| Previous changeset 5:f11ff7be8c78 (2015-04-15) Next changeset 7:8352713cf939 (2016-01-25) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty |
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modified:
test-data/bwa-mem-fastq1.fq test-data/paired_collection_example_pair1_results3.fastqsanger test-data/paired_collection_example_pair2_results3.fastqsanger test-data/paired_collection_example_results3.txt test-data/paired_collection_example_unpair1_results3.fastqsanger test-data/paired_example_pair1_results2.fastqsanger test-data/paired_example_pair2_results2.fastqsanger test-data/paired_example_results2.txt test-data/sanger_full_range_report_results1.txt test-data/sanger_full_range_results2.fastqsanger trim_galore |
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added:
test-data/sanger_full_range_results3.fastqsanger trim_galore.xml |
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removed:
test-data/sanger_full_range_report_results2.txt trim_galore_wrapper.xml |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/bwa-mem-fastq1.fq --- a/test-data/bwa-mem-fastq1.fq Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/bwa-mem-fastq1.fq Wed Oct 07 08:39:59 2015 -0400 |
| b |
| @@ -394,7 +394,3 @@ TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC + CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0 -@M01368:8:000000000-A3GHV:1:1114:9184:6959/1 -GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA -+ -AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF/ |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/paired_collection_example_pair1_results3.fastqsanger --- a/test-data/paired_collection_example_pair1_results3.fastqsanger Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_collection_example_pair1_results3.fastqsanger Wed Oct 07 08:39:59 2015 -0400 |
| b |
| b'@@ -3,9 +3,9 @@\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-GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTAC\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTA\n +\n-CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FF\n @M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGG\n +\n@@ -19,29 +19,29 @@\n +\n ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF\n @M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n-CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTAT\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+>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/\n @M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n-CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACAC\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATT\n +\n-ABBBBFFFFFFFGGGGGGGCGGGHHHHHGHHHHHHHHHGHHHHHHHHHHHGHHHHHGGGGGHGHHHHHHHHHHHHHBGFHHHHGHGHGGHGGGCGGGHHHGGGGGGGHHHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFEDBDFFFFFFFEFFFE0F0FBFFFF0FFFFFFFFFFFFFFFFF\n+ABBBBFFFFFFFGGGGGGGCGGGHHHHHGHHHHHHHHHGHHHHHHHHHHHGHHHHHGGGGGHGHHHHHHHHHHHHHBGFHHHHGHGHGGHGGGCGGGHHHGGGGGGGHHHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFEDBDFFFFFFFEFFFE0F0FBFFFF0FF\n @M01368:8'..b'B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0<FFDGGCC?FF221<BDD11@<11@DDCGEF1<111F1<F1FBGHGHCF-CHHFA./</0CGHF<0CC/;C-:-;;09;FFBFBBFFBC0FFFGGFC0009C00090/-:--9--;-;AFFE;/99\n+AA>1>11F1D1DDFFFFGGG1FH3GHGHGHGHFHEC?EC0B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0<FFDGGCC?FF221<BDD11@<11@DDCGEF1<111F1<F1FBGHGHCF-CHHFA./</0CGHF<0CC/;C-:-;;09;FFBFBB\n @M01368:8:000000000-A3GHV:1:1113:25528:14016/1\n CCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGG\n +\n@@ -371,9 +371,9 @@\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-CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCA\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGAT\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./\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9\n @M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTT\n +\n@@ -387,10 +387,6 @@\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-TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACAT\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCAT\n +\n-CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF\n-@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n-GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTT\n-+\n-AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFF\n' |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/paired_collection_example_pair2_results3.fastqsanger --- a/test-data/paired_collection_example_pair2_results3.fastqsanger Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_collection_example_pair2_results3.fastqsanger Wed Oct 07 08:39:59 2015 -0400 |
| b |
| b'@@ -1,7 +1,7 @@\n @M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n-CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAAT\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA\n +\n-CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFB\n+CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF\n @M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n +\n@@ -15,37 +15,37 @@\n +\n CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA\n @M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n-TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCT\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCAC\n +\n-BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF\n+BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEF\n @M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n-GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCC\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACC\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+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////;///:\n @M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n-AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGT'..b'AATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCC\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGC\n +\n-CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA\n+CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:B\n @M01368:8:000000000-A3GHV:1:1114:15066:16302/2\n-TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAAT\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAG\n +\n-CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;\n @M01368:8:000000000-A3GHV:1:1114:16639:15258/2\n TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n +\n CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF\n @M01368:8:000000000-A3GHV:1:1114:2404:13066/2\n-ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACAT\n+ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGA\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-AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTT\n-+\n-CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B\n+CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFF\n' |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/paired_collection_example_results3.txt --- a/test-data/paired_collection_example_results3.txt Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_collection_example_results3.txt Wed Oct 07 08:39:59 2015 -0400 |
| b |
| @@ -3,84 +3,168 @@ ========================== Input filename: ./input_mate1 Trimming mode: paired-end -Trim Galore version: 0.3.7 +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Length cut-off for read 1: 35 bp (default) +Length cut-off for read 2: 35 bp (default) -cutadapt version 1.1 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1 -Maximum error rate: 10.00% - Processed reads: 100 - Trimmed reads: 20 ( 20.0%) - Total basepairs: 24894 (0.0 Mbp) - Trimmed basepairs: 26 (0.0 Mbp) (0.10% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.00 s - Time per read: 0.03 ms +This is cutadapt 1.8 with Python 2.7.9 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1 +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 99 +Reads with adapters: 52 (52.5%) +Reads written (passing filters): 99 (100.0%) + +Total basepairs processed: 24,849 bp +Quality-trimmed: 205 bp (0.8%) +Total written (filtered): 23,339 bp (93.9%) === Adapter 1 === -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times. +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 9.6% + C: 38.5% + G: 23.1% + T: 28.8% + none/other: 0.0% -Lengths of removed sequences -length count expected -1 16 25.0 -2 2 6.2 -3 2 1.6 +Overview of removed sequences +length count expect max.err error counts +1 11 24.8 0 11 +2 5 6.2 0 5 +3 3 1.5 0 3 +4 3 0.4 0 3 +12 1 0.0 1 1 +13 2 0.0 1 2 +14 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 0 1 +20 2 0.0 1 2 +21 1 0.0 1 1 +24 1 0.0 1 1 +26 2 0.0 1 2 +31 1 0.0 1 1 +33 1 0.0 1 1 +41 2 0.0 1 2 +49 1 0.0 1 1 +50 1 0.0 1 1 +54 1 0.0 1 1 +56 1 0.0 1 1 +58 2 0.0 1 2 +60 1 0.0 1 1 +67 2 0.0 1 2 +68 1 0.0 1 1 +69 1 0.0 1 1 +73 1 0.0 1 1 +80 1 0.0 1 1 +86 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: ./input_mate1 ============================================= -100 sequences processed in total +99 sequences processed in total SUMMARISING RUN PARAMETERS ========================== Input filename: ./input_mate2 Trimming mode: paired-end -Trim Galore version: 0.3.7 +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Length cut-off for read 1: 35 bp (default) +Length cut-off for read 2: 35 bp (default) -cutadapt version 1.1 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate2 -Maximum error rate: 10.00% - Processed reads: 100 - Trimmed reads: 24 ( 24.0%) - Total basepairs: 24354 (0.0 Mbp) - Trimmed basepairs: 36 (0.0 Mbp) (0.15% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.01 s - Time per read: 0.10 ms +This is cutadapt 1.8 with Python 2.7.9 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2 +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 100 +Reads with adapters: 59 (59.0%) +Reads written (passing filters): 100 (100.0%) + +Total basepairs processed: 25,100 bp +Quality-trimmed: 746 bp (3.0%) +Total written (filtered): 23,276 bp (92.7%) === Adapter 1 === -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times. +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 11.9% + C: 39.0% + G: 8.5% + T: 40.7% + none/other: 0.0% -Lengths of removed sequences -length count expected -1 15 25.0 -2 7 6.2 -3 1 1.6 -4 1 0.4 +Overview of removed sequences +length count expect max.err error counts +1 16 25.0 0 16 +2 7 6.2 0 7 +3 1 1.6 0 1 +4 2 0.4 0 2 +6 2 0.0 0 2 +9 2 0.0 0 2 +10 1 0.0 1 1 +13 1 0.0 1 1 +14 2 0.0 1 2 +15 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 1 +19 2 0.0 1 2 +21 1 0.0 1 1 +25 1 0.0 1 1 +30 1 0.0 1 1 +32 2 0.0 1 2 +34 1 0.0 1 1 +36 2 0.0 1 2 +38 1 0.0 1 1 +40 1 0.0 1 1 +41 1 0.0 1 1 +42 1 0.0 1 1 +43 1 0.0 1 1 +49 1 0.0 1 1 +51 1 0.0 1 1 +56 1 0.0 1 1 +57 1 0.0 1 1 +60 1 0.0 1 1 +67 1 0.0 1 1 +80 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: ./input_mate2 ============================================= 100 sequences processed in total -Total number of sequences analysed for the sequence pair length validation: 100 +Total number of sequences analysed for the sequence pair length validation: 99 -Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.00%) +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/paired_collection_example_unpair1_results3.fastqsanger --- a/test-data/paired_collection_example_unpair1_results3.fastqsanger Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_collection_example_unpair1_results3.fastqsanger Wed Oct 07 08:39:59 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +@M01368:8:000000000-A3GHV:1:1101:6911:8255/1 +ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT ++ +BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/paired_example_pair1_results2.fastqsanger --- a/test-data/paired_example_pair1_results2.fastqsanger Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_example_pair1_results2.fastqsanger Wed Oct 07 08:39:59 2015 -0400 |
