| Previous changeset 1:a54de7e658f7 (2014-03-05) Next changeset 3:ceb6467e276c (2015-03-09) |
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Commit message:
Uploaded |
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modified:
bowtie2_wrapper.xml tool_dependencies.xml |
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added:
test-data/bowtie2-fq1.fq test-data/bowtie2-fq2.fq test-data/bowtie2-ref.fasta test-data/bowtie2-test1.bam |
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removed:
test-data/bowtie2/phix_genome.fasta test-data/bowtie2/phix_mapped.bam test-data/bowtie2/phix_reads.fastq |
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| diff -r a54de7e658f7 -r c1ec08cb34f9 bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Wed Mar 05 11:26:50 2014 -0500 +++ b/bowtie2_wrapper.xml Fri Dec 12 11:12:27 2014 -0500 |
| [ |
| b'@@ -1,23 +1,25 @@\n-<tool id="bowtie2" name="Bowtie2" version="0.2">\n- <!-- Wrapper compatible with Bowtie version 2.0.0 -->\n- <description>is a short-read aligner</description>\n+<tool id="bowtie2" name="Bowtie2" version="0.3">\n+ <!-- Wrapper compatible with Bowtie version 2.2.4 -->\n+ <description>- map reads against reference genome</description>\n <version_command>bowtie2 --version</version_command>\n <requirements>\n- <requirement type="package" version="2.1.0">bowtie2</requirement>\n+ <requirement type="package" version="2.2.4">bowtie2</requirement>\n <requirement type="package" version="0.1.18">samtools</requirement>\n </requirements>\n- \n <command>\n+ \n ## prepare bowtie2 index\n #set index_path = \'\'\n #if str($reference_genome.source) == "history":\n- bowtie2-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;\n+ bowtie2-build "$reference_genome.own_file" genome &&\n+ ln -s "$reference_genome.own_file" genome.fa &&\n #set index_path = \'genome\'\n #else:\n #set index_path = $reference_genome.index.fields.path\n #end if\n \n ## execute bowtie2\n+ \n bowtie2\n \n ## number of threads\n@@ -26,75 +28,125 @@\n ## index file path\n -x $index_path\n \n- ## check for single/pair-end\n- #if str( $library.type ) == "single"\n- ## prepare inputs\n- -U $library.input_1\n \n- #if $output_unaligned_reads_l\n+ ## Fastq inputs\n+ #if str( $library.type ) == "single":\n+ -U "${input_1}"\n+ #if str( $library.unaligned_file ) == "true":\n --un $output_unaligned_reads_l\n #end if\n+ #elif str( $library.type ) == "paired":\n+ -1 "${input_1}"\n+ -2 "${input_2}"\n+ #if str( $library.paired_options.paired_options_selector ) == "yes":\n+ -I "${library.paired_options.I}"\n+ -X "${library.paired_options.X}"\n+ ${library.paired_options.fr_rf_ff}\n+ ${library.paired_options.no_mixed}\n+ ${library.paired_options.no_discordant}\n+ ${library.paired_options.dovetail}\n+ ${library.paired_options.no_contain}\n+ ${library.paired_options.no_overlap}\n+ #end if\n+ #if str( $library.unaligned_file ) == "true":\n+ --un-conc $output_unaligned_reads_l\n+ #end if\n #else\n- ## prepare inputs\n- -1 $library.input_1\n- -2 $library.input_2\n- -I $library.min_insert\n- -X $library.max_insert\n-\n- #if $output_unaligned_reads_l\n+ ## prepare collection\n+ -1 $library.input_1.forward\n+ -2 $library.input_1.reverse\n+ #if str( $library.paired_options.paired_options_selector ) == "yes":\n+ -I "${library.paired_options.I}"\n+ -X "${library.paired_options.X}"\n+ ${library.paired_options.fr_rf_ff}\n+ ${library.paired_options.no_mixed}\n+ ${library.paired_options.no_discordant}\n+ ${library.paired_options.dovetail}\n+ ${library.paired_options.no_contain}\n+ ${library.paired_options.no_overlap}\n+ #end if\n+ #if str( $library.unaligned_file ) == "true":\n --un-conc $output_unaligned_reads_l\n #end if\n #end if\n \n- ## configure settings\n- #if str($params.full) == "yes":\n- ## add alignment type\n- $params.align_type\n-\n- ## add performance\n- $params.performance\n- \n- ## add time flag\n- $params.time\n+ ## Readgroups\n+ #if str( $read_group.read_group_selector ) == "yes"'..b'dant. See also: [Mates can overlap, contain or dovetail each other]. \n+ Default: mates can overlap in a concordant alignment.\n+ \n ------\n \n-**SAM options**\n+**SAM options**::\n \n-*--rg-id [text]*\n+ --rg-id <text>\n+ Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be\n+ printed, with `<text>` as the value associated with the `ID:` tag. It also\n+ causes the `RG:Z:` extra field to be attached to each SAM output record, with\n+ value set to `<text>`.\n \n-Set the read group ID to [text]. This causes the SAM @RG header line to be printed, with [text] as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to [text].\n+ --rg <text>\n+ Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the\n+ `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`\n+ must also be specified. This is because the `ID` tag is required by the [SAM\n+ Spec][SAM]. Specify `--rg` multiple times to set multiple fields. See the\n+ [SAM Spec][SAM] for details about what fields are legal.\n \n-*--rg [text]*\n+ --omit-sec-seq\n+ When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`\n+ and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix\n+ in those fields instead.\n+ \n+-----\n \n-Add [text] as a field on the @RG header line. Note: in order for the @RG line to appear, --rg-id must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.\n+**Other options**::\n \n-------\n+ --reorder\n+ Guarantees that output SAM records are printed in an order corresponding to the\n+ order of the reads in the original input file, even when `-p` is set greater\n+ than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie\n+ 2 to run somewhat slower and use somewhat more memory then if `--reorder` were\n+ not specified. Has no effect if `-p` is set to 1, since output order will\n+ naturally correspond to input order in that case.\n \n-**Output options**\n-\n-*--un/--un-conc*\n+ --seed <int>\n+ Use `<int>` as the seed for pseudo-random number generator. Default: 0.\n \n-Write reads that fail to align concordantly to file(s). These reads correspond to the SAM records.\n-\n-*-t/--time (default: off)*\n-\n-Print the wall-clock time required to load the index files and align the reads. This is printed to the "standard error" ("stderr") filehandle.\n+ --non-deterministic\n+ Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It\n+ seeds the generator with a number derived from (a) the read name, (b) the\n+ nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`\n+ option. This means that if two reads are identical (same name, same\n+ nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)\n+ for both, even if there was ambiguity. When `--non-deterministic` is specified,\n+ Bowtie 2 re-initializes its pseudo-random generator for each read using the\n+ current time. This means that Bowtie 2 will not necessarily report the same\n+ alignment for two identical reads. This is counter-intuitive for some users,\n+ but might be more appropriate in situations where the input consists of many\n+ identical reads.\n \n </help>\n+ <citations>\n+ <citation type="doi">10.1186/gb-2009-10-3-r25</citation>\n+ <citation type="doi">10.1038/nmeth.1923</citation>\n+ </citations>\n </tool>\n' |
