| Previous changeset 62:e6c4f3e96e47 (2019-01-17) Next changeset 64:967512924317 (2019-01-28) |
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Commit message:
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a461e07471d3897046e14389171a2c03d09b912d |
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modified:
README.rst sRNAPipe.xml sRNAPipe_User_Manual.pdf test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq_all_mappers.fastq test-data/fastq_dir/reads-sample-small.fastq_unique_mappers.fastq test-data/fastq_dir/reads-sample-small.fastq_unmapped.fastq test-data/reads-sample-small.fastq test-data/res.html test-data/res_files/reads-sample-small.fastq-bonafide_reads-genome.html 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test-data/res_files/reads-sample-small.fastq/dataset_35117_18-29.fastq test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_LTR.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/I_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/MAX_I.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/PROTOP.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_6.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_6.png |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 README.rst --- a/README.rst Thu Jan 17 09:56:52 2019 -0500 +++ b/README.rst Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,3 +1,5 @@ +.. image:: https://travis-ci.org/GReD-Clermont/sRNAPipe.svg?branch=master + :target: https://travis-ci.org/GReD-Clermont/sRNAPipe sRNAPipe ======== @@ -55,9 +57,9 @@ .. raw:: html - <object data="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px"> - <embed src="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"> - This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p> + <object data="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px"> + <embed src="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf"> + This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p> </embed> </object> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 sRNAPipe.xml --- a/sRNAPipe.xml Thu Jan 17 09:56:52 2019 -0500 +++ b/sRNAPipe.xml Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -25,14 +25,12 @@ <requirement type="package" version="0.7.12">bwa</requirement> <requirement type="package" version="2.24">bedtools</requirement> <requirement type="package" version="1.5">samtools</requirement> - <requirement type="package" version="3.3.2">r-base</requirement> - <requirement type="package" version="5.22.0">perl</requirement> <requirement type="package" version="2.50">perl-getopt-long</requirement> <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement> - <requirement type="package" version="0.34" >perl-statistics-r</requirement> + <requirement type="package" version="0.34">perl-statistics-r</requirement> <requirement type="package" version="0.30">perl-string-random</requirement> - <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement> - <requirement type="package" version="0.1" >perl-math-cdf</requirement> + <requirement type="package" version="0.38">perl-file-copy-recursive</requirement> + <requirement type="package" version="0.1">perl-math-cdf</requirement> <requirement type="package" version="3.6">r-plotrix</requirement> <requirement type="package" version="1.14.0">bioconductor-sushi</requirement> <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 sRNAPipe_User_Manual.pdf |
| b |
| Binary file sRNAPipe_User_Manual.pdf has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -2,602 +2,50 @@\n AAAAACACGACCGTTCGCTTTGAAA\n +\n JJJIJJJJJJIHHHHFHFDDBFCC@\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-<<EFECE:?AA,FBADD;;D@@@\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IGGIIGHAIIFAHDDHHDD@4++::\n-@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n-AACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IIIGFCIGGIJGHDCFDFDD?BB?@@\n-@HWI-ST132:678:C1LFKACXX:6:2102:3965:15607\n-TATCTGAACCACTGTGCACG\n-+\n-CJHGEIHHHHDGDFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n-TTCGGCCATTAAAACCAGCGCACT\n-+\n-IIGGDIIHFFIHHHHHFFDDFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n-TCACTCGTTCGGCCATTAAAACCAGC\n-+\n-IHJJIJIHJIIHFC6HHHFFFFFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n-TCATCACTCGTTCGGCCATTAAAAC\n-+\n-JJJHGJIHHFC<HHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n-TTTAATGGCCGAACGAGTGATGACC\n-+\n-B@BDFEFFHHCFHGIIJGHIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIIJJJJJJIIHDHHHDFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIHIIHJJJJJHHHHHDEDDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1310:10470:57499\n-TTAGATTTTTACCCTTTGCT\n-+\n-JIGHGJJHHHGHFFEDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n-GATGAAATCGTTTATGCGCCAAACT\n-+\n-@@@DDDDDHHFHH=GHHIII@GCHI\n-@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n-AGGTGGCTTGAAAGAACTGATCAACA\n-+\n-@CCDDFFFHHHHHHGHIJHIJJCGHI\n-@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n-GTTGATCAGTTCTTTCAAGCCACCT\n-+\n-JIHCIEJIJJJJHHHDD;DDDA?@@\n-@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHGHGHJJGCFHGIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHHHHHJJ<EHIJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CC@FFFFFGDFHGJJIIJIJJJ@HF\n-@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFGHHGFIIJJJJIIJIJH\n-@HWI-ST132:678:C1LFKACXX:6:1307:8164:25340\n-TCTCTAGCTATGCCAAAACTGT\n-+\n-IJJJJJIJJHHDBHFFFFFB@B\n-@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-GGEGIIIJHEFED@FHHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-HHBGIHFGD1JGFAGHHFFFFFC@C\n-@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-GEIGEHGDC1<)HHDDDDBDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-B<GD@?GEEDE>HAFHFDDB=A@@=\n-@HWI-ST132:678:C1LFKACXX:6:1301:18775:28385\n-TATCATCGGCTCGACGGAAA\n-+\n-GHDHGGIGHHHHDDEDBC@@\n-@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-JJIJJIGEAIJHHHFFDFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-?C:?G:E<CF>F>FFC2D;B=+1=\n-@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-HGGHEGFA4IIHHHFBDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-IHFIECJJJJJHGHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n-TTAAACTGTGAATTAAGCGCG\n-+\n-JGHJJJJJHHHFCFFFFF@CB\n-@HWI-ST132:678:C1LFKAC'..b' @HWI-ST132:678:C1LFKACXX:6:1316:14693:8233\n TGAATTGAGAGTCGGCGTTCGTC\n +\n HEJJIJJGJHFFFFFDDDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-HGJJJIJIJIHHHHHBEDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-GCGEIJIIIGHHFDHEFDFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHFGFE1FC<FHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJJJJHGHIHGFAHDHFFFFFBCC\n @HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n GGHJIHHHFECC<DDFFFFDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGJJIIJIHFA3CHHFFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GIHGG?CGFC222F;HFFDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHIJJIIHF:IHHHHHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIIIIGIGGFA<AHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGIHGIIGGIHFHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIIHIGHGHHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHHHGGCD<<BHFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIJIIJJIHGFBFDHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHIIGGCFCHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHGGCCCCAFHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJJJIGHFEHFHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHHJIHBIFCGFCHHHFFFFF@CC\n @HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n EEDIHECF@GEC:DHDFDBAD??@\n-@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHHHE8GHDHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHGIGHGFCHHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIIIIIIHFE@HF?A:DDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GFIHBGGAC@GDDF=HDDFDFC@@\n-@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-HDCHGHGHIGEFAHFFFDDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-DBBIGGDAG?@?FF=FDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-EEIGGHEHDGEFDFDDDEDBD=?@\n-@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JHGJIHGGCC322<2AFFFFD?=:\n-@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIHIGG@HEGHHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIHHJHFFFBHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHEIJHHIHGEHFFHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-@FDFFE@F@F8DD<2+BBDDD??=\n-@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHFE@2@HDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIJIIGFFHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIHGCFC<BHDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGHCIIJIIHF<HGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIJIJJIGG@2<2<DAFFFFF@@=\n @HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n@@ -105346,15 +10706,7 @@\n TGAATTGAGAGTCGGCGTTCGTCAT\n +\n HHD?JHGHHHFEDFHGHFFFFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1303:20279:89985\n-TTTTTAAAATCAAGCAGC\n-+\n-CCCFFFFFHHHHHIJBHH\n @HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n GCTGACATTGCGAAAGTG\n +\n CCCFFFFFHHHHH1EEHH\n-@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n-GCTGACATTGCGAAAGTG\n-+\n-B@BFDFFFHHHAFIJ1CF\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -2,602 +2,50 @@\n AAAAACACGACCGTTCGCTTTGAAA\n +\n JJJIJJJJJJIHHHHFHFDDBFCC@\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-<<EFECE:?AA,FBADD;;D@@@\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IGGIIGHAIIFAHDDHHDD@4++::\n-@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n-AACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IIIGFCIGGIJGHDCFDFDD?BB?@@\n-@HWI-ST132:678:C1LFKACXX:6:2102:3965:15607\n-TATCTGAACCACTGTGCACG\n-+\n-CJHGEIHHHHDGDFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n-TTCGGCCATTAAAACCAGCGCACT\n-+\n-IIGGDIIHFFIHHHHHFFDDFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n-TCACTCGTTCGGCCATTAAAACCAGC\n-+\n-IHJJIJIHJIIHFC6HHHFFFFFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n-TCATCACTCGTTCGGCCATTAAAAC\n-+\n-JJJHGJIHHFC<HHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n-TTTAATGGCCGAACGAGTGATGACC\n-+\n-B@BDFEFFHHCFHGIIJGHIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIIJJJJJJIIHDHHHDFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIHIIHJJJJJHHHHHDEDDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1310:10470:57499\n-TTAGATTTTTACCCTTTGCT\n-+\n-JIGHGJJHHHGHFFEDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n-GATGAAATCGTTTATGCGCCAAACT\n-+\n-@@@DDDDDHHFHH=GHHIII@GCHI\n-@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n-AGGTGGCTTGAAAGAACTGATCAACA\n-+\n-@CCDDFFFHHHHHHGHIJHIJJCGHI\n-@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n-GTTGATCAGTTCTTTCAAGCCACCT\n-+\n-JIHCIEJIJJJJHHHDD;DDDA?@@\n-@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHGHGHJJGCFHGIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHHHHHJJ<EHIJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CC@FFFFFGDFHGJJIIJIJJJ@HF\n-@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFGHHGFIIJJJJIIJIJH\n-@HWI-ST132:678:C1LFKACXX:6:1307:8164:25340\n-TCTCTAGCTATGCCAAAACTGT\n-+\n-IJJJJJIJJHHDBHFFFFFB@B\n-@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-GGEGIIIJHEFED@FHHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-HHBGIHFGD1JGFAGHHFFFFFC@C\n-@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-GEIGEHGDC1<)HHDDDDBDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-B<GD@?GEEDE>HAFHFDDB=A@@=\n-@HWI-ST132:678:C1LFKACXX:6:1301:18775:28385\n-TATCATCGGCTCGACGGAAA\n-+\n-GHDHGGIGHHHHDDEDBC@@\n-@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-JJIJJIGEAIJHHHFFDFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-?C:?G:E<CF>F>FFC2D;B=+1=\n-@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-HGGHEGFA4IIHHHFBDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-IHFIECJJJJJHGHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n-TTAAACTGTGAATTAAGCGCG\n-+\n-JGHJJJJJHHHFCFFFFF@CB\n-@HWI-ST132:678:C1LFKAC'..b' @HWI-ST132:678:C1LFKACXX:6:1316:14693:8233\n TGAATTGAGAGTCGGCGTTCGTC\n +\n HEJJIJJGJHFFFFFDDDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-HGJJJIJIJIHHHHHBEDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-GCGEIJIIIGHHFDHEFDFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHFGFE1FC<FHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJJJJHGHIHGFAHDHFFFFFBCC\n @HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n GGHJIHHHFECC<DDFFFFDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGJJIIJIHFA3CHHFFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GIHGG?CGFC222F;HFFDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHIJJIIHF:IHHHHHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIIIIGIGGFA<AHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGIHGIIGGIHFHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIIHIGHGHHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHHHGGCD<<BHFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIJIIJJIHGFBFDHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHIIGGCFCHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHGGCCCCAFHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJJJIGHFEHFHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHHJIHBIFCGFCHHHFFFFF@CC\n @HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n EEDIHECF@GEC:DHDFDBAD??