| b |
| b'@@ -3,9 +3,9 @@\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-GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTAC\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTA\n +\n-CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FF\n @M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGG\n +\n@@ -19,29 +19,29 @@\n +\n ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF\n @M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n-CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTAT\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+>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/\n @M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n-CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACAC\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATT\n +\n-ABBBBFFFFFFFGGGGGGGCGGGHHHHHGHHHHHHHHHGHHHHHHHHHHHGHHHHHGGGGGHGHHHHHHHHHHHHHBGFHHHHGHGHGGHGGGCGGGHHHGGGGGGGHHHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFEDBDFFFFFFFEFFFE0F0FBFFFF0FFFFFFFFFFFFFFFFF\n+ABBBBFFFFFFFGGGGGGGCGGGHHHHHGHHHHHHHHHGHHHHHHHHHHHGHHHHHGGGGGHGHHHHHHHHHHHHHBGFHHHHGHGHGGHGGGCGGGHHHGGGGGGGHHHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFEDBDFFFFFFFEFFFE0F0FBFFFF0FF\n @M01368:8'..b'B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0<FFDGGCC?FF221<BDD11@<11@DDCGEF1<111F1<F1FBGHGHCF-CHHFA./</0CGHF<0CC/;C-:-;;09;FFBFBBFFBC0FFFGGFC0009C00090/-:--9--;-;AFFE;/99\n+AA>1>11F1D1DDFFFFGGG1FH3GHGHGHGHFHEC?EC0B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0<FFDGGCC?FF221<BDD11@<11@DDCGEF1<111F1<F1FBGHGHCF-CHHFA./</0CGHF<0CC/;C-:-;;09;FFBFBB\n @M01368:8:000000000-A3GHV:1:1113:25528:14016/1\n CCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGG\n +\n@@ -371,9 +371,9 @@\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-CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCA\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGAT\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./\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9\n @M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTT\n +\n@@ -387,10 +387,6 @@\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-TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACAT\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCAT\n +\n-CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF\n-@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n-GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTT\n-+\n-AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFF\n' |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/paired_example_pair2_results2.fastqsanger --- a/test-data/paired_example_pair2_results2.fastqsanger Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_example_pair2_results2.fastqsanger Wed Oct 07 08:39:59 2015 -0400 |
| b |
| b'@@ -1,7 +1,7 @@\n @M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n-CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAAT\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA\n +\n-CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFB\n+CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF\n @M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n +\n@@ -15,37 +15,37 @@\n +\n CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA\n @M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n-TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCT\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCAC\n +\n-BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF\n+BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEF\n @M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n-GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCC\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACC\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+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////;///:\n @M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n-AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGT'..b'AATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCC\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGC\n +\n-CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA\n+CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:B\n @M01368:8:000000000-A3GHV:1:1114:15066:16302/2\n-TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAAT\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAG\n +\n-CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;\n @M01368:8:000000000-A3GHV:1:1114:16639:15258/2\n TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n +\n CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF\n @M01368:8:000000000-A3GHV:1:1114:2404:13066/2\n-ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACAT\n+ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGA\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-AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTT\n-+\n-CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B\n+CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFF\n' |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/paired_example_results2.txt --- a/test-data/paired_example_results2.txt Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_example_results2.txt Wed Oct 07 08:39:59 2015 -0400 |
