Galaxy |

Changeset 0:59a4c97b85d6 (2017-08-05)

Next changeset 1:7a9158bb6f98 (2017-08-07)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380

added:
kallisto_quant.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_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-2.f.fq
test-data/mm10_chrM-2.r.fq
test-data/mm10_chrM-3.f.fq
test-data/mm10_chrM-3.r.fq
test-data/mm10_chrM-4.f.fq
test-data/mm10_chrM-4.r.fq
test-data/mm10_chrM-5.f.fq
test-data/mm10_chrM-5.r.fq
test-data/mm10_chrM.fa
test-data/sacCer2_chrM_F.fq
test-data/sacCer2_chrM_R.fq
tool-data/kallisto_indexes.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test

diff -r 000000000000 -r 59a4c97b85d6 kallisto_quant.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kallisto_quant.xml Sat Aug 05 04:02:28 2017 -0400

[

b'@@ -0,0 +1,197 @@\n+<?xml version="1.0"?>\n+<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.0">\n+ <description>- quantify abundances of 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 = $reference_genome.index.fields.path\n+ #end if\n+ kallisto quant -i \'$index_path\'\n+ $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $pseudobam\n+ #if $pseudobam:\n+ -o .\n+ #else:\n+ --threads \\${GALAXY_SLOTS:-1}\n+ -o .\n+ #end if\n+ #if str($single_paired.single_paired_selector) == \'single\':\n+ --single\n+ #set $single_reads = "\' \'".join(str($single_paired.reads).split(\',\'))\n+ --fragment-length $single_paired.fragment_length\n+ --sd $single_paired.sd\n+ \'$single_reads\'\n+ #else:\n+ #if str($single_paired.collection.collection_selector) == \'datasets\':\n+ #set $forward_reads = str($single_paired.collection.forward).split(\',\')\n+ #set $reverse_reads = str($single_paired.collection.reverse).split(\',\')\n+ #else:\n+ #set $forward_reads = [str($read.forward) for $read in $single_paired.collection.reads]\n+ #set $reverse_reads = [str($read.reverse) for $read in $single_paired.collection.reads]\n+ #end if\n+ #set $tuplexed_reads = zip($forward_reads, $reverse_reads)\n+ #set $multiplexed_reads = []\n+ #for read_pair in $tuplexed_reads:\n+ ${multiplexed_reads.extend([read for read in read_pair])}\n+ #end for\n+ #set $reads = "\' \'".join($multiplexed_reads)\n+ \'$reads\'\n+ #end if\n+ #if $pseudobam:\n+ | samtools sort -O bam -@ \\${GALAXY_SLOTS:-1} -o \'$pseudobam_output\' -\n+ #end if\n+ && cat run_info.json\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="reference_genome">\n+ <param name="reference_genome_source" type="select" label="Reference genome for quantification">\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" label="FASTA reference genome" />\n+ </when>\n+ </conditional>\n+ <conditional name="single_paired">\n+ <param name="single_paired_selector" type="select" label="Single-end or paired reads">\n+ <option value="single" selected="true">Single-end</option>\n+ <option value="paired">Paired</option>\n+ </param>\n+ <when value="single">\n+ <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" />\n+ '..b'\n+ <collection type="paired">\n+ <element name="forward" value="mm10_chrM-3.f.fq" />\n+ <element name="reverse" value="mm10_chrM-3.r.fq" />\n+ </collection>\n+ </element>\n+ <element name="p4">\n+ <collection type="paired">\n+ <element name="forward" value="mm10_chrM-4.f.fq" />\n+ <element name="reverse" value="mm10_chrM-4.r.fq" />\n+ </collection>\n+ </element>\n+ <element name="p5">\n+ <collection type="paired">\n+ <element name="forward" value="mm10_chrM-5.f.fq" />\n+ <element name="reverse" value="mm10_chrM-5.r.fq" />\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" />\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,mm10_chrM-2.f.fq,mm10_chrM-3.f.fq,mm10_chrM-4.f.fq,mm10_chrM-5.f.fq" />\n+ <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />\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="pseudobam" value="true" />\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="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />\n+ <output name="pseudobam_output" file="kallisto_quant_out4.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="pseudobam" value="true" />\n+ <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq" />\n+ <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />\n+ <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />\n+ <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+ kallisto 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. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n'

diff -r 000000000000 -r 59a4c97b85d6 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Aug 05 04:02:28 2017 -0400

@@ -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

diff -r 000000000000 -r 59a4c97b85d6 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 Sat Aug 05 04:02:28 2017 -0400