@\n-@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHHHE8GHDHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHGIGHGFCHHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIIIIIIHFE@HF?A:DDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GFIHBGGAC@GDDF=HDDFDFC@@\n-@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-HDCHGHGHIGEFAHFFFDDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-DBBIGGDAG?@?FF=FDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-EEIGGHEHDGEFDFDDDEDBD=?@\n-@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JHGJIHGGCC322<2AFFFFD?=:\n-@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIHIGG@HEGHHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIHHJHFFFBHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHEIJHHIHGEHFFHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-@FDFFE@F@F8DD<2+BBDDD??=\n-@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHFE@2@HDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIJIIGFFHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIHGCFC<BHDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGHCIIJIIHF<HGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIJIJJIGG@2<2<DAFFFFF@@=\n @HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n@@ -105266,15 +10702,7 @@\n TGAATTGAGAGTCGGCGTTCGTCAT\n +\n HHD?JHGHHHFEDFHGHFFFFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1303:20279:89985\n-TTTTTAAAATCAAGCAGC\n-+\n-CCCFFFFFHHHHHIJBHH\n @HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n GCTGACATTGCGAAAGTG\n +\n CCCFFFFFHHHHH1EEHH\n-@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n-GCTGACATTGCGAAAGTG\n-+\n-B@BFDFFFHHHAFIJ1CF\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,735 +1,67 @@\n-@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n-TTTTTAACGAATCTAGTATACCCT\n-+\n-B@BDFFFFF?<ADFHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n-TAATCGAATGCTAATTGTAATT\n-+\n-=??AAD?B:<CD>,AFAGF9FA\n @HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n TTAACCGTTTTGAGCTCGGCGACCT\n +\n 1=14BDDDHHHFFIIIIFEA??@FH\n-@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n-TCTTTATATTCGTTGGTATTTGGC\n-+\n-CCCFFFFFHHH<2><C<CJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n-CCGGGACTGCACAGACGAAGCGG\n-+\n-@C@FFFFFHHHHHJJJIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n-AGATTCATGTTCGGATCGTCGATAC\n-+\n-@C@FFFFFHHHHHIJBHIJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n-CGCTTCTTTTGAATGCGTCGTGGTG\n-+\n-CCCFFFFFHHHHHJ,AGHI@<?HCG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n-GCTGCCGCGATTCCCAAACCGTCCTG\n-+\n-B@BDDFFFF?@DFEH<EGIGIJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n TCCTGAGAGTCTGGTCACCGTAGAG\n +\n CCCF?EFFHHHFHJHJJJJ3343<A\n-@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n-ACCGTAGAGAATCTGAGCGTCAGAA\n-+\n-@CCFDFFFGFHHHJGDGHGGHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n CACCAGTCGGCAATATAGATCTCCT\n +\n BCBFFFDFHHHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n-TCTATATTGCCGACTGGTGGCTCAGT\n-+\n-BCBFDFFFHHHHHJJHFCFGGGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n-TCCTTGGCGGAGGTATCGTAGTGAG\n-+\n-CCCFFFFFHHFHH?FHJJJJJHJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n-GTACTCGATCGCCTGAAGAAC\n-+\n-@@CFFFFFHHCFHI+AEHHII\n-@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n-TTCCGGATTGGCAATACCCGCCTC\n-+\n-CCCFFFFFHHHHHGI<GHIJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n-TTACAAAGTCAGTGGGGATGC\n-+\n-@@@FFFFFFFHFCGGE<F@A<\n-@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n-TTTGGCAAGAGGCGGCTCCTCCTG\n-+\n-@@BFFFFFHHDFHEHGIJIIIJII\n-@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n-TCTGTTGGCAGCTAGATCAGGGGC\n-+\n-BCCFDFFFHHFHHGIIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n-TCTGTTGGCAGCTAGATCAGGGG\n-+\n-BBCFDEDFHA<DFHFFHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n-TACTTGAGGACATAGACAAACATTG\n-+\n-BBCFFFFFD=CFHH+AEHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n-TCCAGAACAGGTCTGTGGGACTGATC\n-+\n-CCCFFFFFHHHDHI3<EGIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n-TATCCAGAACAGGTCTGTGGGAC\n-+\n-CCCFFFFFHHH?FFHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n-TCCATAATCCTGACCATCCGGGCAG\n-+\n-CC@FFFFFHHHHGIJIJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n-CCCGGATGGTCAGGATTATGGAAGC\n-+\n-CCCFFFFFHFHHHGHIIIIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n-TACGGTAGAACAACTACACCGAGTGGT\n-+\n-@CCFFDDDGBHHHJIIIJJJJJJFHGI\n-@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n-TTTGCTCGACCACTCGGTGTAGTTGT\n-+\n-CCCFFFFFHHHHHJJEE<ACGIIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n-TTTGCTCGACCACTCGGTGTAGT\n-+\n-@C@FFFFFHHHFHIJFEA+@CFH\n @HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n AAAAACACGACCGTTCGCTTTGAAA\n +\n @CCFBDDFHFHHHHIJJJJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-@@@D;;DDABF,AA?:ECEFE<<\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGC'..b'FFFHHHHHIJBHH\n-@HWI-ST132:678:C1LFKACXX:6:2109:19607:31518\n-TCGTGGTGACTCGGTGCCGC\n-+\n-@C@FFFDDHHHHHJCGGH@G\n-@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n-CCGAGCCGACGAACCGTCCCTGGAA\n-+\n-@@@FFF?DHHDHHJJJBHIICAHGI\n-@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n-GCACCATAGACCAACTCTGCCATC\n-+\n-BCCFFFFF+AFHHJJJJIHIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n-CTTTCGATGGCAGAGTTGGTC\n-+\n-@BBFFFDDHHHHHJJGIIGHI\n-@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n-CCACTGTGGAATTATGAGAGC\n-+\n-B@BFFFDDFDHHH4CAEEGII\n-@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n-AAGCAGCCAAAGCTCCAGGGC\n-+\n-CCBFFFFFHHHDFIJJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n-GCAACCAGTTGATTGGGGACT\n-+\n-@CCFFFFFFHHHHJIJEHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n-ATCGTCGTCAACAACGTTGTCAGGAT\n-+\n-CCCFFFFDHGHHHJHHFE+CHHIJII\n-@HWI-ST132:678:C1LFKACXX:6:1307:17701:69811\n-TCGGTTCGGTTCGGATCG\n-+\n-BBCFDDFFHDFFHIHHII\n-@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n-CCGAACCGAACCGAAACCAAACAAAA\n-+\n-=B@D440@@FHHHJJJJJJIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n-TTCCAAAGTTGTGAGGCACTC\n-+\n-@@@F?DDEDFHHHJIHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n-TTAATTTCGCGTTTTTTCTCG\n-+\n-:?BDDF?DFH@00BFHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n-TCGTGTTCGCTCTCAAACTGAAAC\n-+\n-@CCFFFFFGHHHHJJJGIJEIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n-ACCGGACAGCACGGTCGTGTT\n-+\n-@CCFFFFFFHHHGEEGIFGHG\n-@HWI-ST132:678:C1LFKACXX:6:1306:13426:31059\n-ACCGGACAGCACGGTCGT\n-+\n-?@@DA@DDHHHHHIAEEC\n-@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n-TTAACAATCAGTGCGGTGTAC\n-+\n-CCCFFFFEHHHDFGIIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:7124:23190\n-CAAGCGACACGGACTGGAGCCA\n-+\n-@BCFFFFFHHD<CGIFFHHIIJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:19761:27328\n-CAAGCGACACGGACTGGAGCCA\n-+\n-CCCFFFFFHHHHHIJCGHFGIJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:13059:46395\n-AAACTCTAAGCGGTGGATC\n-+\n-CCCFFFFFFHDFFCGHIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1305:16206:81936\n-AAACTCTAAGCGGTGGATCA\n-+\n-CCCFFFFFHHGHHHHIGIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n-AAACTCTAAGCGGTGGATCACTCG\n-+\n-8?<BDDDDDC?88C@<GGDBEH9C\n-@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n-GCATATCGCAGTCCATGCTGT\n-+\n-CCCFFFFFHHHHHJJJJJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1105:14942:89758\n+@HWI-ST132:678:C1LFKACXX:6:1105:13976:35341\n TACATATGGTTGAGGGTTGTAA\n +\n-B@BFFFFFHFHHHEEFCGHHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:12907:27002\n-TACATATGGTTGAGGGTTGTAA\n-+\n-BB@DFFFFHCDA<EHACGE>CH\n-@HWI-ST132:678:C1LFKACXX:6:2108:10584:25180\n-TACATATGGTTGAGGGTTGTAA\n-+\n-B?@DFFFFHADCFACF2AF<CF\n-@HWI-ST132:678:C1LFKACXX:6:1104:5978:95171\n-TATGGTTGAGGGTTGTAA\n-+\n-B@BFFDEFHHGH<EEBFG\n+@?BDDFFFFCFHH<AAAGGFFH\n @HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n GCTGACATTGCGAAAGTG\n +\n CCCFFFFFHHHHH1EEHH\n-@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n-GCTGACATTGCGAAAGTG\n-+\n-B@BFDFFFHHHAFIJ1CF\n-@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n @HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n ATACTAGATTCGTTGAAAAGT\n +\n@@ -122074,47 +12318,3 @@\n TGTTGCGGCAACTTCTTTAAGTTG\n +\n CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n-ACCGTTCTATGCTTTTTTTT\n-+\n-:BBDDDDFHH<2<CFHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n-AAGTAGCAGTCGTGGCCGAGTG\n-+\n-??+4=B?DDHHF<EGHGGGIDG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n-ATCCTACCGGCTGCGAATGA\n-+\n-@CCFFFFFDFFHHJGEHGBG\n-@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n-ACCGGCTGCGAATGAGAA\n-+\n-B@BFFFFFGHDFCFHEGI\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n-@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n-AATGAGAATGTATATTTT\n-+\n-BCBDDFFFHHFHHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n-ATATAGCCTGAGCTTCGACC\n-+\n-CCCFFFDFHHH?FHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n-GTAACTGACCGTGTGGCCCAATGGA\n-+\n-??@DFFFFGHDHGG?GGIEH3<FGH\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,735 +1,67 @@\n-@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n-TTTTTAACGAATCTAGTATACCCT\n-+\n-B@BDFFFFF?<ADFHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n-TAATCGAATGCTAATTGTAATT\n-+\n-=??AAD?B:<CD>,AFAGF9FA\n @HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n TTAACCGTTTTGAGCTCGGCGACCT\n +\n 1=14BDDDHHHFFIIIIFEA??@FH\n-@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n-TCTTTATATTCGTTGGTATTTGGC\n-+\n-CCCFFFFFHHH<2><C<CJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n-CCGGGACTGCACAGACGAAGCGG\n-+\n-@C@FFFFFHHHHHJJJIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n-AGATTCATGTTCGGATCGTCGATAC\n-+\n-@C@FFFFFHHHHHIJBHIJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n-CGCTTCTTTTGAATGCGTCGTGGTG\n-+\n-CCCFFFFFHHHHHJ,AGHI@<?HCG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n-GCTGCCGCGATTCCCAAACCGTCCTG\n-+\n-B@BDDFFFF?