Galaxy |

Changeset 1:7a9158bb6f98 (2017-08-07)

Previous changeset 0:59a4c97b85d6 (2017-08-05) Next changeset 2:552ef00aba90 (2017-08-22)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302

modified:
kallisto_quant.xml
test-data/kallisto_quant_out1.tab
test-data/kallisto_quant_out2.tab
test-data/kallisto_quant_out3.tab

added:
test-data/sacCer2_chrM_F.fq.gz

removed:
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/sacCer2_chrM_F.fq

diff -r 59a4c97b85d6 -r 7a9158bb6f98 kallisto_quant.xml
--- a/kallisto_quant.xml Sat Aug 05 04:02:28 2017 -0400
+++ b/kallisto_quant.xml Mon Aug 07 13:25:33 2017 -0400

[

b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.0">\n+<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.1">\n <description>- quantify abundances of RNA-Seq transcripts</description>\n <macros>\n <import>macros.xml</import>\n@@ -24,25 +24,20 @@\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+ #set $single_reads = $single_paired.reads\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+ #set $forward_reads = $single_paired.collection.forward\n+ #set $reverse_reads = $single_paired.collection.reverse\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+ #set $forward_reads = $single_paired.collection.reads.forward\n+ #set $reverse_reads = $single_paired.collection.reads.reverse\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+ #set $reads = "\'%s\' \'%s\'" % ($forward_reads, $reverse_reads)\n+ $reads\n #end if\n #if $pseudobam:\n | samtools sort -O bam -@ \\${GALAXY_SLOTS:-1} -o \'$pseudobam_output\' -\n@@ -74,7 +69,7 @@\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+ <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />\n <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />\n <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />\n </when>\n@@ -85,11 +80,11 @@\n <option value="collection">Pair or list of pairs</option>\n </param>\n <when value="datasets">\n- <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" />\n- <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" />\n+ <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />\n+ <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />\n </when>\n <when value="collection">\n- <param name="reads" type="data_collection" format="fastq" collection_type="list:paired" label="Collection of reads" />\n+ <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />\n </when>\n </conditional>\n </when>\n@@ -113,8 +108'..b'orward" 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- <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq,mm10_chrM-2.r.fq,mm10_chrM-3.r.fq,mm10_chrM-4.r.fq,mm10_chrM-5.r.fq" />\n+ <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />\n+ <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />\n <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />\n </test>\n <test>\n@@ -123,37 +118,9 @@\n <param name="single_paired_selector" value="paired" />\n <param name="collection_selector" value="collection" />\n <param name="reads">\n- <collection type="list:paired">\n- <element name="p1">\n- <collection type="paired">\n- <element name="forward" value="mm10_chrM-1.f.fq" />\n- <element name="reverse" value="mm10_chrM-1.r.fq" />\n- </collection>\n- </element>\n- <element name="p2">\n- <collection type="paired">\n- <element name="forward" value="mm10_chrM-2.f.fq" />\n- <element name="reverse" value="mm10_chrM-2.r.fq" />\n- </collection>\n- </element>\n- <element name="p3">\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 type="paired">\n+ <element name="forward" value="mm10_chrM-1.f.fq" />\n+ <element name="reverse" value="mm10_chrM-1.r.fq" />\n </collection>\n </param>\n <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" />\n@@ -163,7 +130,7 @@\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+ <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />\n <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />\n </test>\n <test>\n@@ -182,7 +149,7 @@\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="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />\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'

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/kallisto_quant_out1.tab
--- a/test-data/kallisto_quant_out1.tab Sat Aug 05 04:02:28 2017 -0400
+++ b/test-data/kallisto_quant_out1.tab Mon Aug 07 13:25:33 2017 -0400

@@ -1,2 +1,2 @@
target_id length eff_length est_counts tpm
-chrM 16299 15800.9 500 1e+06
+chrM 16299 15800.9 100 1e+06

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/kallisto_quant_out2.tab
--- a/test-data/kallisto_quant_out2.tab Sat Aug 05 04:02:28 2017 -0400
+++ b/test-data/kallisto_quant_out2.tab Mon Aug 07 13:25:33 2017 -0400

@@ -1,2 +1,2 @@
target_id length eff_length est_counts tpm
-chrM 16299 15800.9 500 1e+06
+chrM 16299 15800.9 100 1e+06

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/kallisto_quant_out3.tab
--- a/test-data/kallisto_quant_out3.tab Sat Aug 05 04:02:28 2017 -0400
+++ b/test-data/kallisto_quant_out3.tab Mon Aug 07 13:25:33 2017 -0400

@@ -1,2 +1,2 @@
target_id length eff_length est_counts tpm
-chrM 16299 16100 500 1e+06
+chrM 16299 16100 100 1e+06

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-2.f.fq
--- a/test-data/mm10_chrM-2.f.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,400 +0,0 @@\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 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-2.r.fq
--- a/test-data/mm10_chrM-2.r.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,400 +0,0 @@\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 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-3.f.fq
--- a/test-data/mm10_chrM-3.f.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-3.r.fq
--- a/test-data/mm10_chrM-3.r.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-4.f.fq
--- a/test-data/mm10_chrM-4.f.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-4.r.fq
--- a/test-data/mm10_chrM-4.r.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-5.f.fq
--- a/test-data/mm10_chrM-5.f.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/mm10_chrM-5.r.fq
--- a/test-data/mm10_chrM-5.r.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 59a4c97b85d6 -r 7a9158bb6f98 test-data/sacCer2_chrM_F.fq
--- a/test-data/sacCer2_chrM_F.fq Sat Aug 05 04:02:28 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,792 +0,0 @@\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 59a4c97b85d6 -r 7a9158bb6f98 test-data/sacCer2_chrM_F.fq.gz

Binary file test-data/sacCer2_chrM_F.fq.gz has changed