@@ -0,0 +1,1 @@
+sacCer2_chrX sacCer2 S. cerevisiae Chromosome X (sacCer2_chrX) ${__HERE__}/sacCer2_chrX.kallistei

diff -r 000000000000 -r 59a4c97b85d6 test-data/cached_locally/sacCer2_chrX.kallistei

Binary file test-data/cached_locally/sacCer2_chrX.kallistei has changed

diff -r 000000000000 -r 59a4c97b85d6 test-data/felCat8_chrM.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/felCat8_chrM.fa Sat Aug 05 04:02:28 2017 -0400

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'

diff -r 000000000000 -r 59a4c97b85d6 test-data/felCat8_chrM_F.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/felCat8_chrM_F.fq Sat Aug 05 04:02:28 2017 -0400

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'

diff -r 000000000000 -r 59a4c97b85d6 test-data/felCat8_chrM_R.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/felCat8_chrM_R.fq Sat Aug 05 04:02:28 2017 -0400

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'

diff -r 000000000000 -r 59a4c97b85d6 test-data/kallisto_quant_out1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_quant_out1.tab Sat Aug 05 04:02:28 2017 -0400

@@ -0,0 +1,2 @@
+target_id length eff_length est_counts tpm
+chrM 16299 15800.9 500 1e+06

diff -r 000000000000 -r 59a4c97b85d6 test-data/kallisto_quant_out2.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_quant_out2.tab Sat Aug 05 04:02:28 2017 -0400

@@ -0,0 +1,2 @@
+target_id length eff_length est_counts tpm
+chrM 16299 15800.9 500 1e+06

diff -r 000000000000 -r 59a4c97b85d6 test-data/kallisto_quant_out3.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_quant_out3.tab Sat Aug 05 04:02:28 2017 -0400

@@ -0,0 +1,2 @@
+target_id length eff_length est_counts tpm
+chrM 16299 16100 500 1e+06

diff -r 000000000000 -r 59a4c97b85d6 test-data/kallisto_quant_out4.bam

Binary file test-data/kallisto_quant_out4.bam has changed

diff -r 000000000000 -r 59a4c97b85d6 test-data/kallisto_quant_out4.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_quant_out4.tab Sat Aug 05 04:02:28 2017 -0400

@@ -0,0 +1,2 @@
+target_id length eff_length est_counts tpm
+chrM 17009 16510 200 1e+06

diff -r 000000000000 -r 59a4c97b85d6 test-data/kallisto_quant_out5.bam

Binary file test-data/kallisto_quant_out5.bam has changed

diff -r 000000000000 -r 59a4c97b85d6 test-data/kallisto_quant_out5.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_quant_out5.tab Sat Aug 05 04:02:28 2017 -0400

@@ -0,0 +1,2 @@
+target_id length eff_length est_counts tpm
+chrX 745742 745258 19 1e+06

diff -r 000000000000 -r 59a4c97b85d6 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 Sat Aug 05 04:02:28 2017 -0400

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'

diff -r 000000000000 -r 59a4c97b85d6 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 Sat Aug 05 04:02:28 2017 -0400

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'

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-2.f.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-2.f.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-2.r.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-2.r.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-3.f.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-3.f.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-3.r.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-3.r.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-4.f.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-4.f.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-4.r.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-4.r.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-5.f.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-5.f.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM-5.r.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM-5.r.fq Sat Aug 05 04:02:28 2017 -0400

diff -r 000000000000 -r 59a4c97b85d6 test-data/mm10_chrM.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_chrM.fa Sat Aug 05 04:02:28 2017 -0400

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'

diff -r 000000000000 -r 59a4c97b85d6 test-data/sacCer2_chrM_F.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sacCer2_chrM_F.fq Sat Aug 05 04:02:28 2017 -0400

