATTAAAAAAACCTCTATAATCACCCCCAATACTAAAAA\n+ACCCAAAATTAATCAGTTAGATCCCCAAGTCTCTGGATATTCCTCAGTAG\n+CTATAGCAGTCGTATATCCAAACACAACCAACATCCCCCCTAAATAAATT\n+AAAAAAACTATTAAACCTAAAAACGATCCACCAAACCCTAAAACCATTAA\n+ACAACCAACAAACCCACTAACAATTAAACCTAAACCTCCATAAATAGGTG\n+AAGGCTTTAATGCTAACCCAAGACAACCAACCAAAAATAATGAACTTAAA\n+ACAAAAATATAATTATTCATTATTTCTACACAGCATTCAACTGCGACCAA\n+TGACATGAAAAATCATCGTTGTAATTCAACTACAGAAACACCTAATGACA\n+AACATACGAAAAACACACCCATTATTTAAAATTATTAACCACTCATTCAT\n+TGACCTACCTGCCCCATCCAACATTTCATCATGATGAAACTTTGGGTCCC\n+TTCTAGGAGTCTGCCTAATAGTCCAAATCATTACAGGTCTTTTCTTAGCC\n+ATACACTACACATCAGATACAATAACAGCCTTTTCATCAGTAACACACAT\n+TTGTCGAGACGTAAATTACGGGTGACTAATCCGATATATACACGCAAACG\n+GAGCCTCAATATTTTTTATTTGCTTATTCCTTCATGTCGGACGAGGCTTA\n+TATTATGGATCATATACATTTATAGAAACCTGAAACATTGGAGTACTTCT\n+ACTGTTCGCAGTCATAGCCACAGCATTTATAGGCTACGTCCTTCCATGAG\n+GACAAATATCATTCTGAGGTGCCACAGTTATTACAAACCTCCTATCAGCC\n+ATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGCTTCTC\n+AGTAGACAAAGCCACCTTGACCCGATTCTTCGCTTTCCACTTCATCTTAC\n+CATTTATTATCGCGGCCCTAGCAATCGTTCACCTCCTCTTCCTCCACGAA\n+ACAGGATCAAACAACCCAACAGGATTAAACTCAGATGCAGATAAAATTCC\n+ATTTCACCCCTACTATACAATCAAAGATATCCTAGGTATCCTAATCATAT\n+TCTTAATTCTCATAACCCTAGTATTATTTTTCCCAGACATACTAGGAGAC\n+CCAGACAACTACATACCAGCTAATCCACTAAACACCCCACCCCATATTAA\n+ACCCGAATGATATTTCCTATTTGCATACGCCATTCTACGCTCAATCCCCA\n+ATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAATTTTAGCC\n+CTAATACCTTTCCTTCATACCTCAAAGCAACGAAGCCTAATATTCCGCCC\n+AATCACACAAATTTTGTACTGAATCCTAGTAGCCAACCTACTTATCTTAA\n+CCTGAATTGGGGGCCAACCAGTAGAACACCCATTTATTATCATTGGCCAA\n+CTAGCCTCCATCTCATACTTCTCAATCATCTTAATTCTTATACCAATCTC\n+AGGAATTATCGAAGACAAAATACTAAAATTATATCCATGTCTTGATAGTA\n+TAAACATTACTCTGGTCTTGTAAACCTGAAATGAAGATCTTCTCTTCTCA\n+AGACATCAAGAAGAAGGAGCTACTCCCCACCACCAGCACCCAAAGCTGGT\n+ATTCTAATTAAACTACTTCTTGAGTACATAAATTTACATAGTACAACAGT\n+ACATTTATGTATATCGTACATTAAACTATTTTCCCCAAGCATATAAGCTA\n+GTACATTAAATCAATGGTTCAGGTCATAAAATAATCATCAACATAAATCA\n+ATATATATACCATGAATATTATCTTAAACACATTAAACTAATGTTATAAG\n+GACATATCTGTGTTATCTGACATACACCATACAGTCATAAACTCTTCTCT\n+TCCATATGACTATCCCCTTCCCCATTTGGTCTATTAATCTACCATCCTCC\n+GTGAAACCAACAACCCGCCCACCAATGCCCCTCTTCTCGCTCCGGGCCCA\n+TTAAACTTGGGGGTAGCTAAACTGAAACTTTATCAGACATCTGGTTCTTA\n+CTTCAGGGCCATCAAATGCGTTATCGCCCATACGTTCCCCTTAAATAAGA\n+CATCTCGATGGTATCGGGTCTAATCAGCCCATGACCAACATAACTGTGGT\n+GTCATGCATTTGGTATCTTTTTATTTTGGCCTACTTTCATCAACATAGCC\n+GTCAAGGCATGAAAGGACAGCACACAGTCTAGACGCACCTACGGTGAAGA\n+ATCATTAGTCCGCAAAACCCAATCACCTAAGGCTAATTATTCATGCTTGT\n+TAGACATAAATGCTACTCAATACCAAATTTTAACTCTCCAAACCCCCCAC\n+CCCCTCCTCTTAATGCCAAACCCCAAAAACACTAAGAACTTGAAAGACAT\n+ATAATATTAACTATCAAACCCTATGTCCTGATCAATTCTAGTAGTTCCCA\n+AAATATGACTTATATTTTAGTACTTGTAAAAATTTTACAAAATCATGTTC\n+CGTGAACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAA\n' |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/mm10_chrM.umi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm10_chrM.umi Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,100 @@ +CTAGATTTCC +ATCAACAACC +AACTAAATTT +TTGTAATGCT +TCCTCCAGCG +CTCTAAGTGG +CCAAAAAAAC +TTGTCTTCAT +ATAAGTGGGA +TGACACATGA +TTACTTCACC +GATTTTGGGA +CTAGGAGACC +TCCCCAAGCA +CTCAACTATA +GCGGGGTTCT +ACCTAAACAC +ACCTTGTTCC +CTACGAATAT +TTACTTGCTT +AGACTGTGAA +TCTGACATAC +ATTAGTTCAG +AAAATAGTGA +TGATCCAATA +CAGGTTAAGA +TATCGAAGAG +AACCATTAAT +ATTATAACTT +GTAAATAAGA +AAACAATTTC +ATTGAAGGAA +CCCACTACTT +TCTGTTCTTA +CCTGTACACT +CAGAGCGTTC +TGTTTGTGAT +GCGTAATAGA +ATATAATATT +AAACACCCCA +AAGTTTGAAT +ACACATACAA +GCAAACAAGA +TTCTATATGT +TGATAAATAT +TAGTTGGTTT +CTAAACTCAA +GTTGGTAAAT +ATAAGGCTAT +AATCAGAAGT +AATAACAGCC +TTAGGTGGTT +TTCAAAATTC +AACATTAATA +TAGTATGAGT +ACACATCTGT +ATTCCACTTA +TTATTCTTTA +CAACCAACAA +ATAACCATTG +TCAGGATGAG +TGCCTTCCAG +GGCGTAAAAC +GTATGCTGTA +TTTTGGATTA +GATGTCTTGA +CTTGAAACCA +CCTATGTTCA +TTTATTTAGA +AAAATTATCA +CTCATACATC +AACAAACGAA +ACAAATATTA +AGTACATAAA +GATTAGAATG +ATAGCAACAC +AGCTTAATAT +AGGATAAGCA +CTTTACTGGG +TGCTCTGGCT +GTAGTAGCCC +TAATCTATAT +TACTAGTAAA +GTAATTGATT +TCTCCCAAAC +GGTCTTATCC +ATAAATCAAG +GTTTTGGTTC +GATTAGGAAT +TTATGGAGTT +TTTGACTGAT +AAACGAGGGT +TCGCCCTCCC +TTAGGCGATG +TACTTATTAT +GATTATAGTA +CTAACATTAC +TCACCCAAAA +TTATTCCACT +TAACATTGTT |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/sacCer2_chrM.umi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sacCer2_chrM.umi Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,198 @@ +TAGGCCGTTA +CATCCAATGG +ACCAATGGTT +TGAAAACCAA +TTATATGACT +TTGTTGTTGT +CTCCCCCATG +GAAATGACTC +CCAAACTATG +GCAGATCGTT +AGCCTCCCCT +TTAACAGGCC +TACAAACAGC +TGTAGGCGAA +AATGTTGTTC +ACTGAAGCAT +ATGACTTGTT +TTTTCTCTTT +ATTATTTTCG +GGGTTCTGTG +GTCACATATT +TCCAATTCCT +ATGGTTTGAA +CAGCGTTACC +AGTTTTTCGT +CTGGACCTTC +ATATTATTAG +AGACCACCAA +GAAAATGAAG +AGTTTTGCTA +TGCTCAAATT +AATTCTTTCC +TTCCCAGCTT +CGATAACGGA +CTATCCAGGC +AGAGATCAAA +AATTCTCAGG +TGTCCTCTTG +ATTAATATTC +TCCAACCTGC +TGTTTGTGAA +ACGAGAATCT +AGAACAGAAG +AGTGATGTTC +ATCAGCCCCA +CTCGATGATC +GTCTTCTTTA +GTGGTGGTAA +AGAAGAATCT +AAGGAGGGGT +CATTGATTAA +ACCTGCAGAC +GCATTCCGCT +TAGTTTGAGA +TTAATTTTCT +TCCCTTATCT +TGCTAGCAAG +TCATGCGCTT +TTCTCTCAAA +ATGGATGTGT +TAAAAGAAAT +ATGTCCAGTG +TATTGGTGAA +TTGTAAGGAA +GCACTCATCC +GACTTGAAAT +ACGAACGATA +TTCGAACATT +GACGTTGAAT +AAACAGGACT +ACCAAGAATT +AAGGAAGCCC +TGAATTTGAG +AGTGCCTTAC +AATAGCACGG +GTGACATAGA +TAACGAATTC +GAGAAAAAGC +TGCGTGGATT +CAAACGTATT +GCGAGGTTCT +AGGGTGATTT +CATGGATTAA +GACAGGGTCT +TCTTAAAGTC +TAACCCGGCT +GCGCTTTACA +TATCGTAGTT +AATGCTAGAA +CTACAGGCGG +AGTCATGAAT +GGCAGGAGAA +AATTTTAGAG +GGTGGCGGCA +TATGTTTATG +GTGAGCCCTT +GCACCAAGAG +CAATCTACCG +GCACAAGCGA +ACAGCTCGAA +TTTTCAGCAC +TCAGCATCGT +GGTGGAGGTG +AGGAAAGTCG +ACCTGCTTAT +TCAACCAATT +ATTAACTACT +ATTTTGGCCA +CGGTGAAGAT +CTATGAATCA +AAAGCCTTTG +ATCATCGGTC +TAATCCTTCA +GATGATTTCT +ATCCACTGTT +ATCCATCACC +GACTGTAAAG +TTTTTTTCAC +TACAAGACTA +GAGAGCTACC +ATGGGCGGAG +GACATGAAGC +ATGGTACCAC +TTTGATTAGG +TTTGACGGAA +TACTAAGCAA +AGTCGGCCAA +ATCATTATTT +CTTGGGCGAT +GTTGACATTT +ATTCAAATCA +CCATAGGAGT +AAGTTACCTC +AAATATGTCA +TTAAGGGATG +TTTTTTTCAT +ACTCTACACA +ATGGGCCTTT +CCCCTGTTGC +TAAAAGAACG +GTTCGCATTG +AACATCATTG +CCAAATTGAT +TTCGTATTTT +GTTGCTCAAT +TTTTATACGT +AGATTAAACC +TCCCAATTTT +TATTGGAATG +AACGAGGTGA +ATTCAGTTGC +ACAAATTTTT +CTGACGAGCT +TGGTTGCTCT +TTCTATTAAG +AGAAAATATT +AACCACGTCC +ACATCAGAGC +AACGTTCATG +AATGCATGCG +TTGTTAGGTA +GCTAAATTCA +AAACATGGTT +TAAGACTGAA +TGCACTTGGC +ACGTCATCTG +TAAGTCAGAA +AGTGGAAGGA +TCAAGTGTTG +CTTACAAGGG +TTCCACTCGC +CATAAACATT +CATGGTATAT +GAAAAAGTAT +AAGAAAGGTG +CATAACACCT +TAATGATAGG +TCTCTTTTTC +CCAAACTTTT +GGTCGAGTAC +GCCCTCGTTT +ATTATAGGGT +CAACAAAGAT +AGTTGAGAAT +ATCCTTGACT +TCCTTAGGTT +AGACTTAATC +ATGAGAAGTC +GCAATCTCCC +GGACTACCTT +TTGGGTAACG +GAATATTTAC +AGAGGCAGAT +CTTTTGACCA +GGGCAGCAAC +ATTGGAGGGT +ACGTTCTTGA +GCACGTAACC |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/sacCer2_chrM_F.fq.gz |
| b |