@DFEH<EGIGIJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n TCCTGAGAGTCTGGTCACCGTAGAG\n +\n CCCF?EFFHHHFHJHJJJJ3343<A\n-@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n-ACCGTAGAGAATCTGAGCGTCAGAA\n-+\n-@CCFDFFFGFHHHJGDGHGGHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n CACCAGTCGGCAATATAGATCTCCT\n +\n BCBFFFDFHHHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n-TCTATATTGCCGACTGGTGGCTCAGT\n-+\n-BCBFDFFFHHHHHJJHFCFGGGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n-TCCTTGGCGGAGGTATCGTAGTGAG\n-+\n-CCCFFFFFHHFHH?FHJJJJJHJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n-GTACTCGATCGCCTGAAGAAC\n-+\n-@@CFFFFFHHCFHI+AEHHII\n-@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n-TTCCGGATTGGCAATACCCGCCTC\n-+\n-CCCFFFFFHHHHHGI<GHIJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n-TTACAAAGTCAGTGGGGATGC\n-+\n-@@@FFFFFFFHFCGGE<F@A<\n-@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n-TTTGGCAAGAGGCGGCTCCTCCTG\n-+\n-@@BFFFFFHHDFHEHGIJIIIJII\n-@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n-TCTGTTGGCAGCTAGATCAGGGGC\n-+\n-BCCFDFFFHHFHHGIIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n-TCTGTTGGCAGCTAGATCAGGGG\n-+\n-BBCFDEDFHA<DFHFFHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n-TACTTGAGGACATAGACAAACATTG\n-+\n-BBCFFFFFD=CFHH+AEHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n-TCCAGAACAGGTCTGTGGGACTGATC\n-+\n-CCCFFFFFHHHDHI3<EGIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n-TATCCAGAACAGGTCTGTGGGAC\n-+\n-CCCFFFFFHHH?FFHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n-TCCATAATCCTGACCATCCGGGCAG\n-+\n-CC@FFFFFHHHHGIJIJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n-CCCGGATGGTCAGGATTATGGAAGC\n-+\n-CCCFFFFFHFHHHGHIIIIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n-TACGGTAGAACAACTACACCGAGTGGT\n-+\n-@CCFFDDDGBHHHJIIIJJJJJJFHGI\n-@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n-TTTGCTCGACCACTCGGTGTAGTTGT\n-+\n-CCCFFFFFHHHHHJJEE<ACGIIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n-TTTGCTCGACCACTCGGTGTAGT\n-+\n-@C@FFFFFHHHFHIJFEA+@CFH\n @HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n AAAAACACGACCGTTCGCTTTGAAA\n +\n @CCFBDDFHFHHHHIJJJJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-@@@D;;DDABF,AA?:ECEFE<<\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGC'..b'C\n-+\n-CC@FFFFFHGHHHI3<EHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1212:5835:88214\n-TCTGCAGCGATTCCGAACTC\n-+\n-@CCFFFFFGFHHHIIJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:20279:89985\n-TTTTTAAAATCAAGCAGC\n-+\n-CCCFFFFFHHHHHIJBHH\n-@HWI-ST132:678:C1LFKACXX:6:2109:19607:31518\n-TCGTGGTGACTCGGTGCCGC\n-+\n-@C@FFFDDHHHHHJCGGH@G\n-@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n-CCGAGCCGACGAACCGTCCCTGGAA\n-+\n-@@@FFF?DHHDHHJJJBHIICAHGI\n-@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n-GCACCATAGACCAACTCTGCCATC\n-+\n-BCCFFFFF+AFHHJJJJIHIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n-CTTTCGATGGCAGAGTTGGTC\n-+\n-@BBFFFDDHHHHHJJGIIGHI\n-@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n-CCACTGTGGAATTATGAGAGC\n-+\n-B@BFFFDDFDHHH4CAEEGII\n-@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n-AAGCAGCCAAAGCTCCAGGGC\n-+\n-CCBFFFFFHHHDFIJJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n-GCAACCAGTTGATTGGGGACT\n-+\n-@CCFFFFFFHHHHJIJEHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n-ATCGTCGTCAACAACGTTGTCAGGAT\n-+\n-CCCFFFFDHGHHHJHHFE+CHHIJII\n-@HWI-ST132:678:C1LFKACXX:6:1307:17701:69811\n-TCGGTTCGGTTCGGATCG\n-+\n-BBCFDDFFHDFFHIHHII\n-@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n-CCGAACCGAACCGAAACCAAACAAAA\n-+\n-=B@D440@@FHHHJJJJJJIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n-TTCCAAAGTTGTGAGGCACTC\n-+\n-@@@F?DDEDFHHHJIHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n-TTAATTTCGCGTTTTTTCTCG\n-+\n-:?BDDF?DFH@00BFHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n-TCGTGTTCGCTCTCAAACTGAAAC\n-+\n-@CCFFFFFGHHHHJJJGIJEIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n-ACCGGACAGCACGGTCGTGTT\n-+\n-@CCFFFFFFHHHGEEGIFGHG\n-@HWI-ST132:678:C1LFKACXX:6:1306:13426:31059\n-ACCGGACAGCACGGTCGT\n-+\n-?@@DA@DDHHHHHIAEEC\n-@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n-TTAACAATCAGTGCGGTGTAC\n-+\n-CCCFFFFEHHHDFGIIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:7124:23190\n-CAAGCGACACGGACTGGAGCCA\n-+\n-@BCFFFFFHHD<CGIFFHHIIJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:19761:27328\n-CAAGCGACACGGACTGGAGCCA\n-+\n-CCCFFFFFHHHHHIJCGHFGIJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:13059:46395\n-AAACTCTAAGCGGTGGATC\n-+\n-CCCFFFFFFHDFFCGHIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1305:16206:81936\n-AAACTCTAAGCGGTGGATCA\n-+\n-CCCFFFFFHHGHHHHIGIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n-AAACTCTAAGCGGTGGATCACTCG\n-+\n-8?<BDDDDDC?88C@<GGDBEH9C\n-@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n-GCATATCGCAGTCCATGCTGT\n-+\n-CCCFFFFFHHHHHJJJJJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1105:14942:89758\n+@HWI-ST132:678:C1LFKACXX:6:1105:13976:35341\n TACATATGGTTGAGGGTTGTAA\n +\n-B@BFFFFFHFHHHEEFCGHHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:12907:27002\n-TACATATGGTTGAGGGTTGTAA\n-+\n-BB@DFFFFHCDA<EHACGE>CH\n-@HWI-ST132:678:C1LFKACXX:6:2108:10584:25180\n-TACATATGGTTGAGGGTTGTAA\n-+\n-B?@DFFFFHADCFACF2AF<CF\n-@HWI-ST132:678:C1LFKACXX:6:1104:5978:95171\n-TATGGTTGAGGGTTGTAA\n-+\n-B@BFFDEFHHGH<EEBFG\n+@?BDDFFFFCFHH<AAAGGFFH\n @HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n GCTGACATTGCGAAAGTG\n +\n CCCFFFFFHHHHH1EEHH\n-@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n-GCTGACATTGCGAAAGTG\n-+\n-B@BFDFFFHHHAFIJ1CF\n-@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n @HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n ATACTAGATTCGTTGAAAAGT\n +\n@@ -121998,39 +12314,3 @@\n TGTTGCGGCAACTTCTTTAAGTTG\n +\n CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n-ACCGTTCTATGCTTTTTTTT\n-+\n-:BBDDDDFHH<2<CFHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n-AAGTAGCAGTCGTGGCCGAGTG\n-+\n-??+4=B?DDHHF<EGHGGGIDG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n-ATCCTACCGGCTGCGAATGA\n-+\n-@CCFFFFFDFFHHJGEHGBG\n-@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n-ACCGGCTGCGAATGAGAA\n-+\n-B@BFFFFFGHDFCFHEGI\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n-@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n-AATGAGAATGTATATTTT\n-+\n-BCBDDFFFHHFHHJJJJJ\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,651 +1,55 @@\n-@HWI-ST132:678:C1LFKACXX:6:2105:17359:60231\n-TTTTTTGGCACACGATTTTT\n-+\n-BCBFFFFFHHHHH@FHHIJI\n @HWI-ST132:678:C1LFKACXX:6:1104:3361:38910\n TTTTTTGGCACACGATTTTTTCG\n +\n BCCFFFFFHHHGHF@EHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8271:27021\n-TGGCTCTAGAGGTGGCTCCAGGC\n-+\n-C@CFFFFFHHG3<<ACHIIHGII\n-@HWI-ST132:678:C1LFKACXX:6:1306:9256:39375\n-TGGCTCTAGAGGTGGCTCCAGGC\n-+\n-BBCFFFFFHFHA3+<<EGIIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:12263:15439\n-GCTCTAGAGGTGGCTCCAG\n-+\n-@@@?DEFFHHACFGHJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:8543:80281\n-CTCTAGAGGTGGCTCCAGGCTCT\n-+\n-BBCF=BBDHFHHHIJIIJGIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:13980:18156\n-TCTAGAGGTGGCTCCAGGC\n-+\n-BBBDFFFFCFACDGIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:BBDA2=A=CCFHIJJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?@BDD=BDADHHHHJ3CFGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BDDFFFHHHHFGIJJIIGI\n-@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJJJJJJIHHHFFFFEDDB@@\n-@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B?BDFDFFCFHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:?BDDDFFCF<<<<EGIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJJJJJJJHHHFCFDDDDBBB\n-@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BFFDFFDHFHHJJFIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@BBDFDFFCFHHGHIJIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJJIJJJIHHHDAFDDDDBBB\n-@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?:?DADDD=?::DEEB:<+<:\n-@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCBFFFFFFHHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@CFFFFFFHGHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@@DFFFFF?FHGGIIEHEHG\n-@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBCFFDDFA;DFHIJIIIGII\n-@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFDFFFFFHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JGJJJJJIHD;HHFFFFFBBB\n-@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-IGIIGGIHDCA<44224AB:1\n-@HWI-ST132:678:C1LFKACXX:6:2103:10548:14756\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:B@DFDFFFH<<AEGHHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:2103:3737:60160\n TCTAGAGGTGGCTCCAGGCTC\n +\n B@BDDDEFDFHHHJJJJGIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:8921:19194\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFFFFAFDFHIJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:2104:15981:63048\n TCTAGAGGTGGCTCCAGGCTC\n +\n B@BDDFFFFHHHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:11258:78941\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBFFFFFHH?FHHIJIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:17344:88675\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFFFHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:1224:28968\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-CGCFFGFEC<DAADA2A4=:=\n-@HWI-ST132:678:C1LFKACXX:6:2107:13563:38548\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@@FF?DFHH?HHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:9652:62249\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJIIJIHGHHFHFFFFFDBB@\n-@HWI-ST132:678:C1LFKACXX:6:1212:17696:96425\n-TCTAGAGGTGGCTCCAGGCTCT\n-+\n-B@@DDDFFCFDFHGGIIJIJJI\n-@HWI-ST132:678:C1LFKACXX:6:1302:11655:74544\n-TCTAGAGGTGGCTCCAGGCTCT\n-+\n-:=@BD=+A4AAFFEG@EHIIIG\n-@HWI-ST132:678:C1LFKACXX:6:2103:15155:59922\n-TCTAGAGGTGGCTCCAGGCTCT\n-+\n-BBBDDDFFFHACDHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:12318:50696\n-TCTAGAGGTGGCTCCAGGCTCT\n-+\n-BBBDFFFFFFHHHJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:7049:81574\n-TCTAGAGGTGGCTCCAGGCTCT\n-+\n-BBBDDDFFFHFHHIJJIJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1206:10'..b'CGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJIIHFEIIIHHHHHFFFBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-DIGJIFD?1@@C<0@HHDFFDD??:\n-@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-?HEGHC4HFHG@HFDHHDDD=D@@@\n-@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIIHIHFHHHFFFFF@CC\n-@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIHIJHHHHHFFFFFBCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-FJJIIIGD?FCGHHHHHDDB?FCBB\n-@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJIHF?114C@@CHHFFFFFBB=\n-@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n-TTCGATCGCCGACGTGTGAAGACG\n-+\n-IIIGC<HGGFGHHHHHFFEBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n-ATTCGATCGCCGACGTGTGAAGACG\n-+\n-JJIHGGCGIGJJGHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n-TTCGATCGCCGACGTGTGAAGAC\n-+\n-JJHIGHEGFIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674\n-TCTTCACACGTCGGCGATCGA\n-+\n-@@@DDFFFFHFFDHJGIDD@G\n-@HWI-ST132:678:C1LFKACXX:6:1210:17629:31055\n-TTCACACGTCGGCGATCGA\n-+\n-CCCFFFFFHHHDC<EGHID\n-@HWI-ST132:678:C1LFKACXX:6:1203:18672:91263\n-AATTCGATCGCCGACGTGTGAA\n-+\n-JIJJHHFJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1313:1560:43567\n-GCTTTTTCGTGGGGAGATC\n-+\n-@BCDFFFFFDFFHIJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725\n-TAAGAATTCCGAAACGCCATC\n-+\n-IHEGAG@ED8FDDBBDDD=+?\n-@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n-TGCAAGCTAAGAATTCCGAAACGCC\n-+\n-JJIJJJJJJIHFCAC:HDA==D?B:\n-@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937\n-CGATGTGTTTGTTCGCCCGTC\n-+\n-@@CFFBDBFHHDFHAFHI)@F\n @HWI-ST132:678:C1LFKACXX:6:1209:11809:98806\n AACCTCCTAGTCGCTGTGACT\n +\n JJIJIJIGGHHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841\n-CAGGTTAACCTCCTAGTCGCT\n-+\n-JIJJJJJJHHHHHFFFDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084\n-CAGGTTAACCTCCTAGTCGCT\n-+\n-IIIJIJJIHHHHHFFFDFC@@\n-@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864\n-TTCTTGAACTTGCGAGCACCG\n-+\n-CCCFFFFFHHHAAFC3BEHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094\n-TTCTTGAACTTGCGAGCACCG\n-+\n-CCCFFFFFHHHDHCCFFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n-GTAACACTTTGTAACGGATCGCAAA\n-+\n-@@@DFFFFHHHGHIJJJEIIIIDII\n-@HWI-ST132:678:C1LFKACXX:6:1202:15474:8031\n-TGATGATCAAGTAGTTTCTC\n-+\n-BBCFFFFFHFCAFCHHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705\n-TTGCATTAATCTGAAAGTTGC\n-+\n-IHIGIJJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870\n-CAAATTGGCTTTCCGTCGACT\n-+\n-@@@DFFFFHHGHFHJJEIGHH\n-@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n-TTTCCGTCGACTAACAATAAGCCGT\n-+\n-B@CFFFDDFHHHHJJIJJDHIIIJG\n-@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n-AAAATGTCAGTCACTCAGCCAAAGG\n-+\n-BBCFFFDF?FHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n-TCCTTTGGCTGAGTGACTGACATTT\n-+\n-HEHCFHFFHCA2<<CHFDBDDF@@?\n-@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164\n-CCAAGGAGTCGGCAGCTGAAG\n-+\n-@@@DDDDDCD?FF1)AEGGII\n-@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n-CAAGGAGTCGGCAGCTGAAGTAGCA\n-+\n-=@@DD?DDFF?)@FAH>FEFHHEHE\n-@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805\n-AGTGGGGCCAGAGGGGCTGCT\n-+\n->?:C?:@BFFFCHDADDD@?<\n-@HWI-ST132:678:C1LFKACXX:6:1308:5462:60542\n-TTTGACAGAGAGTGGGGCC\n-+\n-JHHFEFAHGHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042\n-CGGCTTTGTCACTGTTTGATC\n-+\n-@CBFFFFFHHHHHIGHHIGJJ\n-@HWI-ST132:678:C1LFKACXX:6:1108:6289:74344\n-TTTGACAATTGGCGCCGGCG\n-+\n-@C@FFFFFHHDCD8CFIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204\n-TATTGAACTGAAGCCCCCGGC\n-+\n-CCCFFFFFHHHHGJJJJJ@GG\n @HWI-ST132:678:C1LFKACXX:6:2102:9712:32185\n ATTGAACTGAAGCCCCCGGCC\n +\n ?@@BBDBDDFFADHIIIH)?F\n-@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925\n-GAGCGGGTTTGGCCGGGGGCT\n-+\n-JJJJJJJJHGHHHDFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120\n-TGCACGATTCCAATAGTGCTG\n-+\n-IJIGCJIJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1206:15175:27778\n-AATTTGGCGGCTTGGGCTC\n-+\n-C;?1)HHDF??DDDDD???