b'@@ -0,0 +1,792 @@\n+@chrI_176449_177020_5:0:1_5:0:0_0/1\n+TAGGCCGTTATTTCCGTAAAGGATGGTATAATAATAAGAAATTTATCATATTAATAATACCTATATCCAAAAATTTATATTTATATACATGCGCCTAACTATTCATACTATTAATTTCATATTATTAAGCTTTTTTTTTTTCATTTATCATTTTTTTTCGTAACCCTCTCCTACCTGTACAGGTTTCATTCGTAAAGCAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrI_93599_94144_3:1:0_9:0:0_1/1\n+CATCCAATGGTCCTGGATCTTAAGTCCCATAGCTCTTTAACGATCTTGTCCAAATTTGCAATGTTTTTAACAAGGTCATTTTCATCTTTCAGAACCTCATCTTTCAAACTGTGGTTTAGTAAAGCTTCTGTCAGCTGTAACTGGAATCCGATATGAGGCTGATAGTAGTCTAATTCATGTGAATTTAGCGAAAGATTGGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrI_25874_26397_2:0:0_7:1:0_2/1\n+ACCAATGGTTTGCGAACTGATGATAGCATCATTGTCATCAGAACACCAACAACAGCCCCTACTGCCATGACTACAACTCAGCCATGGAACGACACTTTTACCTCTACATCCACTGAAATGACCACCGTCACCGGTTCGAACGGTTTGCCAACTGATGAAACCATCATTGACATCAGAACACCAACAACAGCCACTACAGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrI_139586_140147_6:0:0_3:0:0_3/1\n+TGAAAACCAACCAGGTGTGTTGATTCAAGTCTTTGAAGGTGAAAGATCCAAGACTAAGGACAACAACTTGTTGGGTAAGTTCGAATTGAGTGGTATTCCACCAGCTCCAAGAGGTGTCCCACAAATTGAAGTCACTTTCGATGTCGACTCTAACGGTATTTTGAATGTTTCCGCCGTCGAAAAGGGTACTGGTAAGTCTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_482749_483235_3:0:0_1:0:0_0/1\n+TTATATGACTATGGTCCACCAGGTTGTGCATTCCAAAACAACATCATTGACGGCTGGAGAAAGCATTTTATTTTGGAAGAAGATATGTTGGAAGTTGATTGTACTATGTTAACTCCATATGAGGTTTTGAAGACCTCAGGTCATGTTGACAAATTTTCTGATTGGATGTGTAGAGATTTGAAGACTGGTGAGATTTTCAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_464058_464495_1:0:0_2:0:0_1/1\n+TTGTTGTTGTTGTTGTTGCTGTTGTTGTTGTTGTTGTTGTGCCTGCGCCTGTGCTTGTGCTTGTGCCTGTGCTTGTGCTTGTGCTTGCGCTTGTGCATGTGCTTGTGCTTGTGCTTGTGCCTGTGCTTGCGCCTGTGCTTGTGCTTGTGCTTGCGCTTGTGCTTGTGCTTGTGCTTGAGCTTGTGCTTGTGCTTGAGGTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_551662_552193_3:0:0_4:0:0_2/1\n+CTCCCCCATGAAAAAAGTTTCTCAAAAGTTTAAGTCAATAAACTCCACGGATACTGATATGCAAGAAGCGTTAAGAGATCAATTCTCAGTAAAACATAAAAAAACCAAAAATAATTCACCCAAAGGAAAAAACTCTCGAAAATCCTCTATTCCGAGGTTTGATAAGACTTCTTTGAAGCTAACGACACACAAAAAGCTAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_600174_600690_0:2:0_1:0:0_3/1\n+GAAATGACTCCATTCCCTGAATTTTTTGTGAAACCAATATCTGAGACTCTTCCTTCATCTTATCAACGTATTGTTCAGTCAATTAAGTAAGAAGTATATTTGAGCGCAGCCTTAATCATATATAGCACCAGTTATATGTTTGGCCCTCTCTTGAGTTGAAAAACACATAATACATAGTACTGTACTTTTCTCTTTTTCAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrII_509290_509702_4:0:0_3:0:0_4/1\n+CCAAACTATGGGAAAAGTTTAACTCTTTCTCCAAGACAACCATCTATCCGCTTTTATCTTCCTTGTATCTAGCGCCATCATGGAAAGAATATGTCCCGCTAAAATATCCTTCTAATAACTTCAAGGAATGATACAAAATTTGGGTGAAAAGGTTTACATTGGATTTATTGAAAACAGGTACAACAGAAAATCATCCATTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222'..b'24_680728_0:0:0_3:0:0_7/1\n+GGACTACCTTTGACGCATGATAAGACGGCAAGAGACCTACCACAGCTGTCATCTCAACTAAATTCTATTCCATATTACTCAGCTCCACACGACCCTTCAACGAGACATCATTACCTCAACGTCGCTCAAGCTCAACCAAGGGCTAACTCGACCCCTCAATTGCCCTTTATTTCATCCATTATCAACAACAGCAGTCAAAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_216257_216697_2:0:0_4:0:0_8/1\n+TTGGGTAACGCCTATTAGGGAAAGTAGGTAGTTCCATGACCAACGATTAATGGCAATGATAGTGGGTTCTATATATGTACCGGCTCCATACATCATCTCTGTCCATTCGCTTTTCCATTTTTCGAACTGCAGTTTAGTGTTTTCCCACAATGTTGTGCCCAAAAAGACTTCGTCAAAGTTTACCGTATCAGGACATTCTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_912895_913350_7:0:0_5:0:0_9/1\n+GAATATTTACCAACTGGTTGTATAACTGATCAATTTCTGAATTTTTAATTATTTCCCAGGAGAATGAATTTAGTTTAATTTGATAATGAGGATCACTAGGTTTTAGTTTTAACCTGTTCTGACTAAGGGTCTTACCTATTTCCGTTGTTTCAATATTAGACCGTATCTTTATAAGATTTCATAACGCGTCCTGGGGTGTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_908795_909263_5:0:0_2:0:0_a/1\n+AGAGGCAGATCAGATTGGCACTCACCCTTGCCATCAATATCCCCTTCGATGCATTATGGATCGTTGAACTCGAGAATGTCTCAAGGCGCCAATGCAAGCCATTTGATTGCAAGAGGCGGTGGGAATTCATCTACTAGTGCCTTGAATAGTAGAAGGAATTCTTTAGATAAGAGCTCAAACAAGCAGGGTATGTCATGCTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_766516_767017_5:0:0_7:0:0_b/1\n+CTTTTGACCATTTCATTGATGTTATAATCAGGTTGCACAACAAGTGATGCTGACAATTTTCTATTATCAGCCTTATGCTTTTTGATACCTTCTTTGCTCTGGATACTACGCAAGACCCAAGAGTCAACGTCTTTCGCATCGTACACAGATAAAGAACCGTTATAAAGACTGTGCCGTAACAGTGGAGACGATGAAAAGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_693308_693805_2:0:0_2:0:0_c/1\n+GGGCAGCAACTTCGTTACCATCAGCTGGTCTCCAAACTTGAATGTTTGGTAGGGATCTGAAGTGTGCTAAAGTTTCAATAGGTTGATGTGTTGGACCATCTTCACCGACACCGATAGAGTCATGTGTAGCAACCCAAATAACTGGGTGGCCAGACAAAGCGGACAATCTAACGGCACCAGCAGCATAAGAAACGAAGTTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_289557_289973_4:0:0_3:0:0_d/1\n+ATTGGAGGGTTAGGTAATGTTTACCACTGGAATTTCGAACCTGTTTTTGCCATTTATAACGAGATACATGAGGACTTTCAAGGCATAATATCTGACGAATTGGAGGCCGAAAGCAAGGCATTTTATCACACTGAGGGCTGCAGAAGAGCAATAGGAGAAAATAATAAGTTTAATACCGTTGCTTATCACAAATACATTGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_866925_867424_2:1:0_4:0:0_e/1\n+ACGTTCTTGACGTCCTTTTTCAACCATAGTTTGATAGTATTGTCGATAGAAAAAGTACTTTGACCTGTTCCCACATTTGTAGTAGGAGCCACGGTGGTAATTCTGGAGTTGATAGCTTTAATCATCTTTTCATACTCTGCATAAGCTAAATTAAAATTAAAATATGCGTCTTTCGCCCTTAAGGCAACCCTAGCGGCTGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrXVI_47666_48026_6:0:0_6:1:0_f/1\n+GCACGTAACCGGAAAACTCTTGGCCTAGTGTCAAAGGCGTGGCATCTTGCAAGAGTGTTGTACCGATCATCACAATATGGTCAAATTGCTTGGAATTGGCTTCAAGGGCGTTCTTTAAATTGGTCAACTCAGGTATCAACTCGTTTTGAATTTTCAAACTGGCAGCGATATGCATGACAGTGGGGAAAGTATCATTGGAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 59a4c97b85d6 test-data/sacCer2_chrM_R.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sacCer2_chrM_R.fq Sat Aug 05 04:02:28 2017 -0400

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'

diff -r 000000000000 -r 59a4c97b85d6 tool-data/kallisto_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/kallisto_indexes.loc.sample Sat Aug 05 04:02:28 2017 -0400

@@ -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
+#
+#

diff -r 000000000000 -r 59a4c97b85d6 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sat Aug 05 04:02:28 2017 -0400

@@ -0,0 +1,13 @@
+
+<tables>
+    
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    
+    <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>

diff -r 000000000000 -r 59a4c97b85d6 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Sat Aug 05 04:02:28 2017 -0400

@@ -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>