| Binary file test-data/sacCer2_chrM_F.fq.gz has changed |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/sacCer2_chrM_R.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sacCer2_chrM_R.fq Tue Aug 22 04:16:08 2017 -0400 |
| b |
| b'@@ -0,0 +1,792 @@\n+@chrI_176449_177020_5:0:1_5:0:0_0/2\n+TGGTCAAATTAACTTCAATCGCTGCCGGTGTCGCCGCCATTGCTGCTGTTGCCTCGGCCGCAGGAACCACTACATTAACTCAATCTGACGAAAGAGTTAATTTGGTTGAATTAGGTGTTTATGATTCCGATATCAGAGCTCATTTGGCTGAATACTACTCTTTCTAAGCTGCTCACCCAACTGAAACTTATCCAGTTGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrI_93599_94144_3:1:0_9:0:0_1/2\n+TGTTATATCTAAGCCTTCCAAGCGACCCACACACCATTCGCATTCATCAGACGGGAGTTCTAGCACGCAGACAGATATATCGTTACAGAGCTTGCTTTACCATGATCTTGAAAGCTCACCAAAGAAACATGTTTCGCCGTCAAGACCGCCCTCTGTAGCTTCCGAATCCTCTCCTGCCGTTGCTCATCCCATTGGGCTTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrI_25874_26397_2:0:0_7:1:0_2/2\n+ATTTCAGTGGATGTAGAGGTAAAAGTGTCGTTCCATGGCTGAGTTGTAGTCATGGCAGTAGTGTCTGTTGTTGGTGTTCTGATGACAATGATGGTTTCATCAGTTGGCAAACCGTTGGTACCGGTGACGGTGGTCCTTTCAGTGGATGTAGAGGTAAAAGTGTCGTTCCATGGCTGAGTTGTAGTTATGGCAGTAGTGGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrI_139586_140147_6:0:0_3:0:0_3/2\n+TGCAGCGCCACCTGGAGCACCACCAGCTTTGTACAACTTAGAGATGATTGGGTTGGCAATGTCTTGCAAGTCCTTCAACTTGTCATCGAATTCTTGCTTGCTGGCAGTGGTGTTGCTGTCTAACCAAGAAATAGTCTCTTCAGGCTTCTTGGTGCCGGTGTCCTTGTCAGCTTGTTCCAATTTGTCACCAGCTTCAGAAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_482749_483235_3:0:0_1:0:0_0/2\n+TTGGAGATTCTAAAGTTTCACCGGTGACTGGGTTACCGATATCGTATTTATCCATCAATTCACCTAATTCTGGGCCGGAATAACCATCTATTTTAGCCAAAATTTCTTCCTATTCTTTGACAACGTCGTCATCCAATTTGACTGCTTTAATTTGTTTAACTTTTTTCTTTCTCTTCTTCTTTTCGGCATCGTCCTTAGCA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_464058_464495_1:0:0_2:0:0_1/2\n+GCGCCAACGAATGCCTCTCCTGCCCCACCTCCTGTGATTTTACAACCTACCTTACAACCTAATGATCAAGGAAATCCTTTGAACACTAGAATTTCAGCCCAATCTGCCAATGCTACTGCTTCAATGGTAGCACAACAGCATCCTGCTCAACAAACGCCTATTAACTCTTCTGCAACAATGTACAGTAATGGAGCTTCCCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_551662_552193_3:0:0_4:0:0_2/2\n+AAGGTTTGTAAGCCGATAATTTTTGGATTTACGAGACTCTGGCTTGGAGATGTCAGCAATATTCGGAGAAAGTTTTCTTAATGTTTTCTCTTTAATTTTCAAACGATGTGGCGTTTGCGACGTTGTTAAATTTTTATTTTTATTAGGGGAAATATACGCTTTTGTTGGTCTCCAATAACCTCTTACAGGGCTTTGGTAAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_600174_600690_0:2:0_1:0:0_3/2\n+AAAAATTGTCCCAGCTTTTTGTTGCTGTTTTGTTTCGAGTCAGAACCAGAATGTAGAGAAGAAATTTGCTCATCCTCTCTAAACATACATTTGATAACCCTCAGAGATGATCCTCGCACTTGTAGGTCAACTATGTAGCTCATATCCTTATTTTATGTCTTCAGTTTGAGATCAGAATATTTTTATGAAAATGTTGTCAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_509290_509702_4:0:0_3:0:0_4/2\n+TTCATAGCACATTCTTAACGAATCCACTTGCAAGTTATTCATTGCTTCCAGATTGCACGTGAAAATGCAGTCAAATTCAATAATAATCCCGTTTAAAATATCAGCGTATGGAGTTCCTTTTTCTGCCTTGATCATAATGTCCAGAGAAATATAAGGTAGCAAAAAATTTGATAGTGAGCCATCATCTTCCCTAATCAAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222'..b'24_680728_0:0:0_3:0:0_7/2\n+GAGGAATGTTTTGGTTTGGTATATGAGGAATGTGATGATGCGTAGGGGTAGTTGTGGACAATCGATTGTTCCTGGTGTGAGACAGTGGTTTGACAATATAAGTTGTTCCCATCTGCTTTAGCTGCTGGTACTGATCCAGTTGAAAATCTTGCAGAGAAGGTAATAGAGGGGGAGGAAAATATTGATTTGAATTGTTGATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_216257_216697_2:0:0_4:0:0_8/2\n+ATTCCAGTTGCGATCATTTCATCTCGAGGAGTGATGACTAGAGAACATCCGATCTACACAGTAGAAGACAAATTCGATTTCATCAAAGATAAACTAAGAGACAAAAAGAAGGGAGAGGTACTTTCTGAGATAATGCTATATCTTGTCGAAAAATCACTCGATCTCATTGACGATCCATTCATCCCATTCAGCATATCGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_912895_913350_7:0:0_5:0:0_9/2\n+ATAACCATTTAGCGTGGAAAGGACTTTTTCTCTTATTTAGAACCACTGAGGTTGTCCCAGACATACTTTCGTATGATGAATATTTTGACCTGTGTGGCCAATATGCAGACGCACTTTAAAAGCCGGAACAGTCTCAAGTAGAACTAATAAATGACAAAAAATTACTACAGCAAACGCATCCATATTGTCAAAAAGCCTTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_908795_909263_5:0:0_2:0:0_a/2\n+ATTTCGCCTGAGCTTGAAAGGGCGCAGTAGTTGGTTTAGAGTAATGGTATGGTTGTCTGATAGGTATCCTACTTTTTATGAAAGAACTTGAAATGCTATCAATTGATCTTGGAGATATTGAACTTTTGAATTTTGTAGGACTGTTTCCCATTTGGTTGAGCAAACGGTCATTCTCGTCATCATCATCTTCTTCTACTCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_766516_767017_5:0:0_7:0:0_b/2\n+TTACTTCCTTACAATGTTTCAACCAGCAAGAAAATCCCGTTTACCCTGAATTGCTGGCCCCCTTTTATGAAAATTCATCCTATAATAAGAACGCGCCAATGGTAGAAATATTTTGGATCCTGGGGCCATCAGTTGGAGGTATTTCAGATCTGGAAGATTTGATTGTTTCTCTACATCCATTGATTTTCAAGATGGATCAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_693308_693805_2:0:0_2:0:0_c/2\n+CTAAGTTGCCAACTTACACCGCCAAGGACTCTGCCGTGGCCACTAGAAAATTATCAGAAACTGTTCTTGAGGATGTTTACAATCAATTGCCAGAGTTGATTGGTGGTTCTGCCGATTTAACACCTTCTAACTTGACCAGATGGAAGGAAGGCCTTGACTACCAACCTCCTTCTTCCGGTTCAGGTAACTACTCTGGTAGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_289557_289973_4:0:0_3:0:0_d/2\n+AACATTAAAAACAAATTTTTAGAAAAACAAAAGCTGAATTAAAGACTAAATATTACACAATTTCTTCATACATTTCCGCCCCAAAGTCAAACAGCCTAAATAATATAAAAATTAACTTTTGGCAGCTCCAACCTCTGTACTGCCATCTAAAACTTTTCCAGTAAACGGCTTATATACAGTTAACAACCCGTCACTATCAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_866925_867424_2:1:0_4:0:0_e/2\n+ACAGTTCGCTCTGAAATCTCCCCCTGGGTTTCCCAATGGAATGAAACGTTGGAAAAAGAACTATCCGACCCTCGATCTAATTTGACTAGACATATTAGGATGAATTTCGAAACCTTTAGGTCATTACCTACATTGAAAAATAGCATAATTCCATTAGTAGCGACATCCAAAAATTTTGGTTCACTGTGCACTGCCATAAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_47666_48026_6:0:0_6:1:0_f/2\n+CTAGACGACCACATTCCATTGGTTGTTATGCAAACGGGTTCCGGTACCCAGTCTAACATGAATGGTAATGAAGTTCTTTCCAATCGTGCCATTGAGATCCTAGGAGGCAAGCTTGGATCTAAACAAGTCCATCCAAACAATCATTGCAACCAATCTCAATCATCCAATGATACTTTCCCCACTGTCATGCATATCGCTGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r 000000000000 -r 2953303df011 test-data/sacCer2_chrM_R.fq.gz |
| b |
| Binary file test-data/sacCer2_chrM_R.fq.gz has changed |
| b |
| diff -r 000000000000 -r 2953303df011 tool-data/kallisto_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/kallisto_indexes.loc.sample Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,33 @@ +# kallisto_indexes.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for kallisto. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a kallisto_indexes.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/kallisto_indexes/ +# +# containing sacCer3 genome and sacCer3.*.ht2 files, such as: +# +# -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.fa +# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.kallisto +# +# then the kallisto_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/kallisto_indexes/sacCer3.kallisto +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/kallisto_indexes/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/kallisto_indexes/dm3 +# +# |
| b |
| diff -r 000000000000 -r 2953303df011 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,13 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of indexes in the kallisto mapper format --> + <table name="kallisto_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/kallisto_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 2953303df011 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Aug 22 04:16:08 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="kallisto_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/kallisto_indexes.loc" /> + </table> +</tables> |