| b |
| @@ -3,84 +3,164 @@ ========================== Input filename: ./input_mate1 Trimming mode: paired-end -Trim Galore version: 0.3.7 +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -cutadapt version 1.1 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1 -Maximum error rate: 10.00% - Processed reads: 100 - Trimmed reads: 20 ( 20.0%) - Total basepairs: 24894 (0.0 Mbp) - Trimmed basepairs: 26 (0.0 Mbp) (0.10% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.00 s - Time per read: 0.02 ms +This is cutadapt 1.8 with Python 2.7.9 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1 +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 99 +Reads with adapters: 52 (52.5%) +Reads written (passing filters): 99 (100.0%) + +Total basepairs processed: 24,849 bp +Quality-trimmed: 205 bp (0.8%) +Total written (filtered): 23,339 bp (93.9%) === Adapter 1 === -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times. +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 9.6% + C: 38.5% + G: 23.1% + T: 28.8% + none/other: 0.0% -Lengths of removed sequences -length count expected -1 16 25.0 -2 2 6.2 -3 2 1.6 +Overview of removed sequences +length count expect max.err error counts +1 11 24.8 0 11 +2 5 6.2 0 5 +3 3 1.5 0 3 +4 3 0.4 0 3 +12 1 0.0 1 1 +13 2 0.0 1 2 +14 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 0 1 +20 2 0.0 1 2 +21 1 0.0 1 1 +24 1 0.0 1 1 +26 2 0.0 1 2 +31 1 0.0 1 1 +33 1 0.0 1 1 +41 2 0.0 1 2 +49 1 0.0 1 1 +50 1 0.0 1 1 +54 1 0.0 1 1 +56 1 0.0 1 1 +58 2 0.0 1 2 +60 1 0.0 1 1 +67 2 0.0 1 2 +68 1 0.0 1 1 +69 1 0.0 1 1 +73 1 0.0 1 1 +80 1 0.0 1 1 +86 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: ./input_mate1 ============================================= -100 sequences processed in total +99 sequences processed in total SUMMARISING RUN PARAMETERS ========================== Input filename: ./input_mate2 Trimming mode: paired-end -Trim Galore version: 0.3.7 +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -cutadapt version 1.1 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate2 -Maximum error rate: 10.00% - Processed reads: 100 - Trimmed reads: 24 ( 24.0%) - Total basepairs: 24354 (0.0 Mbp) - Trimmed basepairs: 36 (0.0 Mbp) (0.15% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.01 s - Time per read: 0.12 ms +This is cutadapt 1.8 with Python 2.7.9 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2 +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 100 +Reads with adapters: 59 (59.0%) +Reads written (passing filters): 100 (100.0%) + +Total basepairs processed: 25,100 bp +Quality-trimmed: 746 bp (3.0%) +Total written (filtered): 23,276 bp (92.7%) === Adapter 1 === -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times. +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 11.9% + C: 39.0% + G: 8.5% + T: 40.7% + none/other: 0.0% -Lengths of removed sequences -length count expected -1 15 25.0 -2 7 6.2 -3 1 1.6 -4 1 0.4 +Overview of removed sequences +length count expect max.err error counts +1 16 25.0 0 16 +2 7 6.2 0 7 +3 1 1.6 0 1 +4 2 0.4 0 2 +6 2 0.0 0 2 +9 2 0.0 0 2 +10 1 0.0 1 1 +13 1 0.0 1 1 +14 2 0.0 1 2 +15 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 1 +19 2 0.0 1 2 +21 1 0.0 1 1 +25 1 0.0 1 1 +30 1 0.0 1 1 +32 2 0.0 1 2 +34 1 0.0 1 1 +36 2 0.0 1 2 +38 1 0.0 1 1 +40 1 0.0 1 1 +41 1 0.0 1 1 +42 1 0.0 1 1 +43 1 0.0 1 1 +49 1 0.0 1 1 +51 1 0.0 1 1 +56 1 0.0 1 1 +57 1 0.0 1 1 +60 1 0.0 1 1 +67 1 0.0 1 1 +80 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: ./input_mate2 ============================================= 100 sequences processed in total -Total number of sequences analysed for the sequence pair length validation: 100 +Total number of sequences analysed for the sequence pair length validation: 99 -Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.00%) +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/sanger_full_range_report_results1.txt --- a/test-data/sanger_full_range_report_results1.txt Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/sanger_full_range_report_results1.txt Wed Oct 07 08:39:59 2015 -0400 |
| b |
| @@ -3,34 +3,48 @@ ========================== Input filename: ./input_singles Trimming mode: single-end -Trim Galore version: 0.3.7 +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp -cutadapt version 1.1 +This is cutadapt 1.8 with Python 2.7.9 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_singles -Maximum error rate: 10.00% - Processed reads: 2 - Trimmed reads: 1 ( 50.0%) - Total basepairs: 168 (0.0 Mbp) - Trimmed basepairs: 1 (0.0 Mbp) (0.60% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.00 s - Time per read: 0.32 ms +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (50000 us/read; 0.00 M reads/minute). + +=== Summary === + +Total reads processed: 2 +Reads with adapters: 1 (50.0%) +Reads written (passing filters): 2 (100.0%) + +Total basepairs processed: 188 bp +Quality-trimmed: 20 bp (10.6%) +Total written (filtered): 167 bp (88.8%) === Adapter 1 === -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 1 times. +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 -Lengths of removed sequences -length count expected -1 1 0.5 +Bases preceding removed adapters: + A: 0.0% + C: 100.0% + G: 0.0% + T: 0.0% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 