| Next changeset 1:8c02a91a8680 (2013-04-30) |
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Commit message:
Uploaded v0.0.8, first public release |
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added:
test-data/primers/MID4_GLZRM4E04_rnd30.fasta test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger test-data/primers/MID4_GLZRM4E04_rnd30.sff test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff test-data/primers/dop_primers.fasta tools/primers/seq_primer_clip.py tools/primers/seq_primer_clip.txt tools/primers/seq_primer_clip.xml |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30.fasta Mon Apr 29 06:11:00 2013 -0400 |
| b |
| b'@@ -0,0 +1,60 @@\n+>GLZRM4E04IPVGX\n+CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT\n+>GLZRM4E04I9EJK\n+CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG\n+>GLZRM4E04JHW0A\n+TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC\n+>GLZRM4E04IBNFY\n+CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG\n+>GLZRM4E04IKCQP\n+CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA\n+>GLZRM4E04ITXFU\n+CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT\n+>GLZRM4E04JAY4Z\n+CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC\n+>GLZRM4E04H9M21\n+CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG\n+>GLZRM4E04IQDP5\n+CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG\n+>GLZRM4E04I0CYE\n+TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT\n+>GLZRM4E04I2NA7\n+CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA\n+>GLZRM4E04I5BWJ\n+CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC\n+>GLZRM4E04IK8WX\n+GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG\n+>GLZRM4E04I22QH\n+CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC\n+>GLZRM4E04IVVFA\n+GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG\n+>GLZRM4E04ILU3V\n+CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG\n+>GLZRM4E04IDVJT\n+CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG\n+>GLZRM4E04I3ZJ6\n+CCGACT'..b'AAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG\n+>GLZRM4E04I3UBT\n+CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA\n+>GLZRM4E04H59S1\n+CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG\n+>GLZRM4E04JFA38\n+CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT\n+>GLZRM4E04J4EK3\n+CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG\n+>GLZRM4E04IK96G\n+CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA\n+>GLZRM4E04JVL8Q\n+CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT\n+>GLZRM4E04IOQ36\n+CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT\n+>GLZRM4E04JBJJ1\n+CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG\n+>GLZRM4E04IEFNO\n+CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA\n+>GLZRM4E04JOT5I\n+CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG\n+>GLZRM4E04J4HNG\n+CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT\n+>GLZRM4E04JC544\n+CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC\n' |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger Mon Apr 29 06:11:00 2013 -0400 |
| b |
| b'@@ -0,0 +1,120 @@\n+@GLZRM4E04IPVGX\n+CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT\n++\n+FIIIIIIIIHHHIDDDIIIIIIIIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1\n+@GLZRM4E04I9EJK\n+CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG\n++\n+IIIIGCBCF=422211:882<<9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII\n+@GLZRM4E04JHW0A\n+TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC\n++\n+IIIIIIIIIF;;;;HFDDEHHHIIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,,\n+@GLZRM4E04IBNFY\n+CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG\n++\n+IIIIIIIIIIIIIIIIIIII666IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII\n+@GLZRM4E04IKCQP\n+CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA\n++\n+IIIIIH???GDGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129\n+@GLZRM4E04ITXFU\n+CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT\n++\n+IIIIGDD===@@3111DD@><<DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7\n+@GLZRM4E04JAY4Z\n+CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC\n++\n+FIIIIIIIIIIHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81\n+@GLZRM4E04H9M21\n+CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG\n++\n+IIIIIIII'..b'AACAGAACAAAATTT\n++\n+../42236,,,9:2116../4---3;666?>:>>44...<:9,,,--17,,,,--,,,,,116?44449@A=<<44440..672222../00998?AAAABB=5333=====<<4466AA981118>@:?444>>===>>;;0...:00000..0@<===;;?:AAAA=36333BAAAAB9;==FFFFFF666EFDDDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGF:::DD?FIGGGGIDDFGDDD??==DD:66DDDGDDDDA???=444=>?88///?000<889?AAAD???DDDDDIDDDIIIDD====D:DBA>>??89//---88:86888==DD???>D>>>D:88888>DDDDBBBDDDD33333DD7777D>>>?33331::,:8875222220444::::/:9:99766622226::::98:5:77600..,,,\n+@GLZRM4E04IOQ36\n+CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT\n++\n+HHHGCD@B?0-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998\n+@GLZRM4E04JBJJ1\n+CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG\n++\n+IIIIIIH?;;;@>IIBD@@EII555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHIIIIIIIIIIIIIII\n+@GLZRM4E04IEFNO\n+CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA\n++\n+IIIIIIIIIIIIIIIIIIIE666EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87\n+@GLZRM4E04JOT5I\n+CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG\n++\n+IIIIIIIII=999E144445CCCIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII\n+@GLZRM4E04J4HNG\n+CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT\n++\n+FFHHHHHHFF888??=A6998><44344888877=:433624\n+@GLZRM4E04JC544\n+CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC\n++\n+IIIIHIHIC4------//<=IIIIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=\n' |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30.sff |
| b |
| Binary file test-data/primers/MID4_GLZRM4E04_rnd30.sff has changed |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta Mon Apr 29 06:11:00 2013 -0400 |
| b |
| @@ -0,0 +1,50 @@ +>GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG +>GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC +>GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG +>GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA +>GLZRM4E04ITXFU +CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT +>GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC +>GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG +>GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG +>GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA +>GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC +>GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC +>GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG +>GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG +>GLZRM4E04I3ZJ6 +ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG +>GLZRM4E04I3UBT +AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA +>GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG +>GLZRM4E04JFA38 +GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT +>GLZRM4E04J4EK3 +TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG +>GLZRM4E04IK96G +TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA +>GLZRM4E04IOQ36 +TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT +>GLZRM4E04JBJJ1 +AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG +>GLZRM4E04IEFNO +GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA +>GLZRM4E04JOT5I +GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG +>GLZRM4E04JC544 +ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger Mon Apr 29 06:11:00 2013 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+@GLZRM4E04IPVGX\n+AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT\n++\n+IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1\n+@GLZRM4E04I9EJK\n+TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG\n++\n+9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII\n+@GLZRM4E04JHW0A\n+AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC\n++\n+IIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,,\n+@GLZRM4E04IBNFY\n+GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG\n++\n+6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII\n+@GLZRM4E04IKCQP\n+GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA\n++\n+DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129\n+@GLZRM4E04ITXFU\n+CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT\n++\n+DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7\n+@GLZRM4E04JAY4Z\n+GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC\n++\n+IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81\n+@GLZRM4E04H9M21\n+CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG\n++\n+;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII\n+@GLZRM4E04IQDP5\n+TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGG'..b'TCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG\n++\n+IHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>><D:8544///5544??C24446<BIIIIIIHH\n+@GLZRM4E04IK96G\n+TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA\n++\n+IIIHHHIIIIIIIIIIHHHIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDCCFFFA?666?=ADDDA??????FFDFFFFFFFFFFFFFF???DBAAA::888444?=<;;96667,.--,,12,\n+@GLZRM4E04IOQ36\n+TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT\n++\n+-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998\n+@GLZRM4E04JBJJ1\n+AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG\n++\n+555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHIIIIIIIIIIIIIII\n+@GLZRM4E04IEFNO\n+GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA\n++\n+6EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87\n+@GLZRM4E04JOT5I\n+GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG\n++\n+CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII\n+@GLZRM4E04JC544\n+ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC\n++\n+IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=\n' |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff |
| b |
| Binary file test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff has changed |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta Mon Apr 29 06:11:00 2013 -0400 |
| b |
| @@ -0,0 +1,50 @@ +>GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG +>GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC +>GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG +>GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA +>GLZRM4E04ITXFU +CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACC +>GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC +>GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG +>GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGG +>GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA +>GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC +>GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC +>GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG +>GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACC +>GLZRM4E04I3ZJ6 +ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG +>GLZRM4E04I3UBT +AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA +>GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG +>GLZRM4E04JFA38 +GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT +>GLZRM4E04J4EK3 +TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG +>GLZRM4E04IK96G +TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA +>GLZRM4E04IOQ36 +TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT +>GLZRM4E04JBJJ1 +AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAG +>GLZRM4E04IEFNO +GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA +>GLZRM4E04JOT5I +GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG +>GLZRM4E04JC544 +ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger Mon Apr 29 06:11:00 2013 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+@GLZRM4E04IPVGX\n+AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT\n++\n+IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1\n+@GLZRM4E04I9EJK\n+TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG\n++\n+9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII\n+@GLZRM4E04JHW0A\n+AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC\n++\n+IIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,,\n+@GLZRM4E04IBNFY\n+GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG\n++\n+6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII\n+@GLZRM4E04IKCQP\n+GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA\n++\n+DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129\n+@GLZRM4E04ITXFU\n+CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACC\n++\n+DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>88\n+@GLZRM4E04JAY4Z\n+GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC\n++\n+IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81\n+@GLZRM4E04H9M21\n+CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG\n++\n+;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII\n+@GLZRM4E04IQDP5\n+TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGT'..b'TCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG\n++\n+IHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>><D:8544///5544??C24446<BIIIIIIHH\n+@GLZRM4E04IK96G\n+TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA\n++\n+IIIHHHIIIIIIIIIIHHHIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDCCFFFA?666?=ADDDA??????FFDFFFFFFFFFFFFFF???DBAAA::888444?=<;;96667,.--,,12,\n+@GLZRM4E04IOQ36\n+TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT\n++\n+-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998\n+@GLZRM4E04JBJJ1\n+AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAG\n++\n+555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHI\n+@GLZRM4E04IEFNO\n+GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA\n++\n+6EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87\n+@GLZRM4E04JOT5I\n+GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG\n++\n+CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII\n+@GLZRM4E04JC544\n+ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC\n++\n+IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=\n' |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff |
| b |
| Binary file test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff has changed |
| b |
| diff -r 000000000000 -r 945053d79e60 test-data/primers/dop_primers.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/dop_primers.fasta Mon Apr 29 06:11:00 2013 -0400 |
| b |
| @@ -0,0 +1,16 @@ +>DOP_start +CCGACTCGAG +>DOP1 +CCGACTCGAGNNNNNNATGTGG +>DOP2 +CCGACTCGAGATGNNNNNNTG +>DOP3 +CCGACTCGAGNNNNNNAAATGC +>DOP4 +CCGACTCGAGNNNNNNTTTACG +>DOP5 +CCGACTCGAGNNNNNNTTCAGG +>DOP6 +CCGACTCGAGNNNNNNAAGTCC +>DOP7 +CCGACTCGAGANNNNNNTCTGG |
| b |
| diff -r 000000000000 -r 945053d79e60 tools/primers/seq_primer_clip.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.py Mon Apr 29 06:11:00 2013 -0400 |
| [ |
| b'@@ -0,0 +1,358 @@\n+#!/usr/bin/env python\n+"""Looks for the given primer sequences and clips matching SFF reads.\n+\n+Takes eight command line options, input read filename, input read format,\n+input primer FASTA filename, type of primers (forward, reverse or reverse-\n+complement), number of mismatches (currently only 0, 1 and 2 are supported),\n+minimum length to keep a read (after primer trimming), should primer-less\n+reads be kept (boolean), and finally the output sequence filename.\n+\n+Both the primer and read sequences can contain IUPAC ambiguity codes like N.\n+\n+This supports FASTA, FASTQ and SFF sequence files. Colorspace reads are not\n+supported.\n+\n+The mismatch parameter does not consider gapped alignemnts, however the\n+special case of missing bases at the very start or end of the read is handled.\n+e.g. a primer sequence CCGACTCGAG will match a read starting CGACTCGAG...\n+if one or more mismatches are allowed.\n+\n+This can also be used for stripping off (and optionally filtering on) barcodes.\n+\n+Note that only the trim/clip values in the SFF file are changed, not the flow\n+information of the full read sequence.\n+\n+This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute\n+(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.\n+See accompanying text file for licence details (MIT/BSD style).\n+\n+This is version 0.0.8 of the script. Currently it uses Python\'s regular\n+expression engine for finding the primers, which for my needs is fast enough.\n+"""\n+import sys\n+import re\n+from galaxy_utils.sequence.fasta import fastaReader, fastaWriter\n+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter\n+\n+if "-v" in sys.argv or "--version" in sys.argv:\n+ print "v0.0.5"\n+ sys.exit(0)\n+\n+def stop_err(msg, err=1):\n+ sys.stderr.write(msg)\n+ sys.exit(err)\n+\n+try:\n+ from Bio.Seq import reverse_complement\n+ from Bio.SeqIO.SffIO import SffIterator, SffWriter\n+except ImportError:\n+ stop_err("Requires Biopython 1.54 or later")\n+try:\n+ from Bio.SeqIO.SffIO import ReadRocheXmlManifest\n+except ImportError:\n+ #Prior to Biopython 1.56 this was a private function\n+ from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest\n+\n+#Parse Command Line\n+try:\n+ in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]\n+except ValueError:\n+ stop_err("Expected 8 arguments, got %i:\\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))\n+\n+if in_file == primer_fasta:\n+ stop_err("Same file given as both primer sequences and sequences to clip!")\n+if in_file == out_file:\n+ stop_err("Same file given as both sequences to clip and output!")\n+if primer_fasta == out_file:\n+ stop_err("Same file given as both primer sequences and output!")\n+\n+try:\n+ mm = int(mm)\n+except ValueError:\n+ stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)\n+if mm < 0:\n+ stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)\n+if mm not in [0,1,2]:\n+ raise NotImplementedError\n+\n+try:\n+ min_len = int(min_len)\n+except ValueError:\n+ stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)\n+if min_len < 0:\n+ stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)\n+\n+\n+if keep_negatives.lower() in ["true", "yes", "on"]:\n+ keep_negatives = True\n+elif keep_negatives.lower() in ["false", "no", "off"]:\n+ keep_negatives = False\n+else:\n+ stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)\n+\n+\n+if primer_type.lower() == "forward":\n+ forward = True\n+ rc = False\n+elif primer_type.lower() == "reverse":\n+ forward = False\n+ rc = False\n+elif primer_type.lower() == "reverse-complement":\n+ forward = False\n+ rc = True\n+else:\n+ stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type)\n+\n+\n+ambiguous_dna_values = {\n+ "A": "A",\n+ "C": '..b'e = open(in_file, "rb")\n+ try:\n+ manifest = ReadRocheXmlManifest(in_handle)\n+ except ValueError:\n+ manifest = None\n+ in_handle.seek(0)\n+ out_handle = open(out_file, "wb")\n+ writer = SffWriter(out_handle, xml=manifest)\n+ writer.write_file(process(SffIterator(in_handle)))\n+ #End of SFF code\n+elif seq_format.lower().startswith("fastq"):\n+ in_handle = open(in_file, "rU")\n+ out_handle = open(out_file, "w")\n+ reader = fastqReader(in_handle)\n+ writer = fastqWriter(out_handle)\n+ if forward:\n+ for record in reader:\n+ seq = record.sequence.upper()\n+ result = primer.search(seq)\n+ if result:\n+ #Forward primer, take everything after it\n+ cut = result.end()\n+ record.sequence = seq[cut:]\n+ if len(record.sequence) >= min_len:\n+ record.quality = record.quality[cut:]\n+ clipped += 1\n+ writer.write(record)\n+ else:\n+ short_clipped += 1\n+ elif keep_negatives:\n+ if len(record) >= min_len:\n+ negs += 1\n+ writer.write(record)\n+ else:\n+ short_negs += 1\n+ else:\n+ for record in reader:\n+ seq = record.sequence.upper()\n+ result = primer.search(seq)\n+ if result:\n+ #Reverse primer, take everything before it\n+ cut = result.start()\n+ record.sequence = seq[:cut]\n+ if len(record.sequence) >= min_len:\n+ record.quality = record.quality[:cut]\n+ clipped += 1\n+ writer.write(record)\n+ else:\n+ short_clipped += 1\n+ elif keep_negatives:\n+ if len(record) >= min_len:\n+ negs += 1\n+ writer.write(record)\n+ else:\n+ short_negs += 1\n+elif seq_format.lower()=="fasta":\n+ in_handle = open(in_file, "rU")\n+ out_handle = open(out_file, "w")\n+ reader = fastaReader(in_handle)\n+ writer = fastaWriter(out_handle)\n+ #Following code is identical to that for FASTQ but without editing qualities\n+ if forward:\n+ for record in reader:\n+ seq = record.sequence.upper()\n+ result = primer.search(seq)\n+ if result:\n+ #Forward primer, take everything after it\n+ cut = result.end()\n+ record.sequence = seq[cut:]\n+ if len(record.sequence) >= min_len:\n+ clipped += 1\n+ writer.write(record)\n+ else:\n+ short_clipped += 1\n+ elif keep_negatives:\n+ if len(record) >= min_len:\n+ negs += 1\n+ writer.write(record)\n+ else:\n+ short_negs += 1\n+ else:\n+ for record in reader:\n+ seq = record.sequence.upper()\n+ result = primer.search(seq)\n+ if result:\n+ #Reverse primer, take everything before it\n+ cut = result.start()\n+ record.sequence = seq[:cut]\n+ if len(record.sequence) >= min_len:\n+ clipped += 1\n+ writer.write(record)\n+ else:\n+ short_clipped += 1\n+ elif keep_negatives:\n+ if len(record) >= min_len:\n+ negs += 1\n+ writer.write(record)\n+ else:\n+ short_negs += 1\n+else:\n+ stop_err("Unsupported file type %r" % seq_format)\n+in_handle.close()\n+out_handle.close()\n+\n+print "Kept %i clipped reads," % clipped\n+print "discarded %i short." % short_clipped\n+if keep_negatives:\n+ print "Kept %i non-matching reads," % negs\n+ print "discarded %i short." % short_neg\n' |
| b |
| diff -r 000000000000 -r 945053d79e60 tools/primers/seq_primer_clip.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.txt Mon Apr 29 06:11:00 2013 -0400 |
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| @@ -0,0 +1,103 @@ +Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads +=========================================================== + +This tool is copyright 2011 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This tool is a short Python script (using the Galaxy library functions and +Biopython). There are just two files to install: + +* seq_primer_clip.py (the Python script) +* seq_primer_clip.xml (the Galaxy tool definition) + +The suggested location is a new tools/primers folder. You will also need to +modify the tools_conf.xml file to tell Galaxy to offer the tool and also do +this to tools_conf.xml.sample in order to run the tests: + +<tool file="primers/seq_primer_clip.xml" /> + +There are optionally some example files required to run the functional tests, +put these in the test-data/primers folder. + +test-data/primers/dop_primers.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30.sff +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff + +You should then be able to run the tests with: + +sh run_functional_tests.sh -id seq_primer_clip + +You will also need to install Biopython 1.54 or later. That's it. + + +History +======= + +v0.0.1 - Initial version (not publicly released) +v0.0.2 - Sort primers by length (longest and therefore most specific first) +v0.0.3 - Consider missing bases at start/end of read as mismatches +v0.0.4 - Apply minimum length to sequences with no match too +v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes +v0.0.6 - Added some functional tests +v0.0.7 - Added error check for bad filename arguments +v0.0.8 - Record version of Python script when run from Galaxy. + - Check for errors using Python script's return code. + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +This incorporates the previously used hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder: + +$ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/* + +Check this worked: + +$ tar -tzf seq_primer_clip.tar.gz +tools/primers/seq_primer_clip.py +tools/primers/seq_primer_clip.txt +tools/primers/seq_primer_clip.xml +test-data/primers/dop_primers.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff +test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta +test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff +test-data/primers/MID4_GLZRM4E04_rnd30.sff + + +Licence (MIT/BSD style) +======================= + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. |
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| diff -r 000000000000 -r 945053d79e60 tools/primers/seq_primer_clip.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.xml Mon Apr 29 06:11:00 2013 -0400 |
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| @@ -0,0 +1,137 @@ +<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.8"> + <description>Trim off 5' or 3' primers</description> + <version_command interpreter="python">seq_primer_clip.py --version</version_command> + <command interpreter="python"> +seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/> + <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> + <param name="primer_type" type="select" label="Type of primers"> + <option value="Forward">Forward (5') primers</option> + <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option> + <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option> + </param> + <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)"> + <validator type="in_range" min="0" max="2" /> + </param> + <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/> + <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/> + </inputs> + <outputs> + <data name="output_file" format="data" label="$primer_type primer clipped"> + <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> + <change_format> + <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> + <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" /> + <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> + <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> + <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> + <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> + <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Forward" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="false" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Forward" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="false" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Forward" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="false" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Reverse" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="true" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Reverse" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="true" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Reverse" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="true" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> + </test> + </tests> + <requirements> + <requirement type="python-module">Bio</requirement> + </requirements> + <help> + +**What it does** + +Looks for the given primer sequences (within the existing clipped sequence) and +further clips the reads to remove the primers and any preceding/trailing sequence. + +Reads containing a forward primer are reduced to just the sequence after (and +excluding) the forward primer. + +Reads containing a reverse primer are reduced to just the sequence before (and +excluding) the reverse primer. + +Degenerate primers can be specified using the standard IUPAC ambiguity codes, +thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity +codes) and so on. + +Note that for SFF files only the clip/trim positions are edited - you will still +be able to extract the original full read (with any adapter sequence and poor +quality sequence) if you need to. + +.. class:: warningmark + +**Note**. This tool was initially written for Roche 454 data, and should also +work fine on Sanger or Ion Torrent as well. However, it is probably too slow +for use on large Illumina datasets. + + +**Citation** + +This tool uses Biopython. If you use this tool in scientific work leading to a +publication, please cite: + +Cock et al 2009. Biopython: freely available Python tools for computational +molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. +http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. + + </help> +</tool> |