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| diff -r a54de7e658f7 -r c1ec08cb34f9 test-data/bowtie2-fq1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2-fq1.fq Fri Dec 12 11:12:27 2014 -0500 |
| b |
| b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACC'..b'FHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...//////\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;/////9/////.\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA\n++\n+AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF/\n' |
| b |
| diff -r a54de7e658f7 -r c1ec08cb34f9 test-data/bowtie2-fq2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2-fq2.fq Fri Dec 12 11:12:27 2014 -0500 |
| b |
| b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/2\n+TCGCCTTACCGCTACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG\n++\n+1>11111@11111A111A100000000////011110//>>/12@1@22B/////1@>21/>>/-----9/;////9////--;-;-;-----;--------9/-/-///9-;-------9//////9/////-//-/9-;-;9--/////99-;--9-:-;----/---/-----////---9-/////--;A-//////---------9/-----;-----/-/-----;--;//////////9;///-\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n++\n+BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/2\n+GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\n++\n+3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/2\n+ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT\n++\n+CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA/\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF0/.\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCCA\n++\n+AA?A34BF>AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<BAGHB?11F/FGFGGBFBGBD.11><.<<<C0<A</<<=0GFHC@-.;FF09BFFGB00B0;FE.C/:CCF0;0C0;BBBFF@.9AF.:9EFF.;.BFF/FF/;/./BFB/..;;ABF/9FF//.;AAF9BBBA;-A.B/9///9/BF////;///:9.\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTG'..b'HGGGGGGGGGFEACFFFFFFFFFFFFFFFDFFFAFFFFBFAB@EFAAEFFFFF.ACF.BBFFEBFFFEB;FFFFFFFA/BFBFBBBFFFBFFFFFED.>DFFF.\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/2\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+BBBBCFCCCCCFGGGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF.\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/2\n+ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGAGTTCTGTGGGGCCGGGGATCCTTATAAAAAAAATAGA\n++\n+BCCDDFFFFFFFGGGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGHHGHGAGAEEDG.CGCGHC0CGBFHGFBBF0ABDDEFF@?--:BB@.;:BF;0.0:0.0:000:BF.-.------.9/;000::0;0:--.000\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/2\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC\n++\n+CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A....\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG\n++\n+CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/2\n+ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACATT\n++\n+CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFFFF.9//;FFFFF/BFFB/\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/2\n+AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTTA\n++\n+CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B0\n' |
| b |
| diff -r a54de7e658f7 -r c1ec08cb34f9 test-data/bowtie2-ref.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2-ref.fasta Fri Dec 12 11:12:27 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r a54de7e658f7 -r c1ec08cb34f9 test-data/bowtie2-test1.bam |