\n-@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n-TCGTACCGATCTAGACATCTCTTC\n-+\n-GIJJJJJJIGJHHHGHD<FFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1107:17975:4570\n-GATCGGTACGACTCGTCGGAGT\n-+\n-BCBFFFDFHHHHHJJIJGECFD\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,19 +1,3 @@\n-@HWI-ST132:678:C1LFKACXX:6:2107:14168:54674\n-TATCACTGTATGCGTAGAAAAGAG\n-+\n-CCCFDFFFHHGDFFFHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:20798:12533\n-TCTGCTATCACTGTATGCGTAGAAA\n-+\n-@@@FDDDFHGHHGJIJIG@GCEFDB\n-@HWI-ST132:678:C1LFKACXX:6:2104:13786:79730\n-TCTGCTATCACTGTATGCGTAG\n-+\n-BCCFFFFFHHHHHJHJJJJGIJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:17764:96282\n-TCTGCTATCACTGTATGC\n-+\n-BCBFFFFFHBHHHJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1313:10358:95570\n TAATATAGATTTAAAGTCTAAGAACT\n +\n@@ -22,866 +6,74 @@\n TAATATAGATTTAAAGTCTAAGAACT\n +\n BCCFFFFFGHHHH>GHFHJJJIGJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1301:16563:56958\n-AAGGCAATGCAAAACAAGAATTT\n-+\n-FAA3GHHBEIFHHFDDBDDB@@@\n-@HWI-ST132:678:C1LFKACXX:6:1115:14943:55336\n-TTCTTGTTTTGCATTGCC\n-+\n-:B144ADDHHHHHJIIIG\n-@HWI-ST132:678:C1LFKACXX:6:1107:12070:23186\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-CCCDDEFFHHHHHJJJJJAJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1110:20211:14418\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-CCCFFFFFHHHHHJJJJJIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:13578:65370\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-@8?D=BDFGHHFHIJJJJFGIJIJIJ\n @HWI-ST132:678:C1LFKACXX:6:2101:7667:91449\n TAGTATATTTATTAAATCATTTGACT\n +\n CCCDDEFFHHHHHJJJJJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:12382:29561\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:2107:9787:36481\n TAGTATATTTATTAAATCATTTGACT\n +\n BBBD:ADDHHHHH4HGHIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:14356:68993\n-TAATGTTACATCATATTAAGTCAAATGA\n-+\n-JIJJIHIHJJJJJJJHHHFHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1107:18073:46755\n-AAATATTTCGCTTTTAAAAAATTG\n-+\n-@@CFFFFFHHHGHJIJJBDAGIII\n-@HWI-ST132:678:C1LFKACXX:6:1302:10066:99383\n-AATATTTCGCTTTTAAAAAATTG\n-+\n-BBBDFFFFH@FHHJJJIJGIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:11961:47390\n-ATATTTCGCTTTTAAAAAATTG\n-+\n-CCCFFFFFHHHHHIIHHJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2103:9377:13404\n-TAAATTTGTTTGTTAAAATCGCCG\n-+\n-CCCFFFFFHHHGHIJJJJJHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:5142:10985\n-TTTAAATTTGTTTGTTAAAATCGCC\n-+\n-BCCFDFFFHHHHHIJIJJJJIIIGH\n-@HWI-ST132:678:C1LFKACXX:6:1205:5640:63048\n-TAATAGTCAGGGCGCGAATTTT\n-+\n-=;BD:2=BFHFDFEF6EHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1211:3646:44689\n-TAATAGTCAGGGCGCGAATTTT\n-+\n-@C@FFFDFHHHHGHHJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1108:20386:47976\n-TAATAGTCAGGGCGCGAATTTTT\n-+\n-?@?D;B=B?CAC:2<CFGHIIGI\n-@HWI-ST132:678:C1LFKACXX:6:1207:2583:92360\n-TAATAGTCAGGGCGCGAATTTTT\n-+\n-B@CFFFDDHHDFFGFGHEGHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1102:11267:71435\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@BFFDBDFHHDFIIHJBFFGIGG\n-@HWI-ST132:678:C1LFKACXX:6:1107:9710:51191\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FDF?DHHHDHFGHGGHGJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1108:5610:75509\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFFFFGHGG<DHGHGHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:13565:15908\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFEFHHHCAFGHIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:11179:97926\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FDEBD<FH<DGGIIGGHGIII\n-@HWI-ST132:678:C1LFKACXX:6:1110:18682:30268\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFFFHHHFGIJJIHIIJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1114:13195:76362\n TAATAGTCAGGGCGCGAATTTTTA\n +\n ?@?DDB=DFDDHGIIEBHD=FHIH\n-@HWI-ST132:678:C1LFKACXX:6:1201:9017:61055\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFDFFFHHFFH@BEEGIHJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1201:5418:63606\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@CFBDDEHHA<CFEFHIHIIIII\n-@HWI-ST132:678:C1LFKACXX:6:1213:8541:21411\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@CFFFDDHHFFFFGHIHIJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1214:13791:80762\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FDDDDHFHDHIFII1DFHGGF\n-@HWI-ST132:678:C1LFKACXX:6:1309:8889:7362\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@CFFFFFDHHHHJIJJJHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:17898:28199\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@??DFADDDHCHFFBGGEHIGJGI\n-@HWI-ST132:678:C1LFKACXX:6:2104:10515:36849\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@CCFFFDFHHFHHJIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:6101:64627\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FFFFFHHD:C<@@@CGHIIII\n-@HWI-ST132:678:C1LFKACXX:6:2105:18687:69886\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFFEHHFFH@FHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:16747:90974\n-TAATAGTC'..b'CGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJIIHFEIIIHHHHHFFFBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-DIGJIFD?1@@C<0@HHDFFDD??:\n-@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-?HEGHC4HFHG@HFDHHDDD=D@@@\n-@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIIHIHFHHHFFFFF@CC\n-@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIHIJHHHHHFFFFFBCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-FJJIIIGD?FCGHHHHHDDB?FCBB\n-@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJIHF?114C@@CHHFFFFFBB=\n-@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n-TTCGATCGCCGACGTGTGAAGACG\n-+\n-IIIGC<HGGFGHHHHHFFEBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n-ATTCGATCGCCGACGTGTGAAGACG\n-+\n-JJIHGGCGIGJJGHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n-TTCGATCGCCGACGTGTGAAGAC\n-+\n-JJHIGHEGFIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674\n-TCTTCACACGTCGGCGATCGA\n-+\n-@@@DDFFFFHFFDHJGIDD@G\n-@HWI-ST132:678:C1LFKACXX:6:1210:17629:31055\n-TTCACACGTCGGCGATCGA\n-+\n-CCCFFFFFHHHDC<EGHID\n-@HWI-ST132:678:C1LFKACXX:6:1203:18672:91263\n-AATTCGATCGCCGACGTGTGAA\n-+\n-JIJJHHFJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1313:1560:43567\n-GCTTTTTCGTGGGGAGATC\n-+\n-@BCDFFFFFDFFHIJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725\n-TAAGAATTCCGAAACGCCATC\n-+\n-IHEGAG@ED8FDDBBDDD=+?\n-@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n-TGCAAGCTAAGAATTCCGAAACGCC\n-+\n-JJIJJJJJJIHFCAC:HDA==D?B:\n-@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937\n-CGATGTGTTTGTTCGCCCGTC\n-+\n-@@CFFBDBFHHDFHAFHI)@F\n @HWI-ST132:678:C1LFKACXX:6:1209:11809:98806\n AACCTCCTAGTCGCTGTGACT\n +\n JJIJIJIGGHHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841\n-CAGGTTAACCTCCTAGTCGCT\n-+\n-JIJJJJJJHHHHHFFFDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084\n-CAGGTTAACCTCCTAGTCGCT\n-+\n-IIIJIJJIHHHHHFFFDFC@@\n-@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864\n-TTCTTGAACTTGCGAGCACCG\n-+\n-CCCFFFFFHHHAAFC3BEHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094\n-TTCTTGAACTTGCGAGCACCG\n-+\n-CCCFFFFFHHHDHCCFFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n-GTAACACTTTGTAACGGATCGCAAA\n-+\n-@@@DFFFFHHHGHIJJJEIIIIDII\n-@HWI-ST132:678:C1LFKACXX:6:1202:15474:8031\n-TGATGATCAAGTAGTTTCTC\n-+\n-BBCFFFFFHFCAFCHHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705\n-TTGCATTAATCTGAAAGTTGC\n-+\n-IHIGIJJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870\n-CAAATTGGCTTTCCGTCGACT\n-+\n-@@@DFFFFHHGHFHJJEIGHH\n-@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n-TTTCCGTCGACTAACAATAAGCCGT\n-+\n-B@CFFFDDFHHHHJJIJJDHIIIJG\n-@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n-AAAATGTCAGTCACTCAGCCAAAGG\n-+\n-BBCFFFDF?FHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n-TCCTTTGGCTGAGTGACTGACATTT\n-+\n-HEHCFHFFHCA2<<CHFDBDDF@@?\n-@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164\n-CCAAGGAGTCGGCAGCTGAAG\n-+\n-@@@DDDDDCD?FF1)AEGGII\n-@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n-CAAGGAGTCGGCAGCTGAAGTAGCA\n-+\n-=@@DD?DDFF?)@FAH>FEFHHEHE\n-@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805\n-AGTGGGGCCAGAGGGGCTGCT\n-+\n->?:C?:@BFFFCHDADDD@?<\n-@HWI-ST132:678:C1LFKACXX:6:1308:5462:60542\n-TTTGACAGAGAGTGGGGCC\n-+\n-JHHFEFAHGHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042\n-CGGCTTTGTCACTGTTTGATC\n-+\n-@CBFFFFFHHHHHIGHHIGJJ\n-@HWI-ST132:678:C1LFKACXX:6:1108:6289:74344\n-TTTGACAATTGGCGCCGGCG\n-+\n-@C@FFFFFHHDCD8CFIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204\n-TATTGAACTGAAGCCCCCGGC\n-+\n-CCCFFFFFHHHHGJJJJJ@GG\n @HWI-ST132:678:C1LFKACXX:6:2102:9712:32185\n ATTGAACTGAAGCCCCCGGCC\n +\n ?@@BBDBDDFFADHIIIH)?F\n-@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925\n-GAGCGGGTTTGGCCGGGGGCT\n-+\n-JJJJJJJJHGHHHDFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120\n-TGCACGATTCCAATAGTGCTG\n-+\n-IJIGCJIJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1206:15175:27778\n-AATTTGGCGGCTTGGGCTC\n-+\n-C;?1)HHDF??DDDDD???\n-@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n-TCGTACCGATCTAGACATCTCTTC\n-+\n-GIJJJJJJIGJHHHGHD<FFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1107:17975:4570\n-GATCGGTACGACTCGTCGGAGT\n-+\n-BCBFFFDFHHHHHJJIJGECFD\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,207 +1,23 @@ -@HWI-ST132:678:C1LFKACXX:6:1103:6450:33284 -AACCCGTAAATCCGAACTTG -+ -?@@DD<@DCCABFGF1@GHI -@HWI-ST132:678:C1LFKACXX:6:1104:7735:58473 -AACCCGTAAATCCGAACTTG -+ -:?@DDDDD@<2CAEFHGGIC -@HWI-ST132:678:C1LFKACXX:6:1111:8344:28118 -AACCCGTAAATCCGAACTTG -+ -?@@DDADD@B<ADCAEEGGI -@HWI-ST132:678:C1LFKACXX:6:1201:4901:28957 -AACCCGTAAATCCGAACTTG -+ -@@@FFFFFDAAFHFHGIIJH -@HWI-ST132:678:C1LFKACXX:6:1201:14858:55180 -AACCCGTAAATCCGAACTTG -+ -?B@FDFFFCAHAFGFHIJJJ -@HWI-ST132:678:C1LFKACXX:6:1208:10957:88261 -AACCCGTAAATCCGAACTTG -+ -@@@FFFDDFFFDFCE+CFHI @HWI-ST132:678:C1LFKACXX:6:1211:4119:82063 AACCCGTAAATCCGAACTTG + B?@FFFDF@AACFFAEHHJI -@HWI-ST132:678:C1LFKACXX:6:1301:7756:37290 -AACCCGTAAATCCGAACTTG -+ -=BBDFFFF@<ADFHEGIJJI -@HWI-ST132:678:C1LFKACXX:6:1315:14080:19805 -AACCCGTAAATCCGAACTTG -+ -?@?DDDDFFDDHHJI;EGIE -@HWI-ST132:678:C1LFKACXX:6:2106:14523:50358 -AACCCGTAAATCCGAACTTG -+ -BBBFFFFFH:<ADHGIJJJJ -@HWI-ST132:678:C1LFKACXX:6:2107:6396:35457 -AACCCGTAAATCCGAACTTG -+ -:?BDFFFF<><ADFHIJJJJ -@HWI-ST132:678:C1LFKACXX:6:1106:15354:26782 -AACCCGTAAATCCGAACTTGTG -+ -BB@DFFDFCAADHGIGGHIII? -@HWI-ST132:678:C1LFKACXX:6:1206:3893:47334 -AACCCGTAAATCCGAACTTGTG -+ -?@@F@D@DDDDFHGIBCCHEAB -@HWI-ST132:678:C1LFKACXX:6:1212:8247:60863 -AACCCGTAAATCCGAACTTGTG -+ -?@@FFFDDCA?DFIIGEEHIGH -@HWI-ST132:678:C1LFKACXX:6:2103:20330:81235 -AACCCGTAAATCCGAACTTGTG -+ -=?BDFFFF<<<<D<CEHIJHAF -@HWI-ST132:678:C1LFKACXX:6:2105:18756:21094 -AACCCGTAAATCCGAACTTGTG -+ -CCCFFFFFHFHHHJJJJJJJII -@HWI-ST132:678:C1LFKACXX:6:2108:11590:68948 -AACCCGTAAATCCGAACTTGTG -+ -=?@;DDDD@<ACDGFHHEHAEE -@HWI-ST132:678:C1LFKACXX:6:2109:7213:21129 -AACCCGTAAATCCGAACTTGTG -+ -:B@DFFFF<<<ADBGEFFHIFH @HWI-ST132:678:C1LFKACXX:6:1113:9515:60678 CAAGACCGGCATTATGGGAGTC + ?@;DDFFFDFCFHJJGA8CGEH -@HWI-ST132:678:C1LFKACXX:6:1211:4033:43798 -CAAGACCGGCATTATGGGAGTC -+ -@CCFFFFFHHHHHJGHIJIJFH -@HWI-ST132:678:C1LFKACXX:6:2102:15781:17798 -CAAGACCGGCATTATGGGAGTC -+ -??@DDDDDFFDFFEH<CED:11 -@HWI-ST132:678:C1LFKACXX:6:2105:13568:17777 -CAAGACCGGCATTATGGGAGTC -+ -@BBFBDDD<CFHHHHAGHIJGH -@HWI-ST132:678:C1LFKACXX:6:1116:7415:45912 -TCCCTGAGACCCTAACTTGTG -+ -=?1=ABDDHHGHGICFCEIFF -@HWI-ST132:678:C1LFKACXX:6:1312:17503:22366 -TCCCTGAGACCCTAACTTGTG -+ -@@?DFFFFBHHGHIIIJIGHG @HWI-ST132:678:C1LFKACXX:6:1101:13208:32198 TCCCTGAGACCCTAACTTGTGA + CCCFFFEFFHHHHIJJIIJHHI -@HWI-ST132:678:C1LFKACXX:6:1102:17974:5349 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFDFHGHHHGIJJJJHGI -@HWI-ST132:678:C1LFKACXX:6:1105:10525:58469 -TCCCTGAGACCCTAACTTGTGA -+ -B@CFFFDDDHFHGHIIIGHHIJ -@HWI-ST132:678:C1LFKACXX:6:1106:11675:95913 -TCCCTGAGACCCTAACTTGTGA -+ -@@@DDDDDFHHHHAFH?G+AFH @HWI-ST132:678:C1LFKACXX:6:1107:11700:11209 TCCCTGAGACCCTAACTTGTGA + ?@@DD;==DHFDCGCFEDHHHE -@HWI-ST132:678:C1LFKACXX:6:1109:4618:19903 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHCGGHIJEHH -@HWI-ST132:678:C1LFKACXX:6:1111:16886:54124 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHEHIJJFHIJ -@HWI-ST132:678:C1LFKACXX:6:1113:14917:12939 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHJJJJJIAGH -@HWI-ST132:678:C1LFKACXX:6:1113:15286:60745 -TCCCTGAGACCCTAACTTGTGA -+ -@@@FFFDD2ADFFBHCGGAHHI -@HWI-ST132:678:C1LFKACXX:6:1116:10143:61594 -TCCCTGAGACCCTAACTTGTGA -+ -@B=DDFFFHHHHHIHIJJJHIH @HWI-ST132:678:C1LFKACXX:6:1201:12358:31858 TCCCTGAGACCCTAACTTGTGA + :BBFFF24>ADHHIJJJJHAFH -@HWI-ST132:678:C1LFKACXX:6:1207:19763:6169 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHGIJIJEHHI -@HWI-ST132:678:C1LFKACXX:6:1208:17227:84730 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHGHGHIJIH<CH -@HWI-ST132:678:C1LFKACXX:6:1209:14006:3385 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFFHHHHEHGHHIFGF -@HWI-ST132:678:C1LFKACXX:6:1212:19731:4329 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHJIHIIJHHI -@HWI-ST132:678:C1LFKACXX:6:1212:8981:55837 -TCCCTGAGACCCTAACTTGTGA -+ -@@@D?EFDFFHHHJJIBEGAFC -@HWI-ST132:678:C1LFKACXX:6:1214:16337:65541 -TCCCTGAGACCCTAACTTGTGA -+ -BC?DDFFFGHHHFIIJJIIFGG -@HWI-ST132:678:C1LFKACXX:6:1214:9263:76030 -TCCCTGAGACCCTAACTTGTGA -+ -@@@FFFFFHFHDHEEHIIHAFH -@HWI-ST132:678:C1LFKACXX:6:1215:7321:50488 -TCCCTGAGACCCTAACTTGTGA -+ -@C@DDFDDFFHBDHIIBE@FEH -@HWI-ST132:678:C1LFKACXX:6:1302:17139:90749 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHGHGIJHIIHHI -@HWI-ST132:678:C1LFKACXX:6:1302:8853:99407 -TCCCTGAGACCCTAACTTGTGA -+ -B@BFFFFFHFHHHBFHHIHAFH -@HWI-ST132:678:C1LFKACXX:6:1304:2649:24602 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFDHHHHHGHIJJJFGI -@HWI-ST132:678:C1LFKACXX:6:1304:17263:52290 -TCCCTGAGACCCTAACTTGTGA -+ -@CCFFFFFDHHHH@GIIIIHHI -@HWI-ST132:678:C1LFKACXX:6:1312:12615:9458 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFGHHHH@FIJIF<CH -@HWI-ST132:678:C1LFKACXX:6:1314:17779:75206 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFGHHHHEHJJJJFHJ -@HWI-ST132:678:C1LFKACXX:6:1315:9929:42151 -TCCCTGAGACCCTAACTTGTGA -+ -@@@DDF?D8FHHHGHHIIJEGI -@HWI-ST132:678:C1LFKACXX:6:2103:13958:97727 -TCCCTGAGACCCTAACTTGTGA -+ -@CCFFFFF<FHHHIIJJJJHHJ @HWI-ST132:678:C1LFKACXX:6:2104:10613:2992 TCCCTGAGACCCTAACTTGTGA + @@ -210,14 +26,6 @@ TCCCTGAGACCCTAACTTGTGA + CCCFFFFFHHHHHJJIIIICGI -@HWI-ST132:678:C1LFKACXX:6:2106:15768:75632 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFFHHHHJJJJJ4CFH -@HWI-ST132:678:C1LFKACXX:6:2109:16865:57940 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHIIIJJ<FHH @HWI-ST132:678:C1LFKACXX:6:2109:18750:76156 TCCCTGAGACCCTAACTTGTGA + @@ -226,27 +34,3 @@ TCCCTGAGACCCTAACTTGTGACT + CCCFFFFFGHHHHJJJJI:AFHIJ -@HWI-ST132:678:C1LFKACXX:6:1113:14924:44339 -CCCTGAGACCCTAACTTGTGAC -+ -??@DD;B?DDFHBED?CHGHII -@HWI-ST132:678:C1LFKACXX:6:1107:1375:15117 -TCACAAGTTTTGATCTCCGGTAT -+ -=??D:2A2=?DDCEHBHIJICCG -@HWI-ST132:678:C1LFKACXX:6:2105:17358:56431 -CACAAGTTTTGATCTCCGGTAT -+ -@@@DADDDHH>FHGIGEB@<@F -@HWI-ST132:678:C1LFKACXX:6:1102:6534:83469 -ACAAGTTTTGATCTCCGGTAT -+ -@@CDDDDFHHHHHJJIJJHGI -@HWI-ST132:678:C1LFKACXX:6:1212:17825:83469 -ACAAGTTTTGATCTCCGGTAT -+ -@@@FFFFFHHDFHIJJJIFDH -@HWI-ST132:678:C1LFKACXX:6:1304:1702:48389 -ACAAGTTTTGATCTCCGGTAT -+ -@@@B?=DDHDGFFIIIGGF>E |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,207 +1,23 @@ -@HWI-ST132:678:C1LFKACXX:6:1103:6450:33284 -AACCCGTAAATCCGAACTTG -+ -?@@DD<@DCCABFGF1@GHI -@HWI-ST132:678:C1LFKACXX:6:1104:7735:58473 -AACCCGTAAATCCGAACTTG -+ -:?@DDDDD@<2CAEFHGGIC -@HWI-ST132:678:C1LFKACXX:6:1111:8344:28118 -AACCCGTAAATCCGAACTTG -+ -?@@DDADD@B<ADCAEEGGI -@HWI-ST132:678:C1LFKACXX:6:1201:4901:28957 -AACCCGTAAATCCGAACTTG -+ -@@@FFFFFDAAFHFHGIIJH -@HWI-ST132:678:C1LFKACXX:6:1201:14858:55180 -AACCCGTAAATCCGAACTTG -+ -?B@FDFFFCAHAFGFHIJJJ -@HWI-ST132:678:C1LFKACXX:6:1208:10957:88261 -AACCCGTAAATCCGAACTTG -+ -@@@FFFDDFFFDFCE+CFHI @HWI-ST132:678:C1LFKACXX:6:1211:4119:82063 AACCCGTAAATCCGAACTTG + B?@FFFDF@AACFFAEHHJI -@HWI-ST132:678:C1LFKACXX:6:1301:7756:37290 -AACCCGTAAATCCGAACTTG -+ -=BBDFFFF@<ADFHEGIJJI -@HWI-ST132:678:C1LFKACXX:6:1315:14080:19805 -AACCCGTAAATCCGAACTTG -+ -?@?DDDDFFDDHHJI;EGIE -@HWI-ST132:678:C1LFKACXX:6:2106:14523:50358 -AACCCGTAAATCCGAACTTG -+ -BBBFFFFFH:<ADHGIJJJJ -@HWI-ST132:678:C1LFKACXX:6:2107:6396:35457 -AACCCGTAAATCCGAACTTG -+ -:?BDFFFF<><ADFHIJJJJ -@HWI-ST132:678:C1LFKACXX:6:1106:15354:26782 -AACCCGTAAATCCGAACTTGTG -+ -BB@DFFDFCAADHGIGGHIII? -@HWI-ST132:678:C1LFKACXX:6:1206:3893:47334 -AACCCGTAAATCCGAACTTGTG -+ -?@@F@D@DDDDFHGIBCCHEAB -@HWI-ST132:678:C1LFKACXX:6:1212:8247:60863 -AACCCGTAAATCCGAACTTGTG -+ -?@@FFFDDCA?DFIIGEEHIGH -@HWI-ST132:678:C1LFKACXX:6:2103:20330:81235 -AACCCGTAAATCCGAACTTGTG -+ -=?BDFFFF<<<<D<CEHIJHAF -@HWI-ST132:678:C1LFKACXX:6:2105:18756:21094 -AACCCGTAAATCCGAACTTGTG -+ -CCCFFFFFHFHHHJJJJJJJII -@HWI-ST132:678:C1LFKACXX:6:2108:11590:68948 -AACCCGTAAATCCGAACTTGTG -+ -=?@;DDDD@<ACDGFHHEHAEE -@HWI-ST132:678:C1LFKACXX:6:2109:7213:21129 -AACCCGTAAATCCGAACTTGTG -+ -:B@DFFFF<<<ADBGEFFHIFH @HWI-ST132:678:C1LFKACXX:6:1113:9515:60678 CAAGACCGGCATTATGGGAGTC + ?@;DDFFFDFCFHJJGA8CGEH -@HWI-ST132:678:C1LFKACXX:6:1211:4033:43798 -CAAGACCGGCATTATGGGAGTC -+ -@CCFFFFFHHHHHJGHIJIJFH -@HWI-ST132:678:C1LFKACXX:6:2102:15781:17798 -CAAGACCGGCATTATGGGAGTC -+ -??@DDDDDFFDFFEH<CED:11 -@HWI-ST132:678:C1LFKACXX:6:2105:13568:17777 -CAAGACCGGCATTATGGGAGTC -+ -@BBFBDDD<CFHHHHAGHIJGH -@HWI-ST132:678:C1LFKACXX:6:1116:7415:45912 -TCCCTGAGACCCTAACTTGTG -+ -=?1=ABDDHHGHGICFCEIFF -@HWI-ST132:678:C1LFKACXX:6:1312:17503:22366 -TCCCTGAGACCCTAACTTGTG -+ -@@?DFFFFBHHGHIIIJIGHG @HWI-ST132:678:C1LFKACXX:6:1101:13208:32198 TCCCTGAGACCCTAACTTGTGA + CCCFFFEFFHHHHIJJIIJHHI -@HWI-ST132:678:C1LFKACXX:6:1102:17974:5349 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFDFHGHHHGIJJJJHGI -@HWI-ST132:678:C1LFKACXX:6:1105:10525:58469 -TCCCTGAGACCCTAACTTGTGA -+ -B@CFFFDDDHFHGHIIIGHHIJ -@HWI-ST132:678:C1LFKACXX:6:1106:11675:95913 -TCCCTGAGACCCTAACTTGTGA -+ -@@@DDDDDFHHHHAFH?G+AFH @HWI-ST132:678:C1LFKACXX:6:1107:11700:11209 TCCCTGAGACCCTAACTTGTGA + ?@@DD;==DHFDCGCFEDHHHE -@HWI-ST132:678:C1LFKACXX:6:1109:4618:19903 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHCGGHIJEHH -@HWI-ST132:678:C1LFKACXX:6:1111:16886:54124 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHEHIJJFHIJ -@HWI-ST132:678:C1LFKACXX:6:1113:14917:12939 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHJJJJJIAGH -@HWI-ST132:678:C1LFKACXX:6:1113:15286:60745 -TCCCTGAGACCCTAACTTGTGA -+ -@@@FFFDD2ADFFBHCGGAHHI -@HWI-ST132:678:C1LFKACXX:6:1116:10143:61594 -TCCCTGAGACCCTAACTTGTGA -+ -@B=DDFFFHHHHHIHIJJJHIH @HWI-ST132:678:C1LFKACXX:6:1201:12358:31858 TCCCTGAGACCCTAACTTGTGA + :BBFFF24>ADHHIJJJJHAFH -@HWI-ST132:678:C1LFKACXX:6:1207:19763:6169 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHGIJIJEHHI -@HWI-ST132:678:C1LFKACXX:6:1208:17227:84730 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHGHGHIJIH<CH -@HWI-ST132:678:C1LFKACXX:6:1209:14006:3385 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFFHHHHEHGHHIFGF -@HWI-ST132:678:C1LFKACXX:6:1212:19731:4329 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHJIHIIJHHI -@HWI-ST132:678:C1LFKACXX:6:1212:8981:55837 -TCCCTGAGACCCTAACTTGTGA -+ -@@@D?EFDFFHHHJJIBEGAFC -@HWI-ST132:678:C1LFKACXX:6:1214:16337:65541 -TCCCTGAGACCCTAACTTGTGA -+ -BC?DDFFFGHHHFIIJJIIFGG -@HWI-ST132:678:C1LFKACXX:6:1214:9263:76030 -TCCCTGAGACCCTAACTTGTGA -+ -@@@FFFFFHFHDHEEHIIHAFH -@HWI-ST132:678:C1LFKACXX:6:1215:7321:50488 -TCCCTGAGACCCTAACTTGTGA -+ -@C@DDFDDFFHBDHIIBE@FEH -@HWI-ST132:678:C1LFKACXX:6:1302:17139:90749 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHGHGIJHIIHHI -@HWI-ST132:678:C1LFKACXX:6:1302:8853:99407 -TCCCTGAGACCCTAACTTGTGA -+ -B@BFFFFFHFHHHBFHHIHAFH -@HWI-ST132:678:C1LFKACXX:6:1304:2649:24602 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFDHHHHHGHIJJJFGI -@HWI-ST132:678:C1LFKACXX:6:1304:17263:52290 -TCCCTGAGACCCTAACTTGTGA -+ -@CCFFFFFDHHHH@GIIIIHHI -@HWI-ST132:678:C1LFKACXX:6:1312:12615:9458 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFGHHHH@FIJIF<CH -@HWI-ST132:678:C1LFKACXX:6:1314:17779:75206 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFGHHHHEHJJJJFHJ -@HWI-ST132:678:C1LFKACXX:6:1315:9929:42151 -TCCCTGAGACCCTAACTTGTGA -+ -@@@DDF?D8FHHHGHHIIJEGI -@HWI-ST132:678:C1LFKACXX:6:2103:13958:97727 -TCCCTGAGACCCTAACTTGTGA -+ -@CCFFFFF<FHHHIIJJJJHHJ @HWI-ST132:678:C1LFKACXX:6:2104:10613:2992 TCCCTGAGACCCTAACTTGTGA + @@ -210,14 +26,6 @@ TCCCTGAGACCCTAACTTGTGA + CCCFFFFFHHHHHJJIIIICGI -@HWI-ST132:678:C1LFKACXX:6:2106:15768:75632 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFFHHHHJJJJJ4CFH -@HWI-ST132:678:C1LFKACXX:6:2109:16865:57940 -TCCCTGAGACCCTAACTTGTGA -+ -CCCFFFFFHHHHHIIIJJ<FHH @HWI-ST132:678:C1LFKACXX:6:2109:18750:76156 TCCCTGAGACCCTAACTTGTGA + @@ -226,27 +34,3 @@ TCCCTGAGACCCTAACTTGTGACT + CCCFFFFFGHHHHJJJJI:AFHIJ -@HWI-ST132:678:C1LFKACXX:6:1113:14924:44339 -CCCTGAGACCCTAACTTGTGAC -+ -??@DD;B?DDFHBED?CHGHII -@HWI-ST132:678:C1LFKACXX:6:1107:1375:15117 -TCACAAGTTTTGATCTCCGGTAT -+ -=??D:2A2=?DDCEHBHIJICCG -@HWI-ST132:678:C1LFKACXX:6:2105:17358:56431 -CACAAGTTTTGATCTCCGGTAT -+ -@@@DADDDHH>FHGIGEB@<@F -@HWI-ST132:678:C1LFKACXX:6:1102:6534:83469 -ACAAGTTTTGATCTCCGGTAT -+ -@@CDDDDFHHHHHJJIJJHGI -@HWI-ST132:678:C1LFKACXX:6:1212:17825:83469 -ACAAGTTTTGATCTCCGGTAT -+ -@@@FFFFFHHDFHIJJJIFDH -@HWI-ST132:678:C1LFKACXX:6:1304:1702:48389 -ACAAGTTTTGATCTCCGGTAT -+ -@@@B?=DDHDGFFIIIGGF>E |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -2,498 +2,46 @@\n AAAAACACGACCGTTCGCTTTGAAA\n +\n JJJIJJJJJJIHHHHFHFDDBFCC@\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-<<EFECE:?AA,FBADD;;D@@@\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IGGIIGHAIIFAHDDHHDD@4++::\n-@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n-AACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IIIGFCIGGIJGHDCFDFDD?BB?@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n-TTCGGCCATTAAAACCAGCGCACT\n-+\n-IIGGDIIHFFIHHHHHFFDDFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n-TCACTCGTTCGGCCATTAAAACCAGC\n-+\n-IHJJIJIHJIIHFC6HHHFFFFFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n-TCATCACTCGTTCGGCCATTAAAAC\n-+\n-JJJHGJIHHFC<HHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n-TTTAATGGCCGAACGAGTGATGACC\n-+\n-B@BDFEFFHHCFHGIIJGHIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIIJJJJJJIIHDHHHDFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIHIIHJJJJJHHHHHDEDDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n-GATGAAATCGTTTATGCGCCAAACT\n-+\n-@@@DDDDDHHFHH=GHHIII@GCHI\n-@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n-AGGTGGCTTGAAAGAACTGATCAACA\n-+\n-@CCDDFFFHHHHHHGHIJHIJJCGHI\n-@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n-GTTGATCAGTTCTTTCAAGCCACCT\n-+\n-JIHCIEJIJJJJHHHDD;DDDA?@@\n-@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHGHGHJJGCFHGIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHHHHHJJ<EHIJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CC@FFFFFGDFHGJJIIJIJJJ@HF\n-@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFGHHGFIIJJJJIIJIJH\n-@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-GGEGIIIJHEFED@FHHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-HHBGIHFGD1JGFAGHHFFFFFC@C\n-@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-GEIGEHGDC1<)HHDDDDBDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-B<GD@?GEEDE>HAFHFDDB=A@@=\n-@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-JJIJJIGEAIJHHHFFDFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-?C:?G:E<CF>F>FFC2D;B=+1=\n-@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-HGGHEGFA4IIHHHFBDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-IHFIECJJJJJHGHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1106:6262:61387\n-TTTTTTGATCTTTGGAGATTTATC\n-+\n-JJJJJIIIHIHHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1310:7732:65923\n-TCCTGTTGATCATTTGGCCGTGGT\n-+\n-IJHGIJIIHJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1103:7321:66631\n-TCCTGTTGATCATTTGGCCGTGG\n-+\n-HFCIHFC:IJHHHHHFFDFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1205:14661:3569\n-TCCTGTTGATCATTTGGCCGTGG\n-+\n-HGGJJJJIJJHHHHHFEDFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1204:8331:100236\n-CAAATGATCAACAGGACTCCACAAC\n-+\n-=@BFFF?=C:=>AFGCGGGIGHIII\n-@HWI-ST132:678:C1LFKACXX:6:1113:18652:10806\n-AATGATCAACAGGACTCCACAACT\n-+\n-@@@ABDDFHH'..b'-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-IHIIHFFB<@HDHBHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1304:17315:89761\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-JIIIIIHFE@HHFHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1307:8460:50243\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-JIIIHIGC8GHFHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1308:10034:23861\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-IIIIEEE@)CC2DDDDDDDD???