1 0.5 0 1 RUN STATISTICS FOR INPUT FILE: ./input_singles |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/sanger_full_range_report_results2.txt --- a/test-data/sanger_full_range_report_results2.txt Wed Apr 15 17:31:52 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,40 +0,0 @@ - -SUMMARISING RUN PARAMETERS -========================== -Input filename: ./input_mate1 -Quality Phred score cutoff: 20 -Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' -Maximum trimming error rate: 0.1 (default) -Minimum required adapter overlap (stringency): 1 bp -Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp - - -cutadapt version 1.1 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1 -Maximum error rate: 10.00% - Processed reads: 100 - Trimmed reads: 20 ( 20.0%) - Total basepairs: 24894 (0.0 Mbp) - Trimmed basepairs: 26 (0.0 Mbp) (0.10% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.01 s - Time per read: 0.05 ms - -=== Adapter 1 === - -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times. - -Lengths of removed sequences -length count expected -1 16 25.0 -2 2 6.2 -3 2 1.6 - - -RUN STATISTICS FOR INPUT FILE: ./input_mate1 -============================================= -100 sequences processed in total -Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%) - |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/sanger_full_range_results2.fastqsanger --- a/test-data/sanger_full_range_results2.fastqsanger Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/sanger_full_range_results2.fastqsanger Wed Oct 07 08:39:59 2015 -0400 |
| [ |
| b'@@ -1,396 +1,8 @@\n-@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n-GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTG\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-GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTAC\n-+\n-CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF\n-@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n-ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGG\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-ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTT\n-+\n-ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF\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-CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACAC\n-+\n-ABBBBFFFFFFFGGGGGGGCGGGHHHHHGHHHHHHHHHGHHHHHHHHHHHGHHHHHGGGGGHGHHHHHHHHHHHHHBGFHHHHGHGHGGHGGGCGGGHHHGGGGGGGHHHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFEDBDFFFFFFFEFFFE0F0FBFFFF0FFFFFFFFFFFFFFFFF\n-@M01368:8:000000000-A3GHV:1:1102:13809:1733/1\n-ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGA'..b'?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n-@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n-TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTAT\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-CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCA\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./\n-@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n-CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTT\n-+\n-AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE\n-@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n-TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATT\n-+\n-BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;\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-TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACAT\n-+\n-CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF\n-@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n-GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTT\n-+\n-AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF\n+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876\n' |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 test-data/sanger_full_range_results3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_results3.fastqsanger Wed Oct 07 08:39:59 2015 -0400 |
| [ |
| @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876 |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 trim_galore --- a/trim_galore Wed Apr 15 17:31:52 2015 -0400 +++ b/trim_galore Wed Oct 07 08:39:59 2015 -0400 |
| [ |
| b'@@ -23,33 +23,146 @@\n ## along with this program. If not, see <http://www.gnu.org/licenses/>.\n \n \n+## this script is taking in FastQ sequences and trims them using Cutadapt\n \n-## this script is taking in FastQ sequences and trims them with Cutadapt\n+## last modified on 01 May 2015\n+\n+my $DOWARN = 1; # print on screen warning and text by default\n+BEGIN { $SIG{\'__WARN__\'} = sub { warn $_[0] if $DOWARN } };\n+\n+my $trimmer_version = \'0.4.0\';\n+\n+\n+my ($cutoff,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$a2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2,$three_prime_clip_r1,$three_prime_clip_r2,$nextera,$small_rna,$path_to_cutadapt,$illumina) = process_commandline();\n+\n+my @filenames = @ARGV;\n+die "\\nPlease provide the filename(s) of one or more FastQ file(s) to launch Trim Galore!\\n\n+USAGE: \'trim_galore [options] <filename(s)>\' or \'trim_galore --help\' for more options\\n\\n" unless (@filenames);\n+file_sanity_check($filenames[0]);\n+\n+\n+########################################################################\n+\n+my $path_to_fastqc = \'fastqc\';\n \n-## last modified on 16 July 2014\n+# Before we start let\'s have quick look if Cutadapt seems to be working with the path information provided\n+# To change the path to Cutadapt use --path_to_cutadapt /full/path/to/the/Cutadapt/executable\n \n+if(defined $path_to_cutadapt){\n+ warn "Path to Cutadapt set as: \'$path_to_cutadapt\' (user defined)\\n";\n+ # we\'ll simply use this\n+}\n+else{\n+ $path_to_cutadapt = \'cutadapt\'; # default, assuming it is in the PATH\n+ warn "Path to Cutadapt set as: \'$path_to_cutadapt\' (default)\\n";\n+}\n+my $cutadapt_version;\n+my $return = system "$path_to_cutadapt --version"; #>/dev/null 2>&1";\n+if ($return == -1){\n+ die "Failed to execute Cutadapt porperly. Please install Cutadapt first and make sure it is in the PATH, or specify the path to the Cutadapt executable using --path_to_cutadapt /path/to/cutadapt\\n\\n";\n+}\n+else{\n+ warn "Cutadapt seems to be working fine (tested command \'$path_to_cutadapt --version\')\\n";\n+ $cutadapt_version = `$path_to_cutadapt --version`;\n+ chomp $cutadapt_version;\n+ # warn "Cutadapt version: $cutadapt_version\\n";\n+}\n \n \n ########################################################################\n \n-# change these paths if needed\n+sub autodetect_adapter_type{\n+ warn "\\n\\nAUTO-DETECTING ADAPTER TYPE\\n===========================\\n";\n+ warn "Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> $ARGV[0] <<)\\n\\n";\n \n-my $path_to_cutadapt = \'cutadapt\';\n-my $path_to_fastqc = \'fastqc\';\n-\n-########################################################################\n+ if ($ARGV[0] =~ /gz$/){\n+ open (AUTODETECT,"zcat $ARGV[0] |") or die "Failed to read from file $ARGV[0]\\n";\n+ }\n+ else{\n+ open (AUTODETECT,$ARGV[0]) or die "Failed to read from file $ARGV[0]\\n";\n+ }\n \n-my $trimmer_version = \'0.3.7\';\n-my $DOWARN = 1; # print on screen warning and text by default\n-BEGIN { $SIG{\'__WARN__\'} = sub { warn $_[0] if $DOWARN } };\n+ my %adapters;\n+\n+ $adapters{\'Illumina\'} -> {seq} = \'AGATCGGAAGAGC\';\n+ $adapters{\'Illumina\'} -> {count}= 0;\n+ $adapters{\'Illumina\'} -> {name}= \'Illumina TruSeq, Sanger iPCR; auto-detected\';\n \n-my ($cutoff,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$a2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2,$three_prime_clip_r1,$three_prime_clip_r2) = process_commandline();\n+ $adapters{\'Nextera\'} -> {seq} = \'CTGTCTCTTATA\';\n+ $adapters{\'Nextera\'} -> {count}= 0;\n+ $adapters{\'Nextera\'} -> {name}= \'Nextera Transposase sequence; auto-detected\';\n \n-my @filenames = @ARGV;\n+ $adapters{\'smallRNA\'} -> {seq} = \'ATGGAATTCTCG\';\n+ $adapters{\'smallRNA\'} -> {count}= 0;\n+ $adapters{\'smallRNA\'} -> {name}= \'Illumina smal'..b"lidate,$retain,$length_read_1,$length_read_2,$adapter2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2,$three_prime_clip_r1,$three_prime_clip_r2);\n+ return ($quality,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$adapter2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2,$three_prime_clip_r1,$three_prime_clip_r2,$nextera,$small_rna,$path_to_cutadapt,$illumina);\n }\n \n \n@@ -1284,12 +1462,24 @@\n automatically invoke FastQC, so --fastqc does not have to be specified\n separately.\n \n--a/--adapter <STRING> Adapter sequence to be trimmed. If not specified explicitely, the first 13\n- bp of the Illumina adapter 'AGATCGGAAGAGC' will be used by default.\n+-a/--adapter <STRING> Adapter sequence to be trimmed. If not specified explicitly, Trim Galore will\n+ try to auto-detect whether the Illumina universal, Nextera transposase or Illumina\n+ small RNA adapter sequence was used. Also see '--illumina', '--nextera' and\n+ '--small_rna'. If no adapter can be detected within the first 1 million sequences\n+ of the first file specified Trim Galore defaults to '--illumina'.\n \n -a2/--adapter2 <STRING> Optional adapter sequence to be trimmed off read 2 of paired-end files. This\n option requires '--paired' to be specified as well.\n \n+--illumina Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter\n+ 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.\n+\n+--nextera Adapter sequence to be trimmed is the first 12bp of the Nextera adapter\n+ 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.\n+\n+--small_rna Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA Adapter\n+ 'ATGGAATTCTCG' instead of the default auto-detection of adapter sequence.\n+\n \n --stringency <INT> Overlap with adapter sequence required to trim a sequence. Defaults to a\n very stringent setting of 1, i.e. even a single bp of overlapping sequence\n@@ -1331,16 +1521,20 @@\n methylation. Please refer to the M-bias plot section in the Bismark User Guide for\n some examples. Default: OFF.\n \n---three_prime_clip_R1 <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end\n+--three_prime_clip_R1 <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end\n reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted\n bias from the 3' end that is not directly related to adapter sequence or basecall quality.\n Default: OFF.\n \n---three_prime_clip_R2 <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 2 AFTER\n+--three_prime_clip_R2 <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 2 AFTER\n adapter/quality trimming has been performed. This may remove some unwanted bias from\n the 3' end that is not directly related to adapter sequence or basecall quality.\n Default: OFF.\n \n+--path_to_cutadapt </path/to/cutadapt> You may use this option to specify a path to the Cutadapt executable,\n+ e.g. /my/home/cutadapt-1.7.1/bin/cutadapt. Else it is assumed that Cutadapt is in\n+ the PATH.\n+\n \n RRBS-specific options (MspI digested material):\n \n@@ -1408,7 +1602,7 @@\n Default: 35 bp.\n \n \n-Last modified on 16 July 2014.\n+Last modified on 06 May 2015.\n \n HELP\n exit;\n" |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 trim_galore.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trim_galore.xml Wed Oct 07 08:39:59 2015 -0400 |
| [ |
| b'@@ -0,0 +1,372 @@\n+<tool id="trim_galore" name="Trim Galore!" version="0.4.0">\n+ <!-- Wrapper compatible with Trim Galore! version 0.4 -->\n+ <description>adaptive quality and adapter trimmer</description>\n+ <macros>\n+ <macro name="adapter_trimming">\n+ <conditional name="trimming">\n+ <param name="trimming_select" type="select" label="Trimming reads?">\n+ <option value="">Automatic detection</option>\n+ <option value="--illumina">Illumina universal</option>\n+ <option value="--nextera">Nextera transposase</option>\n+ <option value="--small_rna">Illumina small RNA adapters</option>\n+ <option value="user">User defined adapter trimming</option>\n+ </param>\n+ <when value="auto"/>\n+ <when value="--illumina"/>\n+ <when value="--nextera"/>\n+ <when value="--small_rna"/>\n+ <when value="user">\n+ <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">\n+ <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n+ </param>\n+ <yield/>\n+ </when>\n+ </conditional>\n+ </macro>\n+ <macro name="paired_adapter_trimming">\n+\n+ <expand macro="adapter_trimming">\n+ <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">\n+ <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n+ </param>\n+ </expand>\n+ <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3\' end." help="" />\n+ <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n+ <help>Instructs Trim Galore! to remove N bp from the 3\' end of read 1 after adapter/quality trimming has been performed.\n+ This may remove some unwanted bias from the 3\' end that is not directly related to adapter sequence or basecall quality.\n+ (--three_prime_clip_R1)</help>\n+ </param>\n+ <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n+ <help>Instructs Trim Galore! to remove N bp from the 3\' end of read 2 after\n+ adapter/quality trimming has been performed. This may remove some unwanted bias from\n+ the 3\' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help>\n+ </param>\n+ </macro>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="1.8">cutadapt</requirement>\n+ </requirements>\n+ <version_command interpreter="perl">trim_galore --version</version_command>\n+ <command>\n+<![CDATA[\n+\n+ ## trim_galore removes .fastq and .fq file extensions of input files.\n+ ## This is essential if Galaxy provides links to files (with real extensions)\n+ ## but that behaviour is causing an inconsistency in output filenaming.\n+ ## We work around this by linking every file to cwd without file extension\n+\n+ #if $singlePaired.sPaired == "single":\n+ ln -s "${singlePaired.input_singles}" ./input_singles;\n+ #elif $singlePaired.sPaired == "paired":\n+ ln -s "${singlePaired.input_mate1}" ./input_mate1;\n+ ln -s "${singlePaired.input_mate2}" ./input_mate2;\n+ #else:\n+ ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1;\n+ ln -s "${singlePaired.input_mate_'..b' <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ <param name="sPaired" value="paired" />\n+ <param name="settingsType" value="custom" />\n+ <param name="report" value="true" />\n+ <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>\n+ <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>\n+ <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="8" />\n+ </test>\n+\n+ <test>\n+ <param name="input_mate_pairs">\n+ <collection type="paired">\n+ <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n+ <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ </collection>\n+ </param>\n+\n+ <param name="sPaired" value="paired_collection" />\n+ <param name="settingsType" value="custom" />\n+ <param name="report" value="true" />\n+ <param name="retain_unpaired_select" value="retain_unpaired_output" />\n+\n+ <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="8" />\n+\n+ <output_collection name="trimmed_reads_paired_collection" type="paired">\n+ <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>\n+ <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>\n+ </output_collection>\n+\n+ <output_collection name="trimmed_reads_unpaired_collection" type="paired">\n+ <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>\n+ <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>\n+ </output_collection>\n+\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+**What it does**\n+\n+`Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It\'s main features are:\n+\n+ * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters (\'AGATCGGAAGAGC\') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too\n+ * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation\n+ * For any kind of FASTQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter and quality trimming\n+ * The Phred quality of basecalls and the stringency for adapter removal can be specified individually\n+ * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality\n+ * Trim Galore! can trim paired-end files by 1 additional bp from the 3\' end of all reads to avoid problems with invalid alignments with Bowtie 1\n+\n+.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\n+\n+It is developed by Felix Krueger at the Babraham Institute.\n+]]>\n+ </help>\n+ <citations></citations>\n+</tool>\n' |
| b |
| diff -r f11ff7be8c78 -r 11962ce40855 trim_galore_wrapper.xml --- a/trim_galore_wrapper.xml Wed Apr 15 17:31:52 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,350 +0,0 @@\n-<tool id="trim_galore" name="Trim Galore" version="0.3.7.0">\n- <!-- Wrapper compatible with Trim Galore version 0.3.7 -->\n- <description>adaptive quality and adapter trimmer</description>\n- <version_command interpreter="perl">trim_galore --version</version_command>\n- <requirements>\n- <requirement type="package" version="1.8">cutadapt</requirement>\n- </requirements>\n- <macros>\n- <macro name="paired_adapter_trimming">\n- <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3\' end." help="" />\n- <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off read 1">\n- <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n- </param>\n- <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">\n- <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n- </param>\n-\n- <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n- <help>Instructs Trim Galore to remove N bp from the 3\' end of read 1 after adapter/quality trimming has been performed. \n- This may remove some unwanted bias from the 3\' end that is not directly related to adapter sequence or basecall quality.\n- (--three_prime_clip_R1)</help>\n- </param>\n- <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n- <help>Instructs Trim Galore to remove N bp from the 3\' end of read 2 after\n- adapter/quality trimming has been performed. This may remove some unwanted bias from\n- the 3\' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help>\n- </param>\n- </macro>\n- </macros>\n- <command>\n-<![CDATA[\n-\n- ## trim_galore removes .fastq and .fq file extensions of input files.\n- ## This is essential if Galaxy provides links to files (with real extensions)\n- ## but that behaviour is causing an inconsitency in output filenaming.\n- ## We work around this by linking every file to cwd without file extension\n-\n- #if $singlePaired.sPaired == "single":\n- ln -s "${singlePaired.input_singles}" ./input_singles;\n- #elif $singlePaired.sPaired == "paired":\n- ln -s "${singlePaired.input_mate1}" ./input_mate1;\n- ln -s "${singlePaired.input_mate2}" ./input_mate2;\n- #else:\n- ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1;\n- ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2;\n- #end if\n-\n- perl $__tool_directory__/trim_galore\n-\n- ## we only support fastqsanger\n- --phred33\n-\n- #if $params.settingsType == "custom":\n-\n- ## default 20\n- --quality $params.quality\n-\n- ## default 1\n- --stringency $params.stringency\n-\n- ## default 0.1\n- -e $params.error_rate\n-\n- ## default 20\n- --length $params.min_length\n-\n- #if int($params.clip_R1) > 0:\n- --clip_R1 $params.clip_R1\n- #end if\n-\n- #if int($params.clip_R2) > 0:\n- --clip_R2 $params.clip_R2\n- #end if\n-\n- #if $params.retain_unpaired.settingsType == "retain_unpaired_output":\n- --retain_unpaired\n- --length_1 $params.retain_unpaired.length_1\n- --length_2 $params.retain_unpaired.length_2\n- #end if\n-\n- #end if\n-\n- '..b' <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_val_2.fq"\n- label="${tool.name} on ${on_string}: unpaired reads (2)">\n- <filter>\n- ((\n- params[\'settingsType\'] == "custom" and\n- params[\'retain_unpaired\'][\'settingsType\'] == "retain_unpaired_output" and\n- singlePaired[\'sPaired\'] == "paired"\n- ))\n- </filter>\n- </data>\n-\n- <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">\n- <filter>\n- ((\n- params[\'settingsType\'] == "custom" and\n- params[\'report\'] == True\n- ))\n- </filter>\n- </data>\n-\n- </outputs>\n- <tests>\n- <test>\n- <!-- Trim entire sequences; keep empty reads -->\n- <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n- <param name="sPaired" value="single" />\n- <param name="settingsType" value="custom" />\n- <param name="report" value="true" />\n- <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>\n- <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="2" />\n- </test>\n-\n- <test>\n- <!-- Trim entire sequences; keep empty reads -->\n- <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n- <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n- <param name="sPaired" value="paired" />\n- <param name="settingsType" value="custom" />\n- <param name="report" value="true" />\n- <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>\n- <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>\n- <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="8" />\n- </test>\n-\n- <test>\n- <!-- Trim entire sequences; keep empty reads -->\n- <param name="input_mate_pairs">\n- <collection type="paired">\n- <element name="forward" value="bwa-mem-fastq1.fq" />\n- <element name="reverse" value="bwa-mem-fastq2.fq" />\n- </collection>\n- </param>\n- <param name="sPaired" value="paired_collection" />\n- <param name="settingsType" value="custom" />\n- <param name="report" value="true" />\n- <param name="retain_unpaired" value="retain_unpaired_output" />\n-\n- <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="8" />\n-\n- <output_collection name="trimmed_reads_paired_collection" type="paired">\n- <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>\n- <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>\n- </output_collection>\n-\n- <output_collection name="trimmed_reads_unpaired_collection" type="paired">\n- <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>\n- <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>\n- </output_collection>\n- </test>\n- </tests>\n- <help>\n-<![CDATA[\n-\n-**What it does**\n-\n-TrimGalore_ is a wrapper script that makes use of the publically available\n-adapter trimming tool Cutadapt.\n-\n-.. _TrimGalore: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\n-\n-\n-It is developed by Felix Krueger at the Babraham Institute.\n-\n-\n-]]>\n- </help>\n-</tool>\n' |