| b |
| Binary file test-data/bowtie2-test1.bam has changed |
| b |
| diff -r a54de7e658f7 -r c1ec08cb34f9 test-data/bowtie2/phix_genome.fasta --- a/test-data/bowtie2/phix_genome.fasta Wed Mar 05 11:26:50 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,78 +0,0 @@ ->gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174, complete genome -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA \ No newline at end of file |
| b |
| diff -r a54de7e658f7 -r c1ec08cb34f9 test-data/bowtie2/phix_mapped.bam |
| b |
| Binary file test-data/bowtie2/phix_mapped.bam has changed |
| b |
| diff -r a54de7e658f7 -r c1ec08cb34f9 test-data/bowtie2/phix_reads.fastq --- a/test-data/bowtie2/phix_reads.fastq Wed Mar 05 11:26:50 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,260 +0,0 @@\n-@HWI-EAS210R_0001:4:10:890:1882#0/1\n-AATCTCATCTCTCTTTTTGCGTTCTGCTTCAATATCTG\n-+HWI-EAS210R_0001:4:10:890:1882#0/1\n-fcceeggggggggggggffghggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:890:1010#0/1\n-GTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGA\n-+HWI-EAS210R_0001:4:10:890:1010#0/1\n-gggggggggggggghgggggggggfggggggggggggg\n-@HWI-EAS210R_0001:4:10:890:1780#0/1\n-GAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTAT\n-+HWI-EAS210R_0001:4:10:890:1780#0/1\n-ggfhggggggggggggggggghgggggfggggggdggg\n-@HWI-EAS210R_0001:4:10:890:1348#0/1\n-TTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT\n-+HWI-EAS210R_0001:4:10:890:1348#0/1\n-ggggggggggggggggggggggggghfggeggggggdg\n-@HWI-EAS210R_0001:4:10:890:1707#0/1\n-AAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCC\n-+HWI-EAS210R_0001:4:10:890:1707#0/1\n-gfgfgfgggggggfggeggggffgcgggdfggfggdgg\n-@HWI-EAS210R_0001:4:10:890:1527#0/1\n-CGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC\n-+HWI-EAS210R_0001:4:10:890:1527#0/1\n-gggggggggggggggggggggggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:890:781#0/1\n-CGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCAT\n-+HWI-EAS210R_0001:4:10:890:781#0/1\n-gggggggggggggggggggggggggggggggghggggg\n-@HWI-EAS210R_0001:4:10:890:568#0/1\n-GTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT\n-+HWI-EAS210R_0001:4:10:890:568#0/1\n-gggggggfgggggggggggggggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:890:1365#0/1\n-CCAACATAAACATTATTGCCCGGCGTACGAGGAAGGAC\n-+HWI-EAS210R_0001:4:10:890:1365#0/1\n-eggggdggfghggggggggghgfgfegghfggfgggge\n-@HWI-EAS210R_0001:4:10:890:161#0/1\n-GTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCT\n-+HWI-EAS210R_0001:4:10:890:161#0/1\n-ggggfg_gggfegggfgeggaefefdbfddeedgcgg`\n-@HWI-EAS210R_0001:4:10:890:1920#0/1\n-TTTATCAATACCATGAAAAATATCAACCACACCAGAAG\n-+HWI-EAS210R_0001:4:10:890:1920#0/1\n-gggggggggggggggggggggffggggggggggggggg\n-@HWI-EAS210R_0001:4:10:890:61#0/1\n-GTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCA\n-+HWI-EAS210R_0001:4:10:890:61#0/1\n-eede[egfggfggggggggggggegggggfgggggggg\n-@HWI-EAS210R_0001:4:10:890:1284#0/1\n-AAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA\n-+HWI-EAS210R_0001:4:10:890:1284#0/1\n-gggggggggggggggggggggggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:890:208#0/1\n-CAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC\n-+HWI-EAS210R_0001:4:10:890:208#0/1\n-gggeggggggggggggggggggggggggggggddgggg\n-@HWI-EAS210R_0001:4:10:890:859#0/1\n-CAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGC\n-+HWI-EAS210R_0001:4:10:890:859#0/1\n-ggggcgggggggggggdgfggggggggfggggghgggh\n-@HWI-EAS210R_0001:4:10:890:1947#0/1\n-TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGAT\n-+HWI-EAS210R_0001:4:10:890:1947#0/1\n-ggggggggggggggggggeggggggggggggfgfgggg\n-@HWI-EAS210R_0001:4:10:890:416#0/1\n-AATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTG\n-+HWI-EAS210R_0001:4:10:890:416#0/1\n-eggggggggggdcgggggfggfgggggfcgfggggggg\n-@HWI-EAS210R_0001:4:10:890:654#0/1\n-GCAGCAAGGTCCATATCTGACTTTTTGTTAACGTATTT\n-+HWI-EAS210R_0001:4:10:890:654#0/1\n-ggggghggggghggggghgfggggfgdfffgggggggg\n-@HWI-EAS210R_0001:4:10:890:269#0/1\n-CTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGG\n-+HWI-EAS210R_0001:4:10:890:269#0/1\n-eecaadggggggggggggggggdgg\\ffffgggggggg\n-@HWI-EAS210R_0001:4:10:890:657#0/1\n-TACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGG\n-+HWI-EAS210R_0001:4:10:890:657#0/1\n-ggggghggggffgggfggggggfggfggggfffgfggg\n-@HWI-EAS210R_0001:4:10:890:1449#0/1\n-TTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTA\n-+HWI-EAS210R_0001:4:10:890:1449#0/1\n-ggggggggggggggggfgggghgggggggggggghhfh\n-@HWI-EAS210R_0001:4:10:890:305#0/1\n-CACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATA\n-+HWI-EAS210R_0001:4:10:890:305#0/1\n-gggegggfgggfggggggdgggdggfgffggggggfhg\n-@HWI-EAS210R_0001:4:10:890:1190#0/1\n-AATAAGCAATGACGGCAGCAATAAACTCAACAGGAGCA\n-+HWI-EAS210R_0001:4:10:890:1190#0/1\n-bbecb_gggggggggggggggggggcgggfVgggeggg\n-@HWI-EAS210R_0001:4:10:890:1586#0/1\n-ATTAGCTGTACCATACTCAGGCACACAAAAATACTGAT\n-+HWI-EAS210R_0001:4:10:890:1586#0/1\n-eggWgaa^O[\\`[\\_]J_^][`W`\\]K^BBBBBBBBBB\n-@HWI-EAS210R_0001:4:10:890:617#0/1\n-AAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGG\n-+HWI-EAS210R_0001:4:10:890:617#0/1\n-gggggggggggggggggggggggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:890:1562#0/1\n-GTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATC\n-+HWI-EAS210R_0001:4:10:890:1562#0/1\n-hggffggggdgggggaageef`Waegggbgggcgddgg\n-@H'..b'ggggggggggggggggggggggggfggggg\n-@HWI-EAS210R_0001:4:10:890:287#0/1\n-GTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCA\n-+HWI-EAS210R_0001:4:10:890:287#0/1\n-ggggggfcggggg^fbe``egggggggdgg`dddfggg\n-@HWI-EAS210R_0001:4:10:890:335#0/1\n-AAGAGGTTTTACCTCCAAATGAAGAAATAACATCATGG\n-+HWI-EAS210R_0001:4:10:890:335#0/1\n-`^_``Q[cccggfgggggggbddg\\dXdbegggddfg`\n-@HWI-EAS210R_0001:4:10:891:149#0/1\n-TTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAG\n-+HWI-EAS210R_0001:4:10:891:149#0/1\n-ggggghgggggghggggggggggggfgggggggffggg\n-@HWI-EAS210R_0001:4:10:891:445#0/1\n-ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACT\n-+HWI-EAS210R_0001:4:10:891:445#0/1\n-gggggggddggggggggggggggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:891:1476#0/1\n-GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCG\n-+HWI-EAS210R_0001:4:10:891:1476#0/1\n-ggegggffghhggfhggfgeggffgggffggagfggfg\n-@HWI-EAS210R_0001:4:10:891:323#0/1\n-TGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGT\n-+HWI-EAS210R_0001:4:10:891:323#0/1\n-gggcgfefghgggghgfgfgggggggggegaaeeagge\n-@HWI-EAS210R_0001:4:10:891:69#0/1\n-CTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTAC\n-+HWI-EAS210R_0001:4:10:891:69#0/1\n-gggefgggfgafP_Vdbacbgegebd`fbaeggaggQd\n-@HWI-EAS210R_0001:4:10:891:1379#0/1\n-GACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAAT\n-+HWI-EAS210R_0001:4:10:891:1379#0/1\n-gggggggggggggggggggggggggggggfgefggggg\n-@HWI-EAS210R_0001:4:10:891:608#0/1\n-CTTATGCTAATTTGCATACTGACCAAGAACGTGATTAC\n-+HWI-EAS210R_0001:4:10:891:608#0/1\n-ggggggggggggggggggggggggfggggggggggggg\n-@HWI-EAS210R_0001:4:10:891:1831#0/1\n-GTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTA\n-+HWI-EAS210R_0001:4:10:891:1831#0/1\n-ggggggggggggggggghggggggggghgggggfgggg\n-@HWI-EAS210R_0001:4:10:891:412#0/1\n-TAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACG\n-+HWI-EAS210R_0001:4:10:891:412#0/1\n-gggggggggggggggggggggggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:891:346#0/1\n-AATTCATCCATTAACTTCTCATCAACATATACAAACTC\n-+HWI-EAS210R_0001:4:10:891:346#0/1\n-^W][_b^be_cRgaggdgdgbL_^_\\ZN\\R]]`W]cYe\n-@HWI-EAS210R_0001:4:10:891:174#0/1\n-AGTGGAGGCCTCCAGCAATCTTGAACACTCATCCTTAA\n-+HWI-EAS210R_0001:4:10:891:174#0/1\n-ggggggggggggggggggggggcgggggfgggghghcg\n-@HWI-EAS210R_0001:4:10:891:1415#0/1\n-ACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATC\n-+HWI-EAS210R_0001:4:10:891:1415#0/1\n-gggggggggggdghgggggggggggggggggggggggg\n-@HWI-EAS210R_0001:4:10:891:705#0/1\n-TTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTC\n-+HWI-EAS210R_0001:4:10:891:705#0/1\n-gfgggggggggfgggggggggggfgddgggggggeggg\n-@HWI-EAS210R_0001:4:10:891:1398#0/1\n-GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAA\n-+HWI-EAS210R_0001:4:10:891:1398#0/1\n-ebehggdhdfgffdda`e\\ecgfggedgegeggdfdfg\n-@HWI-EAS210R_0001:4:10:891:971#0/1\n-TAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCCAC\n-+HWI-EAS210R_0001:4:10:891:971#0/1\n-ggfgggghggggggfggfgghggfggggfghggffghg\n-@HWI-EAS210R_0001:4:10:891:627#0/1\n-GTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAA\n-+HWI-EAS210R_0001:4:10:891:627#0/1\n-dfdffaeaaagggg[bgggghgghgggfgg\\efefggd\n-@HWI-EAS210R_0001:4:10:891:1822#0/1\n-GAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCA\n-+HWI-EAS210R_0001:4:10:891:1822#0/1\n-gggeggfggegggggdggggghgfgedgggggcfgdcg\n-@HWI-EAS210R_0001:4:10:891:1103#0/1\n-AAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGA\n-+HWI-EAS210R_0001:4:10:891:1103#0/1\n-ggeggfggggggggghggggggggggfffgdggggggb\n-@HWI-EAS210R_0001:4:10:891:586#0/1\n-TATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC\n-+HWI-EAS210R_0001:4:10:891:586#0/1\n-ggggggggggggegfgggfcgggggffggggggggggg\n-@HWI-EAS210R_0001:4:10:891:1620#0/1\n-TTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCT\n-+HWI-EAS210R_0001:4:10:891:1620#0/1\n-gggggfggggghgggggghcgggdgggegggefgfT``\n-@HWI-EAS210R_0001:4:10:891:42#0/1\n-CTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTA\n-+HWI-EAS210R_0001:4:10:891:42#0/1\n-ggefggggggfggggfaf_fggggdfggggfaYbfd]b\n-@HWI-EAS210R_0001:4:10:891:1609#0/1\n-GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCATC\n-+HWI-EAS210R_0001:4:10:891:1609#0/1\n-gggghgggghfgghgggggfffggggcgggfdggfggf\n-@HWI-EAS210R_0001:4:10:891:1028#0/1\n-AATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAAT\n-+HWI-EAS210R_0001:4:10:891:1028#0/1\n-gfgggggggdgbggfgegeeggggggggdggegggddg\n-@HWI-EAS210R_0001:4:10:891:902#0/1\n-ATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCG\n-+HWI-EAS210R_0001:4:10:891:902#0/1\n-ggggggfgggggggggggggggggfddggggggggggg\n' |
| b |
| diff -r a54de7e658f7 -r c1ec08cb34f9 tool_dependencies.xml --- a/tool_dependencies.xml Wed Mar 05 11:26:50 2014 -0500 +++ b/tool_dependencies.xml Fri Dec 12 11:12:27 2014 -0500 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="bowtie2" version="2.1.0"> - <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="bowtie2" version="2.2.4"> + <repository changeset_revision="2b25b6e8d108" name="package_bowtie_2_2_4" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |