# HG changeset patch # User peterjc # Date 1367334283 14400 # Node ID 8c02a91a868019bbb9e57ea03a05a6f5b86d4df6 # Parent 945053d79e605c207c354fb2df3494bf1657b613 Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation. diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MID4_GLZRM4E04_rnd30.fasta Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,60 @@ +>GLZRM4E04IPVGX +CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I9EJK +CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG +>GLZRM4E04JHW0A +TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC +>GLZRM4E04IBNFY +CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG +>GLZRM4E04IKCQP +CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA +>GLZRM4E04ITXFU +CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT +>GLZRM4E04JAY4Z +CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC +>GLZRM4E04H9M21 +CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG +>GLZRM4E04IQDP5 +CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG +>GLZRM4E04I0CYE +TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I2NA7 +CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA +>GLZRM4E04I5BWJ +CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC +>GLZRM4E04IK8WX +GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG +>GLZRM4E04I22QH +CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC +>GLZRM4E04IVVFA +GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG +>GLZRM4E04ILU3V +CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG +>GLZRM4E04IDVJT +CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG +>GLZRM4E04I3ZJ6 +CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG +>GLZRM4E04I3UBT +CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA +>GLZRM4E04H59S1 +CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG +>GLZRM4E04JFA38 +CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT +>GLZRM4E04J4EK3 +CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG +>GLZRM4E04IK96G +CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA +>GLZRM4E04JVL8Q +CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT +>GLZRM4E04IOQ36 +CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT +>GLZRM4E04JBJJ1 +CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG +>GLZRM4E04IEFNO +CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA +>GLZRM4E04JOT5I +CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG +>GLZRM4E04J4HNG +CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT +>GLZRM4E04JC544 +CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MID4_GLZRM4E04_rnd30.fastqsanger Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,120 @@ +@GLZRM4E04IPVGX +CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ++ +FIIIIIIIIHHHIDDDIIIIIIIIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 +@GLZRM4E04I9EJK +CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ++ +IIIIGCBCF=422211:882<<9992/..//399662444/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII +@GLZRM4E04JHW0A +TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ++ +IIIIIIIIIF;;;;HFDDEHHHIIIAA??9998665333DEA<>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, +@GLZRM4E04IBNFY +CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ++ +IIIIIIIIIIIIIIIIIIII666IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII +@GLZRM4E04IKCQP +CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ++ +IIIIIH???GDGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEHBGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7 +@GLZRM4E04JAY4Z +CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ++ +FIIIIIIIIIIHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<>>>332766,,,2--,,./../8>==?5555A81 +@GLZRM4E04H9M21 +CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ++ +IIIIIIIIIIIIIGGGIIII;;;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII +@GLZRM4E04IQDP5 +CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG ++ +IIHIIIIE@111177?@88@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=:111----,- +@GLZRM4E04IK8WX +GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG ++ +IIIIIIIIIIIIIIH??;;;HIIICCGIIIIIIH????IIIIIIIIII?666HIIIIII +@GLZRM4E04I22QH +CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ++ +444:<:34466,,--1585--,,,,,/,57:7524--..22?><<<9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- +@GLZRM4E04IVVFA +GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG ++ +HHIICCBBIIIIIIIIIHHHIIIIIIIIGGGIIIIIIIH6666IIIAAIIIIH;;;IHHHHIIBBCCIIIIIIIIIIIIII +@GLZRM4E04ILU3V +CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ++ +DDDDFECADBBA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 +@GLZRM4E04IDVJT +CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG ++ +IIIIIIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, +@GLZRM4E04H59S1 +CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ++ +IIIIIIIII???IIGG;;;HIIIIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC +@GLZRM4E04JFA38 +CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT ++ +:8875782222..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III>>>8888DIIIIIHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>>:>>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..,,, +@GLZRM4E04IOQ36 +CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT ++ +HHHGCD@B?0-,,,,.../<<<733856=;?////001//9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8:@9333=BBB?AAA>>=899=>55;55=9998 +@GLZRM4E04JBJJ1 +CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG ++ +IIIIIIH?;;;@>IIBD@@EII555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 +@GLZRM4E04JOT5I +CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG ++ +IIIIIIIII=999E144445CCCIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII +@GLZRM4E04J4HNG +CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT ++ +FFHHHHHHFF888??=A6998><44344888877=:433624 +@GLZRM4E04JC544 +CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC ++ +IIIIHIHIC4------//<=IIIIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777= diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30.sff Binary file test-data/MID4_GLZRM4E04_rnd30.sff has changed diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MID4_GLZRM4E04_rnd30_fclip.fasta Tue Apr 30 11:04:43 2013 -0400 @@ -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 diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,100 @@ +@GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ++ +IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 +@GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ++ +9992/..//399662444/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII +@GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ++ +IIIAA??9998665333DEA<>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, +@GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ++ +6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII +@GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ++ +DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEHBGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7 +@GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ++ +IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<>>>332766,,,2--,,./../8>==?5555A81 +@GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ++ +;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII +@GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG ++ +88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CCIIIIIIIIIIIIII +@GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA ++ +21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113, +@GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC ++ +IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=:111----,- +@GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ++ +6,,--1585--,,,,,/,57:7524--..22?><<<9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- +@GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ++ +BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 +@GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG ++ +CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, +@GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ++ +IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC +@GLZRM4E04JFA38 +GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT ++ +2..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8:@9333=BBB?AAA>>=899=>55;55=9998 +@GLZRM4E04JBJJ1 +AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG ++ +555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 +@GLZRM4E04JOT5I +GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG ++ +CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII +@GLZRM4E04JC544 +ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC ++ +IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777= diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30_fclip.sff Binary file test-data/MID4_GLZRM4E04_rnd30_fclip.sff has changed diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MID4_GLZRM4E04_rnd30_frclip.fasta Tue Apr 30 11:04:43 2013 -0400 @@ -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 diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,100 @@ +@GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ++ +IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 +@GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ++ +9992/..//399662444/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII +@GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ++ +IIIAA??9998665333DEA<>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, +@GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ++ +6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII +@GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ++ +DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEHBGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>88 +@GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ++ +IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<>>>332766,,,2--,,./../8>==?5555A81 +@GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ++ +;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII +@GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGG ++ +88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CC +@GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA ++ +21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113, +@GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC ++ +IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=:111----,- +@GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ++ +6,,--1585--,,,,,/,57:7524--..22?><<<9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- +@GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ++ +BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 +@GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACC ++ +CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, +@GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ++ +IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC +@GLZRM4E04JFA38 +GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT ++ +2..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8:@9333=BBB?AAA>>=899=>55;55=9998 +@GLZRM4E04JBJJ1 +AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAG ++ +555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 +@GLZRM4E04JOT5I +GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG ++ +CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII +@GLZRM4E04JC544 +ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC ++ +IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777= diff -r 945053d79e60 -r 8c02a91a8680 test-data/MID4_GLZRM4E04_rnd30_frclip.sff Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.sff has changed diff -r 945053d79e60 -r 8c02a91a8680 test-data/dop_primers.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dop_primers.fasta Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,16 @@ +>DOP_start +CCGACTCGAG +>DOP1 +CCGACTCGAGNNNNNNATGTGG +>DOP2 +CCGACTCGAGATGNNNNNNTG +>DOP3 +CCGACTCGAGNNNNNNAAATGC +>DOP4 +CCGACTCGAGNNNNNNTTTACG +>DOP5 +CCGACTCGAGNNNNNNTTCAGG +>DOP6 +CCGACTCGAGNNNNNNAAGTCC +>DOP7 +CCGACTCGAGANNNNNNTCTGG diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30.fasta --- a/test-data/primers/MID4_GLZRM4E04_rnd30.fasta Mon Apr 29 06:11:00 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ ->GLZRM4E04IPVGX -CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ->GLZRM4E04I9EJK -CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ->GLZRM4E04JHW0A -TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ->GLZRM4E04IBNFY -CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ->GLZRM4E04IKCQP -CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ->GLZRM4E04ITXFU -CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT ->GLZRM4E04JAY4Z -CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ->GLZRM4E04H9M21 -CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ->GLZRM4E04IQDP5 -CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG ->GLZRM4E04I0CYE -TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT ->GLZRM4E04I2NA7 -CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA ->GLZRM4E04I5BWJ -CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC ->GLZRM4E04IK8WX -GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG ->GLZRM4E04I22QH -CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ->GLZRM4E04IVVFA -GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG ->GLZRM4E04ILU3V -CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ->GLZRM4E04IDVJT -CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG ->GLZRM4E04I3ZJ6 -CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG ->GLZRM4E04I3UBT -CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA ->GLZRM4E04H59S1 -CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ->GLZRM4E04JFA38 -CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT ->GLZRM4E04J4EK3 -CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG ->GLZRM4E04IK96G -CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA ->GLZRM4E04JVL8Q -CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT ->GLZRM4E04IOQ36 -CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT ->GLZRM4E04JBJJ1 -CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG ->GLZRM4E04IEFNO -CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA ->GLZRM4E04JOT5I -CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG ->GLZRM4E04J4HNG -CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT ->GLZRM4E04JC544 -CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger --- a/test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger Mon Apr 29 06:11:00 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,120 +0,0 @@ -@GLZRM4E04IPVGX -CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT -+ -FIIIIIIIIHHHIDDDIIIIIIIIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 -@GLZRM4E04I9EJK -CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG -+ -IIIIGCBCF=422211:882<<9992/..//399662444/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII -@GLZRM4E04JHW0A -TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC -+ -IIIIIIIIIF;;;;HFDDEHHHIIIAA??9998665333DEA<>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, -@GLZRM4E04IBNFY -CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG -+ -IIIIIIIIIIIIIIIIIIII666IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII -@GLZRM4E04IKCQP -CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA -+ -IIIIIH???GDGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEHBGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7 -@GLZRM4E04JAY4Z -CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC -+ -FIIIIIIIIIIHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<>>>332766,,,2--,,./../8>==?5555A81 -@GLZRM4E04H9M21 -CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG -+ -IIIIIIIIIIIIIGGGIIII;;;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII -@GLZRM4E04IQDP5 -CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG -+ -IIHIIIIE@111177?@88@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=:111----,- -@GLZRM4E04IK8WX -GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG -+ -IIIIIIIIIIIIIIH??;;;HIIICCGIIIIIIH????IIIIIIIIII?666HIIIIII -@GLZRM4E04I22QH -CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC -+ -444:<:34466,,--1585--,,,,,/,57:7524--..22?><<<9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- -@GLZRM4E04IVVFA -GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG -+ -HHIICCBBIIIIIIIIIHHHIIIIIIIIGGGIIIIIIIH6666IIIAAIIIIH;;;IHHHHIIBBCCIIIIIIIIIIIIII -@GLZRM4E04ILU3V -CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG -+ -DDDDFECADBBA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 -@GLZRM4E04IDVJT -CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG -+ -IIIIIIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, -@GLZRM4E04H59S1 -CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG -+ -IIIIIIIII???IIGG;;;HIIIIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC -@GLZRM4E04JFA38 -CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT -+ -:8875782222..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III>>>8888DIIIIIHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>>:>>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..,,, -@GLZRM4E04IOQ36 -CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT -+ -HHHGCD@B?0-,,,,.../<<<733856=;?////001//9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8:@9333=BBB?AAA>>=899=>55;55=9998 -@GLZRM4E04JBJJ1 -CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG -+ -IIIIIIH?;;;@>IIBD@@EII555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 -@GLZRM4E04JOT5I -CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG -+ -IIIIIIIII=999E144445CCCIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII -@GLZRM4E04J4HNG -CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT -+ -FFHHHHHHFF888??=A6998><44344888877=:433624 -@GLZRM4E04JC544 -CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC -+ -IIIIHIHIC4------//<=IIIIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777= diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30.sff Binary file test-data/primers/MID4_GLZRM4E04_rnd30.sff has changed diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta --- a/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta Mon Apr 29 06:11:00 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ ->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 diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger --- a/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger Mon Apr 29 06:11:00 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -@GLZRM4E04IPVGX -AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT -+ -IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 -@GLZRM4E04I9EJK -TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG -+ -9992/..//399662444/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII -@GLZRM4E04JHW0A -AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC -+ -IIIAA??9998665333DEA<>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, -@GLZRM4E04IBNFY -GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG -+ -6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII -@GLZRM4E04IKCQP -GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA -+ -DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEHBGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7 -@GLZRM4E04JAY4Z -GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC -+ -IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<>>>332766,,,2--,,./../8>==?5555A81 -@GLZRM4E04H9M21 -CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG -+ -;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII -@GLZRM4E04IQDP5 -TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG -+ -88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CCIIIIIIIIIIIIII -@GLZRM4E04I2NA7 -TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA -+ -21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113, -@GLZRM4E04I5BWJ -TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC -+ -IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=:111----,- -@GLZRM4E04I22QH -CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC -+ -6,,--1585--,,,,,/,57:7524--..22?><<<9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- -@GLZRM4E04ILU3V -CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG -+ -BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 -@GLZRM4E04IDVJT -GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG -+ -CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, -@GLZRM4E04H59S1 -TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG -+ -IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC -@GLZRM4E04JFA38 -GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT -+ -2..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8:@9333=BBB?AAA>>=899=>55;55=9998 -@GLZRM4E04JBJJ1 -AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG -+ -555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 -@GLZRM4E04JOT5I -GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG -+ -CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII -@GLZRM4E04JC544 -ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC -+ -IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777= diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff Binary file test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff has changed diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta --- a/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta Mon Apr 29 06:11:00 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ ->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 diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger --- a/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger Mon Apr 29 06:11:00 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -@GLZRM4E04IPVGX -AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT -+ -IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 -@GLZRM4E04I9EJK -TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG -+ -9992/..//399662444/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII -@GLZRM4E04JHW0A -AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC -+ -IIIAA??9998665333DEA<>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, -@GLZRM4E04IBNFY -GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG -+ -6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII -@GLZRM4E04IKCQP -GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA -+ -DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEHBGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>88 -@GLZRM4E04JAY4Z -GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC -+ -IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<>>>332766,,,2--,,./../8>==?5555A81 -@GLZRM4E04H9M21 -CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG -+ -;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII -@GLZRM4E04IQDP5 -TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGG -+ -88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CC -@GLZRM4E04I2NA7 -TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA -+ -21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113, -@GLZRM4E04I5BWJ -TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC -+ -IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=:111----,- -@GLZRM4E04I22QH -CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC -+ -6,,--1585--,,,,,/,57:7524--..22?><<<9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- -@GLZRM4E04ILU3V -CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG -+ -BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 -@GLZRM4E04IDVJT -GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACC -+ -CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, -@GLZRM4E04H59S1 -TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG -+ -IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC -@GLZRM4E04JFA38 -GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT -+ -2..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8:@9333=BBB?AAA>>=899=>55;55=9998 -@GLZRM4E04JBJJ1 -AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAG -+ -555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 -@GLZRM4E04JOT5I -GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG -+ -CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII -@GLZRM4E04JC544 -ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC -+ -IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777= diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff Binary file test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff has changed diff -r 945053d79e60 -r 8c02a91a8680 test-data/primers/dop_primers.fasta --- a/test-data/primers/dop_primers.fasta Mon Apr 29 06:11:00 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ ->DOP_start -CCGACTCGAG ->DOP1 -CCGACTCGAGNNNNNNATGTGG ->DOP2 -CCGACTCGAGATGNNNNNNTG ->DOP3 -CCGACTCGAGNNNNNNAAATGC ->DOP4 -CCGACTCGAGNNNNNNTTTACG ->DOP5 -CCGACTCGAGNNNNNNTTCAGG ->DOP6 -CCGACTCGAGNNNNNNAAGTCC ->DOP7 -CCGACTCGAGANNNNNNTCTGG diff -r 945053d79e60 -r 8c02a91a8680 tools/primers/seq_primer_clip.py.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.py.orig Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,358 @@ +#!/usr/bin/env python +"""Looks for the given primer sequences and clips matching SFF reads. + +Takes eight command line options, input read filename, input read format, +input primer FASTA filename, type of primers (forward, reverse or reverse- +complement), number of mismatches (currently only 0, 1 and 2 are supported), +minimum length to keep a read (after primer trimming), should primer-less +reads be kept (boolean), and finally the output sequence filename. + +Both the primer and read sequences can contain IUPAC ambiguity codes like N. + +This supports FASTA, FASTQ and SFF sequence files. Colorspace reads are not +supported. + +The mismatch parameter does not consider gapped alignemnts, however the +special case of missing bases at the very start or end of the read is handled. +e.g. a primer sequence CCGACTCGAG will match a read starting CGACTCGAG... +if one or more mismatches are allowed. + +This can also be used for stripping off (and optionally filtering on) barcodes. + +Note that only the trim/clip values in the SFF file are changed, not the flow +information of the full read sequence. + +This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute +(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. +See accompanying text file for licence details (MIT/BSD style). + +This is version 0.0.8 of the script. Currently it uses Python's regular +expression engine for finding the primers, which for my needs is fast enough. +""" +import sys +import re +from galaxy_utils.sequence.fasta import fastaReader, fastaWriter +from galaxy_utils.sequence.fastq import fastqReader, fastqWriter + +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.5" + sys.exit(0) + +def stop_err(msg, err=1): + sys.stderr.write(msg) + sys.exit(err) + +try: + from Bio.Seq import reverse_complement + from Bio.SeqIO.SffIO import SffIterator, SffWriter +except ImportError: + stop_err("Requires Biopython 1.54 or later") +try: + from Bio.SeqIO.SffIO import ReadRocheXmlManifest +except ImportError: + #Prior to Biopython 1.56 this was a private function + from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest + +#Parse Command Line +try: + in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:] +except ValueError: + stop_err("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) + +if in_file == primer_fasta: + stop_err("Same file given as both primer sequences and sequences to clip!") +if in_file == out_file: + stop_err("Same file given as both sequences to clip and output!") +if primer_fasta == out_file: + stop_err("Same file given as both primer sequences and output!") + +try: + mm = int(mm) +except ValueError: + stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm) +if mm < 0: + stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm) +if mm not in [0,1,2]: + raise NotImplementedError + +try: + min_len = int(min_len) +except ValueError: + stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len) +if min_len < 0: + stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len) + + +if keep_negatives.lower() in ["true", "yes", "on"]: + keep_negatives = True +elif keep_negatives.lower() in ["false", "no", "off"]: + keep_negatives = False +else: + stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives) + + +if primer_type.lower() == "forward": + forward = True + rc = False +elif primer_type.lower() == "reverse": + forward = False + rc = False +elif primer_type.lower() == "reverse-complement": + forward = False + rc = True +else: + stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type) + + +ambiguous_dna_values = { + "A": "A", + "C": "C", + "G": "G", + "T": "T", + "M": "ACM", + "R": "AGR", + "W": "ATW", + "S": "CGS", + "Y": "CTY", + "K": "GTK", + "V": "ACGMRSV", + "H": "ACTMWYH", + "D": "AGTRWKD", + "B": "CGTSYKB", + "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC] + "N": ".", + } + +ambiguous_dna_re = {} +for letter, values in ambiguous_dna_values.iteritems(): + if len(values) == 1: + ambiguous_dna_re[letter] = values + else: + ambiguous_dna_re[letter] = "[%s]" % values + + +def make_reg_ex(seq): + return "".join(ambiguous_dna_re[letter] for letter in seq) + +def make_reg_ex_mm(seq, mm): + if mm > 2: + raise NotImplementedError("At most 2 mismatches allowed!") + seq = seq.upper() + yield make_reg_ex(seq) + for i in range(1,mm+1): + #Missing first/last i bases at very start/end of sequence + for reg in make_reg_ex_mm(seq[i:], mm-i): + yield "^" + reg + for reg in make_reg_ex_mm(seq[:-i], mm-i): + yield "$" + reg + if mm >= 1: + for i,letter in enumerate(seq): + #We'll use a set to remove any duplicate patterns + #if letter not in "NX": + pattern = seq[:i] + "N" + seq[i+1:] + assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \ + % (pattern, len(pattern), seq, len(seq)) + yield make_reg_ex(pattern) + if mm >=2: + for i,letter in enumerate(seq): + #We'll use a set to remove any duplicate patterns + #if letter not in "NX": + for k,letter in enumerate(seq[i+1:]): + #We'll use a set to remove any duplicate patterns + #if letter not in "NX": + pattern = seq[:i] + "N" + seq[i+1:i+1+k] + "N" + seq[i+k+2:] + assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \ + % (pattern, len(pattern), seq, len(seq)) + yield make_reg_ex(pattern) + +def load_primers_as_re(primer_fasta, mm, rc=False): + #Read primer file and record all specified sequences + primers = set() + in_handle = open(primer_fasta, "rU") + reader = fastaReader(in_handle) + count = 0 + for record in reader: + if rc: + seq = reverse_complement(record.sequence) + else: + seq = record.sequence + #primers.add(re.compile(make_reg_ex(seq))) + count += 1 + for pattern in make_reg_ex_mm(seq, mm): + primers.add(pattern) + in_handle.close() + #Use set to avoid duplicates, sort to have longest first + #(so more specific primers found before less specific ones) + primers = sorted(set(primers), key=lambda p: -len(p)) + return count, re.compile("|".join(primers)) #make one monster re! + + + +#Read primer file and record all specified sequences +count, primer = load_primers_as_re(primer_fasta, mm, rc) +print "%i primer sequences" % count + +short_neg = 0 +short_clipped = 0 +clipped = 0 +negs = 0 + +if seq_format.lower()=="sff": + #SFF is different because we just change the trim points + if forward: + def process(records): + global short_clipped, short_neg, clipped, negs + for record in records: + left_clip = record.annotations["clip_qual_left"] + right_clip = record.annotations["clip_qual_right"] + seq = str(record.seq)[left_clip:right_clip].upper() + result = primer.search(seq) + if result: + #Forward primer, take everything after it + #so move the left clip along + if len(seq) - result.end() >= min_len: + record.annotations["clip_qual_left"] = left_clip + result.end() + clipped += 1 + yield record + else: + short_clipped += 1 + elif keep_negatives: + if len(seq) >= min_len: + negs += 1 + yield record + else: + short_neg += 1 + else: + def process(records): + global short_clipped, short_neg, clipped, negs + for record in records: + left_clip = record.annotations["clip_qual_left"] + right_clip = record.annotations["clip_qual_right"] + seq = str(record.seq)[left_clip:right_clip].upper() + result = primer.search(seq) + if result: + #Reverse primer, take everything before it + #so move the right clip back + new_len = result.start() + if new_len >= min_len: + record.annotations["clip_qual_right"] = left_clip + new_len + clipped += 1 + yield record + else: + short_clipped += 1 + elif keep_negatives: + if len(seq) >= min_len: + negs += 1 + yield record + else: + short_neg += 1 + + in_handle = open(in_file, "rb") + try: + manifest = ReadRocheXmlManifest(in_handle) + except ValueError: + manifest = None + in_handle.seek(0) + out_handle = open(out_file, "wb") + writer = SffWriter(out_handle, xml=manifest) + writer.write_file(process(SffIterator(in_handle))) + #End of SFF code +elif seq_format.lower().startswith("fastq"): + in_handle = open(in_file, "rU") + out_handle = open(out_file, "w") + reader = fastqReader(in_handle) + writer = fastqWriter(out_handle) + if forward: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Forward primer, take everything after it + cut = result.end() + record.sequence = seq[cut:] + if len(record.sequence) >= min_len: + record.quality = record.quality[cut:] + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 + else: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Reverse primer, take everything before it + cut = result.start() + record.sequence = seq[:cut] + if len(record.sequence) >= min_len: + record.quality = record.quality[:cut] + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 +elif seq_format.lower()=="fasta": + in_handle = open(in_file, "rU") + out_handle = open(out_file, "w") + reader = fastaReader(in_handle) + writer = fastaWriter(out_handle) + #Following code is identical to that for FASTQ but without editing qualities + if forward: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Forward primer, take everything after it + cut = result.end() + record.sequence = seq[cut:] + if len(record.sequence) >= min_len: + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 + else: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Reverse primer, take everything before it + cut = result.start() + record.sequence = seq[:cut] + if len(record.sequence) >= min_len: + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 +else: + stop_err("Unsupported file type %r" % seq_format) +in_handle.close() +out_handle.close() + +print "Kept %i clipped reads," % clipped +print "discarded %i short." % short_clipped +if keep_negatives: + print "Kept %i non-matching reads," % negs + print "discarded %i short." % short_neg diff -r 945053d79e60 -r 8c02a91a8680 tools/primers/seq_primer_clip.txt --- a/tools/primers/seq_primer_clip.txt Mon Apr 29 06:11:00 2013 -0400 +++ b/tools/primers/seq_primer_clip.txt Tue Apr 30 11:04:43 2013 -0400 @@ -12,25 +12,14 @@ * 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: +modify the tools_conf.xml file to tell Galaxy to offer the tool: -There are optionally some example files required to run the functional tests, -put these in the test-data/primers folder. +If you wish to run the unit tests, also add this to tools_conf.xml.sample +and move/copy the test-data files under Galaxy's test-data folder. Then: -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 +$ ./run_functional_tests.sh -id seq_primer_clip You will also need to install Biopython 1.54 or later. That's it. @@ -47,6 +36,7 @@ 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. +v0.0.9 - Moved test data to workaround Galaxy Tool Shed limititation. Developers @@ -61,7 +51,7 @@ 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/* +$ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30* Check this worked: @@ -69,16 +59,16 @@ 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 +test-data/dop_primers.fasta +test-data/MID4_GLZRM4E04_rnd30.fasta +test-data/MID4_GLZRM4E04_rnd30.fastqsanger +test-data/MID4_GLZRM4E04_rnd30_fclip.fasta +test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger +test-data/MID4_GLZRM4E04_rnd30_fclip.sff +test-data/MID4_GLZRM4E04_rnd30_frclip.fasta +test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger +test-data/MID4_GLZRM4E04_rnd30_frclip.sff +test-data/MID4_GLZRM4E04_rnd30.sff Licence (MIT/BSD style) diff -r 945053d79e60 -r 8c02a91a8680 tools/primers/seq_primer_clip.txt.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.txt.orig Tue Apr 30 11:04:43 2013 -0400 @@ -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: + + + +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. diff -r 945053d79e60 -r 8c02a91a8680 tools/primers/seq_primer_clip.xml --- a/tools/primers/seq_primer_clip.xml Mon Apr 29 06:11:00 2013 -0400 +++ b/tools/primers/seq_primer_clip.xml Tue Apr 30 11:04:43 2013 -0400 @@ -1,4 +1,4 @@ - + Trim off 5' or 3' primers seq_primer_clip.py --version @@ -39,58 +39,58 @@ - - + + - + - - + + - + - - + + - + - - + + - + - - + + - + - - + + - + diff -r 945053d79e60 -r 8c02a91a8680 tools/primers/seq_primer_clip.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.xml.orig Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,137 @@ + + Trim off 5' or 3' primers + seq_primer_clip.py --version + +seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bio + + + +**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. + + +