\n @HWI-ST132:678:C1LFKACXX:6:1316:14693:8233\n TGAATTGAGAGTCGGCGTTCGTC\n +\n HEJJIJJGJHFFFFFDDDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-HGJJJIJIJIHHHHHBEDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-GCGEIJIIIGHHFDHEFDFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHFGFE1FC<FHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJJJJHGHIHGFAHDHFFFFFBCC\n @HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n GGHJIHHHFECC<DDFFFFDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGJJIIJIHFA3CHHFFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GIHGG?CGFC222F;HFFDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHIJJIIHF:IHHHHHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIIIIGIGGFA<AHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGIHGIIGGIHFHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIIHIGHGHHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHHHGGCD<<BHFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIJIIJJIHGFBFDHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHIIGGCFCHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHGGCCCCAFHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJJJIGHFEHFHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHHJIHBIFCGFCHHHFFFFF@CC\n @HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n EEDIHECF@GEC:DHDFDBAD??@\n-@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHHHE8GHDHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHGIGHGFCHHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIIIIIIHFE@HF?A:DDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GFIHBGGAC@GDDF=HDDFDFC@@\n-@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-HDCHGHGHIGEFAHFFFDDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-DBBIGGDAG?@?FF=FDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-EEIGGHEHDGEFDFDDDEDBD=?@\n-@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JHGJIHGGCC322<2AFFFFD?=:\n-@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIHIGG@HEGHHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIHHJHFFFBHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHEIJHHIHGEHFFHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-@FDFFE@F@F8DD<2+BBDDD??=\n-@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHFE@2@HDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIJIIGFFHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIHGCFC<BHDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGHCIIJIIHF<HGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIJIJJIGG@2<2<DAFFFFF@@=\n @HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -2,498 +2,46 @@\n AAAAACACGACCGTTCGCTTTGAAA\n +\n JJJIJJJJJJIHHHHFHFDDBFCC@\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-<<EFECE:?AA,FBADD;;D@@@\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IGGIIGHAIIFAHDDHHDD@4++::\n-@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n-AACCGCACGAGAGCAGTCTGCACGCT\n-+\n-IIIGFCIGGIJGHDCFDFDD?BB?@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n-TTCGGCCATTAAAACCAGCGCACT\n-+\n-IIGGDIIHFFIHHHHHFFDDFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n-TCACTCGTTCGGCCATTAAAACCAGC\n-+\n-IHJJIJIHJIIHFC6HHHFFFFFB@@\n-@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n-TCATCACTCGTTCGGCCATTAAAAC\n-+\n-JJJHGJIHHFC<HHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n-TTTAATGGCCGAACGAGTGATGACC\n-+\n-B@BDFEFFHHCFHGIIJGHIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIIJJJJJJIIHDHHHDFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n-TGCTAGGTCATCACTCGTTCGGCC\n-+\n-JIHIIHJJJJJHHHHHDEDDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n-GATGAAATCGTTTATGCGCCAAACT\n-+\n-@@@DDDDDHHFHH=GHHIII@GCHI\n-@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n-AGGTGGCTTGAAAGAACTGATCAACA\n-+\n-@CCDDFFFHHHHHHGHIJHIJJCGHI\n-@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n-GTTGATCAGTTCTTTCAAGCCACCT\n-+\n-JIHCIEJIJJJJHHHDD;DDDA?@@\n-@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHGHGHJJGCFHGIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFHHHHHJJ<EHIJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CC@FFFFFGDFHGJJIIJIJJJ@HF\n-@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n-TGGCTTGAAAGAACTGATCAACAGT\n-+\n-CCCFFFFFGHHGFIIJJJJIIJIJH\n-@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-GGEGIIIJHEFED@FHHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n-TCATCGGCTCGACGGAAACAATCTC\n-+\n-HHBGIHFGD1JGFAGHHFFFFFC@C\n-@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-GEIGEHGDC1<)HHDDDDBDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n-TATCATCGGCTCGACGGAAACAATC\n-+\n-B<GD@?GEEDE>HAFHFDDB=A@@=\n-@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-JJIJJIGEAIJHHHFFDFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n-TAAACTGTGAATTAAGCGCGCACA\n-+\n-?C:?G:E<CF>F>FFC2D;B=+1=\n-@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-HGGHEGFA4IIHHHFBDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n-TTAAACTGTGAATTAAGCGCGCAC\n-+\n-IHFIECJJJJJHGHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1106:6262:61387\n-TTTTTTGATCTTTGGAGATTTATC\n-+\n-JJJJJIIIHIHHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1310:7732:65923\n-TCCTGTTGATCATTTGGCCGTGGT\n-+\n-IJHGIJIIHJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1103:7321:66631\n-TCCTGTTGATCATTTGGCCGTGG\n-+\n-HFCIHFC:IJHHHHHFFDFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1205:14661:3569\n-TCCTGTTGATCATTTGGCCGTGG\n-+\n-HGGJJJJIJJHHHHHFEDFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1204:8331:100236\n-CAAATGATCAACAGGACTCCACAAC\n-+\n-=@BFFF?=C:=>AFGCGGGIGHIII\n-@HWI-ST132:678:C1LFKACXX:6:1113:18652:10806\n-AATGATCAACAGGACTCCACAACT\n-+\n-@@@ABDDFHH'..b'-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-IHIIHFFB<@HDHBHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1304:17315:89761\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-JIIIIIHFE@HHFHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1307:8460:50243\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-JIIIHIGC8GHFHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1308:10034:23861\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-IIIIEEE@)CC2DDDDDDDD???\n @HWI-ST132:678:C1LFKACXX:6:1316:14693:8233\n TGAATTGAGAGTCGGCGTTCGTC\n +\n HEJJIJJGJHFFFFFDDDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-HGJJJIJIJIHHHHHBEDA4+:1\n-@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n-TGAATTGAGAGTCGGCGTTCGTC\n-+\n-GCGEIJIIIGHHFDHEFDFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHFGFE1FC<FHFFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJJJJHGHIHGFAHDHFFFFFBCC\n @HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n GGHJIHHHFECC<DDFFFFDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGJJIIJIHFA3CHHFFFFFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GIHGG?CGFC222F;HFFDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHIJJIIHF:IHHHHHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIIIIGIGGFA<AHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGIHGIIGGIHFHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIIHIGHGHHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHHHGGCD<<BHFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JJIJIIJJIHGFBFDHFFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHIIGGCFCHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIIHGGCCCCAFHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJJJIGHFEHFHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHHJIHBIFCGFCHHHFFFFF@CC\n @HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n EEDIHECF@GEC:DHDFDBAD??@\n-@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJJHHHE8GHDHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHGIGHGFCHHHFFFFFBB@\n-@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIIIIIIHFE@HF?A:DDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-GFIHBGGAC@GDDF=HDDFDFC@@\n-@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-HDCHGHGHIGEFAHFFFDDFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-DBBIGGDAG?@?FF=FDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-EEIGGHEHDGEFDFDDDEDBD=?@\n-@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JHGJIHGGCC322<2AFFFFD?=:\n-@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIHIGG@HEGHHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIHHJHFFFBHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHEIJHHIHGEHFFHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-@FDFFE@F@F8DD<2+BBDDD??=\n-@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IJIJIHFE@2@HDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHJIJIIGFFHFHGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-JIHIHGCFC<BHDHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IHGHCIIJIIHF<HGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n-TGAATTGAGAGTCGGCGTTCGTCA\n-+\n-IIJIJJIGG@2<2<DAFFFFF@@=\n @HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n TGAATTGAGAGTCGGCGTTCGTCA\n +\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,619 +1,63 @@\n-@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n-TTTTTAACGAATCTAGTATACCCT\n-+\n-B@BDFFFFF?<ADFHHIJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n TTAACCGTTTTGAGCTCGGCGACCT\n +\n 1=14BDDDHHHFFIIIIFEA??@FH\n-@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n-TCTTTATATTCGTTGGTATTTGGC\n-+\n-CCCFFFFFHHH<2><C<CJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n-CCGGGACTGCACAGACGAAGCGG\n-+\n-@C@FFFFFHHHHHJJJIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n-AGATTCATGTTCGGATCGTCGATAC\n-+\n-@C@FFFFFHHHHHIJBHIJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n-CGCTTCTTTTGAATGCGTCGTGGTG\n-+\n-CCCFFFFFHHHHHJ,AGHI@<?HCG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n-GCTGCCGCGATTCCCAAACCGTCCTG\n-+\n-B@BDDFFFF?@DFEH<EGIGIJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n TCCTGAGAGTCTGGTCACCGTAGAG\n +\n CCCF?EFFHHHFHJHJJJJ3343<A\n-@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n-ACCGTAGAGAATCTGAGCGTCAGAA\n-+\n-@CCFDFFFGFHHHJGDGHGGHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n CACCAGTCGGCAATATAGATCTCCT\n +\n BCBFFFDFHHHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n-TCTATATTGCCGACTGGTGGCTCAGT\n-+\n-BCBFDFFFHHHHHJJHFCFGGGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n-TCCTTGGCGGAGGTATCGTAGTGAG\n-+\n-CCCFFFFFHHFHH?FHJJJJJHJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n-TTCCGGATTGGCAATACCCGCCTC\n-+\n-CCCFFFFFHHHHHGI<GHIJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n-TTTGGCAAGAGGCGGCTCCTCCTG\n-+\n-@@BFFFFFHHDFHEHGIJIIIJII\n-@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n-TCTGTTGGCAGCTAGATCAGGGGC\n-+\n-BCCFDFFFHHFHHGIIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n-TCTGTTGGCAGCTAGATCAGGGG\n-+\n-BBCFDEDFHA<DFHFFHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n-TACTTGAGGACATAGACAAACATTG\n-+\n-BBCFFFFFD=CFHH+AEHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n-TCCAGAACAGGTCTGTGGGACTGATC\n-+\n-CCCFFFFFHHHDHI3<EGIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n-TATCCAGAACAGGTCTGTGGGAC\n-+\n-CCCFFFFFHHH?FFHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n-TCCATAATCCTGACCATCCGGGCAG\n-+\n-CC@FFFFFHHHHGIJIJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n-CCCGGATGGTCAGGATTATGGAAGC\n-+\n-CCCFFFFFHFHHHGHIIIIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n-TACGGTAGAACAACTACACCGAGTGGT\n-+\n-@CCFFDDDGBHHHJIIIJJJJJJFHGI\n-@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n-TTTGCTCGACCACTCGGTGTAGTTGT\n-+\n-CCCFFFFFHHHHHJJEE<ACGIIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n-TTTGCTCGACCACTCGGTGTAGT\n-+\n-@C@FFFFFHHHFHIJFEA+@CFH\n @HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n AAAAACACGACCGTTCGCTTTGAAA\n +\n @CCFBDDFHFHHHHIJJJJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-@@@D;;DDABF,AA?:ECEFE<<\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGCACGCT\n-+\n-::++4@DDHHDDHAFIIAHGIIGGI\n-@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n-AACCGCACGAGAGCAGTCTGCACGCT\n-+\n-@@?BB?DDFDFCDHGJIGGICFGIII\n @HWI-ST132:678:C1LFKACXX:6:1206:10939:52268\n TAGCTGTTAAAACCGCACGAGAGC\n +\n BCCFFFFFHHHFHJIIJJIIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1206:12272:27806\n-ATGCTTATCTGAACCACTGTGCACG\n-+\n-CC@FFFFFHHHHHIIEHH<IIIHII\n-@HWI-ST132:678:C1LFKACXX:6:1309:'..b'678:C1LFKACXX:6:1311:5489:31007\n-ACATGGTCTTCGGGTAGCTCCAGT\n-+\n-@@BDFFADFHHGHJGGGHIJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:2108:4142:4308\n-TTACGAAATGGAACTAGTTTAGTCC\n-+\n-@@CFFFFFHH?FDIJIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1307:5088:23177\n-TGCGGGTTAAACACTGCCTTGGTG\n-+\n-=B@DB@0<CFHHHJJGEGIHIJGH\n-@HWI-ST132:678:C1LFKACXX:6:1111:13371:74417\n-TGTTTACTCAAGTCCGTGCACTCG\n-+\n-B@BFFFFFH:=AAEHIHJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:8994:56073\n-TCCAGGGGAGCGGACCAAGTCGATC\n-+\n-CCCFFFFFHHH<02:CGHHHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1206:9820:97666\n-CAATTCGAGTGGGATTTCTGATCCA\n-+\n-1:1=ADDEHF<ACAFHHIJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:17211:43697\n-TCCAGGACAAGATGCAACGCCAAAT\n-+\n-CCCFFFFFHHHHHIJGIIFHIJGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:4977:37967\n-TCTGCAGATTCTTTTGGTGTGTCTG\n-+\n-@C@FFFFFGHHHHJJJHGGGIGGHH\n-@HWI-ST132:678:C1LFKACXX:6:1211:6239:25199\n-CGCGCGGCTGCTTTTCACTTTCTGCA\n-+\n-CCCFFFFFHHGHHJJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:18450:76819\n-TTGGTTAGCCTGGTACCTGCGAA\n-+\n-CCCFDDEFHHHAA<<EFHICHII\n-@HWI-ST132:678:C1LFKACXX:6:2108:15223:32156\n-ATCGTGCAATCGTTCTCTGCCCGGA\n-+\n-B@CFFFFFHHHHFIJJJJFFHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:12241:76580\n-CTAGGCAAAAACTCAGAAGAAGG\n-+\n-@CCFFFFF8DHHHIJHJJJJGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1311:13842:17572\n-TAAATTACGGTGCGGGCAGCACT\n-+\n-@@@DDDEF:DAFDGG@GGFHIIG\n-@HWI-ST132:678:C1LFKACXX:6:1311:3626:78835\n-TTGAATAAGTTATCAGTCGGCGC\n-+\n-<@@DFFFFHFHFHJJIIIIJJIF\n-@HWI-ST132:678:C1LFKACXX:6:1108:16423:60929\n-CACCGCCGAATGCGCATAATTAAT\n-+\n-CCBFFFFFHHHHH@FHHGHIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:5257:5545\n-TGAGGAGTAGCGCTCCACCCCAACC\n-+\n-BBCFDEFDDFHFFIIIJJIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:17133:15596\n-TAGCCAGGAATCGGCAAGACAGGAAC\n-+\n-CCCFFFFFHHHHHJJIJJIIIJJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:4415:33661\n-CAAAGTCGTCTGGCAGACGGACTT\n-+\n-@@@FFBDDHHH+CGIGHI<FHIII\n-@HWI-ST132:678:C1LFKACXX:6:1302:1520:97310\n-CAAAGTCGTCTGGCAGACGGACTT\n-+\n-B@CFFFFFHHHHGJJFFGFHIJII\n-@HWI-ST132:678:C1LFKACXX:6:1206:19361:50379\n-TGCTGATGGACGGCAGCTCCTCCTC\n-+\n-BCCFFFFFGHH@HGHIIJJJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1215:10959:84025\n-CTTTTGTGTTCGGGGCTAAAGTA\n-+\n-B@BADEDDFHHDHJJJJHJJJCG\n-@HWI-ST132:678:C1LFKACXX:6:1112:17895:2328\n-TGTCGATGTTGGCGCGATTGTCT\n-+\n-BCCFFDFFHHHGHHGIIJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1110:11426:42306\n-TGCGGCTGAGCTGCGACCCCCGAG\n-+\n-@@@AFFFF3CFHHJIIJJJIJJGH\n-@HWI-ST132:678:C1LFKACXX:6:1109:4127:92377\n-TTTCGAGATGACGCTGGCTGACTG\n-+\n-CCCFFFFFHHHHHIIJIHJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1301:3941:50559\n-TAAAACGAAGTCGAACTGAGAGGA\n-+\n-B@BF?A@DFHDHHGIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1307:9525:53853\n-TTTGTGGGTCTAGACGCCAGCAAGG\n-+\n-@@@DDDFFHHHHH4E@@C@FGIIII\n-@HWI-ST132:678:C1LFKACXX:6:1304:6688:77081\n-CGTAAACAGGAAAGGAGTCCGTGG\n-+\n-@CCFDFFFHHHHGJIJIGHIJIJI\n-@HWI-ST132:678:C1LFKACXX:6:1304:15559:58628\n-TTTGCCTTTTTCTGCTTTCTTGCTG\n-+\n-@CBF;DFFHHHHHJHIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2103:8015:68812\n-TCATGTCGTTTGAATCTATTTTCATT\n-+\n-BC@FFDFFHHHHHIIJJIJJJJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1107:10110:3863\n-CCGAGTGACTGAGTGCGGACGAGCGC\n-+\n-B@@FFDDFHBFHHEHIGIIIHGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:7295:27446\n-TCCAGTATCTGATGTCCGCTGTC\n-+\n-@CCFFBDDHHHHHC<CHDHGIIG\n-@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n-CCGAGCCGACGAACCGTCCCTGGAA\n-+\n-@@@FFF?DHHDHHJJJBHIICAHGI\n-@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n-GCACCATAGACCAACTCTGCCATC\n-+\n-BCCFFFFF+AFHHJJJJIHIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n-ATCGTCGTCAACAACGTTGTCAGGAT\n-+\n-CCCFFFFDHGHHHJHHFE+CHHIJII\n-@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n-CCGAACCGAACCGAAACCAAACAAAA\n-+\n-=B@D440@@FHHHJJJJJJIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n-TCGTGTTCGCTCTCAAACTGAAAC\n-+\n-@CCFFFFFGHHHHJJJGIJEIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n-AAACTCTAAGCGGTGGATCACTCG\n-+\n-8?<BDDDDDC?88C@<GGDBEH9C\n @HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n TGTTGCGGCAACTTCTTTAAGTTG\n +\n CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n-@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n-GTAACTGACCGTGTGGCCCAATGGA\n-+\n-??@DFFFFGHDHGG?GGIEH3<FGH\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,619 +1,63 @@\n-@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n-TTTTTAACGAATCTAGTATACCCT\n-+\n-B@BDFFFFF?<ADFHHIJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n TTAACCGTTTTGAGCTCGGCGACCT\n +\n 1=14BDDDHHHFFIIIIFEA??@FH\n-@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n-TCTTTATATTCGTTGGTATTTGGC\n-+\n-CCCFFFFFHHH<2><C<CJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n-CCGGGACTGCACAGACGAAGCGG\n-+\n-@C@FFFFFHHHHHJJJIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n-AGATTCATGTTCGGATCGTCGATAC\n-+\n-@C@FFFFFHHHHHIJBHIJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n-CGCTTCTTTTGAATGCGTCGTGGTG\n-+\n-CCCFFFFFHHHHHJ,AGHI@<?HCG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n-GCTGCCGCGATTCCCAAACCGTCCTG\n-+\n-B@BDDFFFF?@DFEH<EGIGIJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n TCCTGAGAGTCTGGTCACCGTAGAG\n +\n CCCF?EFFHHHFHJHJJJJ3343<A\n-@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n-ACCGTAGAGAATCTGAGCGTCAGAA\n-+\n-@CCFDFFFGFHHHJGDGHGGHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n CACCAGTCGGCAATATAGATCTCCT\n +\n BCBFFFDFHHHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n-TCTATATTGCCGACTGGTGGCTCAGT\n-+\n-BCBFDFFFHHHHHJJHFCFGGGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n-TCCTTGGCGGAGGTATCGTAGTGAG\n-+\n-CCCFFFFFHHFHH?FHJJJJJHJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n-TTCCGGATTGGCAATACCCGCCTC\n-+\n-CCCFFFFFHHHHHGI<GHIJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n-TTTGGCAAGAGGCGGCTCCTCCTG\n-+\n-@@BFFFFFHHDFHEHGIJIIIJII\n-@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n-TCTGTTGGCAGCTAGATCAGGGGC\n-+\n-BCCFDFFFHHFHHGIIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n-TCTGTTGGCAGCTAGATCAGGGG\n-+\n-BBCFDEDFHA<DFHFFHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n-TACTTGAGGACATAGACAAACATTG\n-+\n-BBCFFFFFD=CFHH+AEHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n-TCCAGAACAGGTCTGTGGGACTGATC\n-+\n-CCCFFFFFHHHDHI3<EGIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n-TATCCAGAACAGGTCTGTGGGAC\n-+\n-CCCFFFFFHHH?FFHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n-TCCATAATCCTGACCATCCGGGCAG\n-+\n-CC@FFFFFHHHHGIJIJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n-CCCGGATGGTCAGGATTATGGAAGC\n-+\n-CCCFFFFFHFHHHGHIIIIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n-TACGGTAGAACAACTACACCGAGTGGT\n-+\n-@CCFFDDDGBHHHJIIIJJJJJJFHGI\n-@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n-TTTGCTCGACCACTCGGTGTAGTTGT\n-+\n-CCCFFFFFHHHHHJJEE<ACGIIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n-TTTGCTCGACCACTCGGTGTAGT\n-+\n-@C@FFFFFHHHFHIJFEA+@CFH\n @HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n AAAAACACGACCGTTCGCTTTGAAA\n +\n @CCFBDDFHFHHHHIJJJJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-@@@D;;DDABF,AA?:ECEFE<<\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGCACGCT\n-+\n-::++4@DDHHDDHAFIIAHGIIGGI\n-@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n-AACCGCACGAGAGCAGTCTGCACGCT\n-+\n-@@?BB?DDFDFCDHGJIGGICFGIII\n @HWI-ST132:678:C1LFKACXX:6:1206:10939:52268\n TAGCTGTTAAAACCGCACGAGAGC\n +\n BCCFFFFFHHHFHJIIJJIIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1206:12272:27806\n-ATGCTTATCTGAACCACTGTGCACG\n-+\n-CC@FFFFFHHHHHIIEHH<IIIHII\n-@HWI-ST132:678:C1LFKACXX:6:1309:'..b'2:678:C1LFKACXX:6:1307:2988:76332\n-TCGAAAGTCCAACTGGAATGGCCC\n-+\n-@CCFFFFDHHHHHJJIJGIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1311:5489:31007\n-ACATGGTCTTCGGGTAGCTCCAGT\n-+\n-@@BDFFADFHHGHJGGGHIJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:2108:4142:4308\n-TTACGAAATGGAACTAGTTTAGTCC\n-+\n-@@CFFFFFHH?FDIJIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1307:5088:23177\n-TGCGGGTTAAACACTGCCTTGGTG\n-+\n-=B@DB@0<CFHHHJJGEGIHIJGH\n-@HWI-ST132:678:C1LFKACXX:6:1111:13371:74417\n-TGTTTACTCAAGTCCGTGCACTCG\n-+\n-B@BFFFFFH:=AAEHIHJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:8994:56073\n-TCCAGGGGAGCGGACCAAGTCGATC\n-+\n-CCCFFFFFHHH<02:CGHHHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1206:9820:97666\n-CAATTCGAGTGGGATTTCTGATCCA\n-+\n-1:1=ADDEHF<ACAFHHIJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:17211:43697\n-TCCAGGACAAGATGCAACGCCAAAT\n-+\n-CCCFFFFFHHHHHIJGIIFHIJGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:4977:37967\n-TCTGCAGATTCTTTTGGTGTGTCTG\n-+\n-@C@FFFFFGHHHHJJJHGGGIGGHH\n-@HWI-ST132:678:C1LFKACXX:6:1211:6239:25199\n-CGCGCGGCTGCTTTTCACTTTCTGCA\n-+\n-CCCFFFFFHHGHHJJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:18450:76819\n-TTGGTTAGCCTGGTACCTGCGAA\n-+\n-CCCFDDEFHHHAA<<EFHICHII\n-@HWI-ST132:678:C1LFKACXX:6:2108:15223:32156\n-ATCGTGCAATCGTTCTCTGCCCGGA\n-+\n-B@CFFFFFHHHHFIJJJJFFHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:12241:76580\n-CTAGGCAAAAACTCAGAAGAAGG\n-+\n-@CCFFFFF8DHHHIJHJJJJGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1311:13842:17572\n-TAAATTACGGTGCGGGCAGCACT\n-+\n-@@@DDDEF:DAFDGG@GGFHIIG\n-@HWI-ST132:678:C1LFKACXX:6:1311:3626:78835\n-TTGAATAAGTTATCAGTCGGCGC\n-+\n-<@@DFFFFHFHFHJJIIIIJJIF\n-@HWI-ST132:678:C1LFKACXX:6:1108:16423:60929\n-CACCGCCGAATGCGCATAATTAAT\n-+\n-CCBFFFFFHHHHH@FHHGHIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:5257:5545\n-TGAGGAGTAGCGCTCCACCCCAACC\n-+\n-BBCFDEFDDFHFFIIIJJIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:17133:15596\n-TAGCCAGGAATCGGCAAGACAGGAAC\n-+\n-CCCFFFFFHHHHHJJIJJIIIJJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:4415:33661\n-CAAAGTCGTCTGGCAGACGGACTT\n-+\n-@@@FFBDDHHH+CGIGHI<FHIII\n-@HWI-ST132:678:C1LFKACXX:6:1302:1520:97310\n-CAAAGTCGTCTGGCAGACGGACTT\n-+\n-B@CFFFFFHHHHGJJFFGFHIJII\n-@HWI-ST132:678:C1LFKACXX:6:1206:19361:50379\n-TGCTGATGGACGGCAGCTCCTCCTC\n-+\n-BCCFFFFFGHH@HGHIIJJJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1215:10959:84025\n-CTTTTGTGTTCGGGGCTAAAGTA\n-+\n-B@BADEDDFHHDHJJJJHJJJCG\n-@HWI-ST132:678:C1LFKACXX:6:1112:17895:2328\n-TGTCGATGTTGGCGCGATTGTCT\n-+\n-BCCFFDFFHHHGHHGIIJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1110:11426:42306\n-TGCGGCTGAGCTGCGACCCCCGAG\n-+\n-@@@AFFFF3CFHHJIIJJJIJJGH\n-@HWI-ST132:678:C1LFKACXX:6:1109:4127:92377\n-TTTCGAGATGACGCTGGCTGACTG\n-+\n-CCCFFFFFHHHHHIIJIHJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1301:3941:50559\n-TAAAACGAAGTCGAACTGAGAGGA\n-+\n-B@BF?A@DFHDHHGIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1307:9525:53853\n-TTTGTGGGTCTAGACGCCAGCAAGG\n-+\n-@@@DDDFFHHHHH4E@@C@FGIIII\n-@HWI-ST132:678:C1LFKACXX:6:1304:6688:77081\n-CGTAAACAGGAAAGGAGTCCGTGG\n-+\n-@CCFDFFFHHHHGJIJIGHIJIJI\n-@HWI-ST132:678:C1LFKACXX:6:1304:15559:58628\n-TTTGCCTTTTTCTGCTTTCTTGCTG\n-+\n-@CBF;DFFHHHHHJHIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2103:8015:68812\n-TCATGTCGTTTGAATCTATTTTCATT\n-+\n-BC@FFDFFHHHHHIIJJIJJJJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1107:10110:3863\n-CCGAGTGACTGAGTGCGGACGAGCGC\n-+\n-B@@FFDDFHBFHHEHIGIIIHGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:7295:27446\n-TCCAGTATCTGATGTCCGCTGTC\n-+\n-@CCFFBDDHHHHHC<CHDHGIIG\n-@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n-CCGAGCCGACGAACCGTCCCTGGAA\n-+\n-@@@FFF?DHHDHHJJJBHIICAHGI\n-@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n-GCACCATAGACCAACTCTGCCATC\n-+\n-BCCFFFFF+AFHHJJJJIHIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n-ATCGTCGTCAACAACGTTGTCAGGAT\n-+\n-CCCFFFFDHGHHHJHHFE+CHHIJII\n-@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n-CCGAACCGAACCGAAACCAAACAAAA\n-+\n-=B@D440@@FHHHJJJJJJIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n-TCGTGTTCGCTCTCAAACTGAAAC\n-+\n-@CCFFFFFGHHHHJJJGIJEIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n-AAACTCTAAGCGGTGGATCACTCG\n-+\n-8?<BDDDDDC?88C@<GGDBEH9C\n @HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n TGTTGCGGCAACTTCTTTAAGTTG\n +\n CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -2,438 +2,42 @@\n TTTTTTGGCACACGATTTTTTCG\n +\n BCCFFFFFHHHGHF@EHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8271:27021\n-TGGCTCTAGAGGTGGCTCCAGGC\n-+\n-C@CFFFFFHHG3<<ACHIIHGII\n-@HWI-ST132:678:C1LFKACXX:6:1306:9256:39375\n-TGGCTCTAGAGGTGGCTCCAGGC\n-+\n-BBCFFFFFHFHA3+<<EGIIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:8543:80281\n-CTCTAGAGGTGGCTCCAGGCTCT\n-+\n-BBCF=BBDHFHHHIJIIJGIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1206:10520:35802\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-BBBDFFFFFHAADGHIIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:16796:70859\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-BBBDFDFFFFHHDIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1312:8034:92577\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-=?8ABBDDAFHHHIJIIIIJJII\n-@HWI-ST132:678:C1LFKACXX:6:2103:6868:77512\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-BBBDDDFFCHHHHJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:8058:54317\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-:BBDFDFFCF<<AAF?GHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:4030:77058\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-BCBFDFFFDFHHHJJJIIIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:2108:19158:37021\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-BCBDFFFFFFHHHIJJIJJJJJI\n @HWI-ST132:678:C1LFKACXX:6:2108:4761:89781\n TCTAGAGGTGGCTCCAGGCTCTC\n +\n @BBDFFFFADHFHEIIIJJIJJI\n-@HWI-ST132:678:C1LFKACXX:6:2109:17544:31829\n-TCTAGAGGTGGCTCCAGGCTCTC\n-+\n-BCBFFFFFFHHHHJJIJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1211:11818:23477\n-TCTAGAGGTGGCTCCAGGCTCTCT\n-+\n-IHJIJIJIDGIFFDFFFFFFDBBB\n-@HWI-ST132:678:C1LFKACXX:6:1310:1057:72917\n-GAGAGCCTGGAGCCACCTCTAGA\n-+\n-IHJJJJJIJJHHFFHFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:2107:14168:54674\n-TATCACTGTATGCGTAGAAAAGAG\n-+\n-CCCFDFFFHHGDFFFHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:20798:12533\n-TCTGCTATCACTGTATGCGTAGAAA\n-+\n-@@@FDDDFHGHHGJIJIG@GCEFDB\n-@HWI-ST132:678:C1LFKACXX:6:1115:5746:10371\n-TATGCTCATGCATTGTAAATTTGACA\n-+\n-=@B=BDEFGH>FHGGAFHEJIJIHJJ\n-@HWI-ST132:678:C1LFKACXX:6:1115:5725:10377\n-TATGCTCATGCATTGTAAATTTGACA\n-+\n-=?1A4=BDADD<<AF<C:CIHAHJIB\n-@HWI-ST132:678:C1LFKACXX:6:1204:5988:3191\n-TTTTGTCAAATTTACAATGCATGAGC\n-+\n-@CCFFDFFH4DHHIIGII<@IIIIII\n-@HWI-ST132:678:C1LFKACXX:6:1112:17845:55327\n-TTTTGTCAAATTTACAATGCATG\n-+\n-JJJIGIHEEBHHHHDFFDFFCC@\n @HWI-ST132:678:C1LFKACXX:6:1116:8060:21154\n TTTTGTCAAATTTACAATGCATG\n +\n GGIJIJJJJIHHHHGFFDDD@B@\n-@HWI-ST132:678:C1LFKACXX:6:1202:12362:65139\n-TTTTGTCAAATTTACAATGCATG\n-+\n-BCCFFDFFHHHHHJJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:10333:80069\n-TTTTGTCAAATTTACAATGCATG\n-+\n-JJJJJJJJJJHHHHHFFDFFBCC\n-@HWI-ST132:678:C1LFKACXX:6:1115:14316:97559\n-TGCATTGTAAATTTGACAAAATATG\n-+\n-GCGIDEJJIGIJHHHHFDFDDB:@?\n-@HWI-ST132:678:C1LFKACXX:6:1210:19160:87047\n-TGCATTGTAAATTTGACAAAATATG\n-+\n-CCCFFFFDHHHHHJJHJIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:14990:61179\n-TTTGACAAAATATGCCCTTCACC\n-+\n-@@@D+ADEHAHHHIIIIIIIGII\n-@HWI-ST132:678:C1LFKACXX:6:1103:12540:8868\n-TTTGACAAAATATGCCCTTCACC\n-+\n-GHIGIIGFA,HF>FFB>DAF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1103:6815:14215\n-TTTGACAAAATATGCCCTTCACC\n-+\n-CIIIIIIIIIHHHFHEDB+F@@@\n-@HWI-ST132:678:C1LFKACXX:6:1107:5684:28828\n-TTTGACAAAATATGCCCTTCACC\n-+\n-BCCFFFFFFCFHHEGHJIJJIIG\n-@HWI-ST132:678:C1LFKACXX:6:1108:15125:97763\n-TTTGACAAAATATGCCCTTCACC\n-+\n-CCCFFFFFHHHHH<CGIJJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1110:20123:8967\n-TTTGACAAAATATGCCCTTCACC\n-+\n-JJJJJJJJIJHHHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1111:4327:25202\n-TTTGACAAAATATGCCCTTCACC\n-+\n-@@@FFDFDHHA?FEBHF@HIGGG\n-@HWI-ST132:678:C1LFKACXX:6:1112:16367:41504\n-TTTGACAAAATATGCCCTTCACC\n-+\n-@@CFDFFFHGFHHJIJIIJJIIE\n-@HWI-ST132:678:C1LFKACXX:6:1115:12597:83379\n-TTTGACAAAATATGCCCTTCACC\n-+\n-IHIGGEGGGGCDFFHFFEADB;@\n-@HWI-ST132:678:C1LFKACXX:6:1202:11500:85997\n-TTTGACAAAATATGCCCTTCACC\n-+\n-BBBF=DEFHHHHHIIJJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1203:7440:86465\n TTTGACAAAATATGCCCTTCACC\n +\n JJJIIIIHFHHHDFHFDDAFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1208:5601:13037\n-TTTGACAAAATATGCCCTTCACC\n-+\n-CCCFFFFFHHHHHFFHIJJJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1208:3642:37562\n-TTTGACAAAATATGCCCTTCACC\n-+\n-CCCFFFFFHGHHHGIJJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:15199:72310\n-TTTGACAAAATATGCCCTTCACC\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:10211:42145\n-TTTGACAAAATATGCCCTTCACC\n-+\n-@BBDDFDEFDFHGHIIJJJ'..b':678:C1LFKACXX:6:1304:10404:89803\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJIIGE?CGHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1305:13291:74216\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJIHGC?1:E@HHHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1305:14099:91760\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-GIGIIIEHFC?EHGHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1306:4852:79972\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJIIIGFC:?FJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1306:14526:93144\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIIIIIHFC8EHHF<HFFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1306:12830:100458\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJIIGIGHEE:CHHHFHFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1307:3341:79302\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIIIHG<HEGHIHFFHHDDD=D@@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:20666:8951\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIHCBD?C:C?EDDHHGFFFDF@@@\n @HWI-ST132:678:C1LFKACXX:6:1310:20517:19080\n TTCGATCGCCGACGTGTGAAGACGT\n +\n FHGGGF?GGFEHHHFHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1310:19552:89269\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJIJJIHFCCHHGHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1310:11672:92080\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIJIHFGHHGHJHHHHHFFFDFCCC\n @HWI-ST132:678:C1LFKACXX:6:1312:14124:76448\n TTCGATCGCCGACGTGTGAAGACGT\n +\n@@ -7026,111 +710,7 @@\n TTCGATCGCCGACGTGTGAAGACGT\n +\n AIIJJJIHFFGDHHHHHFFFDFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1315:9373:25299\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-G>FDCC4;;EEIFDFDFDD=+D?@@\n-@HWI-ST132:678:C1LFKACXX:6:1315:12968:32460\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-BD9FGFFBF?GGF<FFFDDDB=1@@\n-@HWI-ST132:678:C1LFKACXX:6:2101:18316:34316\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJJJJIHHEIHHFHHFFEDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2101:18438:36839\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJJJJHGG?HHHDHHFFDDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2101:14608:56807\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJJIHHHFIIHHHHHFFFDDBCB\n-@HWI-ST132:678:C1LFKACXX:6:2103:7602:64596\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-GHIIHFBC??:@FCCDF@+A;D??=\n @HWI-ST132:678:C1LFKACXX:6:2103:17863:69050\n TTCGATCGCCGACGTGTGAAGACGT\n +\n GIJJJJIIHFGIHFHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2104:5137:4251\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJIJJIHEHHJHHDHGFFEFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2104:20272:16658\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJIHHJIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:8336:35547\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJIHHDC?C@F@@HGFFFFD@B=\n-@HWI-ST132:678:C1LFKACXX:6:2104:17454:68818\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJIIHFEIIIHHHHHFFFBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-DIGJIFD?1@@C<0@HHDFFDD??:\n-@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-?HEGHC4HFHG@HFDHHDDD=D@@@\n-@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIIHIHFHHHFFFFF@CC\n-@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIHIJHHHHHFFFFFBCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-FJJIIIGD?FCGHHHHHDDB?FCBB\n-@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJIHF?114C@@CHHFFFFFBB=\n-@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n-TTCGATCGCCGACGTGTGAAGACG\n-+\n-IIIGC<HGGFGHHHHHFFEBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n-ATTCGATCGCCGACGTGTGAAGACG\n-+\n-JJIHGGCGIGJJGHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n-TTCGATCGCCGACGTGTGAAGAC\n-+\n-JJHIGHEGFIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n-TGCAAGCTAAGAATTCCGAAACGCC\n-+\n-JJIJJJJJJIHFCAC:HDA==D?B:\n-@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n-GTAACACTTTGTAACGGATCGCAAA\n-+\n-@@@DFFFFHHHGHIJJJEIIIIDII\n-@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n-TTTCCGTCGACTAACAATAAGCCGT\n-+\n-B@CFFFDDFHHHHJJIJJDHIIIJG\n-@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n-AAAATGTCAGTCACTCAGCCAAAGG\n-+\n-BBCFFFDF?FHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n-TCCTTTGGCTGAGTGACTGACATTT\n-+\n-HEHCFHFFHCA2<<CHFDBDDF@@?\n-@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n-CAAGGAGTCGGCAGCTGAAGTAGCA\n-+\n-=@@DD?DDFF?)@FAH>FEFHHEHE\n-@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n-TCGTACCGATCTAGACATCTCTTC\n-+\n-GIJJJJJJIGJHHHGHD<FFD@@@\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,11 +1,3 @@\n-@HWI-ST132:678:C1LFKACXX:6:2107:14168:54674\n-TATCACTGTATGCGTAGAAAAGAG\n-+\n-CCCFDFFFHHGDFFFHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:20798:12533\n-TCTGCTATCACTGTATGCGTAGAAA\n-+\n-@@@FDDDFHGHHGJIJIG@GCEFDB\n @HWI-ST132:678:C1LFKACXX:6:1313:10358:95570\n TAATATAGATTTAAAGTCTAAGAACT\n +\n@@ -14,742 +6,70 @@\n TAATATAGATTTAAAGTCTAAGAACT\n +\n BCCFFFFFGHHHH>GHFHJJJIGJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1301:16563:56958\n-AAGGCAATGCAAAACAAGAATTT\n-+\n-FAA3GHHBEIFHHFDDBDDB@@@\n-@HWI-ST132:678:C1LFKACXX:6:1107:12070:23186\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-CCCDDEFFHHHHHJJJJJAJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1110:20211:14418\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-CCCFFFFFHHHHHJJJJJIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:13578:65370\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-@8?D=BDFGHHFHIJJJJFGIJIJIJ\n @HWI-ST132:678:C1LFKACXX:6:2101:7667:91449\n TAGTATATTTATTAAATCATTTGACT\n +\n CCCDDEFFHHHHHJJJJJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:12382:29561\n-TAGTATATTTATTAAATCATTTGACT\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:2107:9787:36481\n TAGTATATTTATTAAATCATTTGACT\n +\n BBBD:ADDHHHHH4HGHIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:14356:68993\n-TAATGTTACATCATATTAAGTCAAATGA\n-+\n-JIJJIHIHJJJJJJJHHHFHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1107:18073:46755\n-AAATATTTCGCTTTTAAAAAATTG\n-+\n-@@CFFFFFHHHGHJIJJBDAGIII\n-@HWI-ST132:678:C1LFKACXX:6:1302:10066:99383\n-AATATTTCGCTTTTAAAAAATTG\n-+\n-BBBDFFFFH@FHHJJJIJGIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:2103:9377:13404\n-TAAATTTGTTTGTTAAAATCGCCG\n-+\n-CCCFFFFFHHHGHIJJJJJHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:5142:10985\n-TTTAAATTTGTTTGTTAAAATCGCC\n-+\n-BCCFDFFFHHHHHIJIJJJJIIIGH\n-@HWI-ST132:678:C1LFKACXX:6:1108:20386:47976\n-TAATAGTCAGGGCGCGAATTTTT\n-+\n-?@?D;B=B?CAC:2<CFGHIIGI\n-@HWI-ST132:678:C1LFKACXX:6:1207:2583:92360\n-TAATAGTCAGGGCGCGAATTTTT\n-+\n-B@CFFFDDHHDFFGFGHEGHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1102:11267:71435\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@BFFDBDFHHDFIIHJBFFGIGG\n-@HWI-ST132:678:C1LFKACXX:6:1107:9710:51191\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FDF?DHHHDHFGHGGHGJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1108:5610:75509\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFFFFGHGG<DHGHGHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:13565:15908\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFEFHHHCAFGHIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:11179:97926\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FDEBD<FH<DGGIIGGHGIII\n-@HWI-ST132:678:C1LFKACXX:6:1110:18682:30268\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFFFHHHFGIJJIHIIJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1114:13195:76362\n TAATAGTCAGGGCGCGAATTTTTA\n +\n ?@?DDB=DFDDHGIIEBHD=FHIH\n-@HWI-ST132:678:C1LFKACXX:6:1201:9017:61055\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFDFFFHHFFH@BEEGIHJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1201:5418:63606\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@CFBDDEHHA<CFEFHIHIIIII\n-@HWI-ST132:678:C1LFKACXX:6:1213:8541:21411\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@CFFFDDHHFFFFGHIHIJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1214:13791:80762\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FDDDDHFHDHIFII1DFHGGF\n-@HWI-ST132:678:C1LFKACXX:6:1309:8889:7362\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@CFFFFFDHHHHJIJJJHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:17898:28199\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@??DFADDDHCHFFBGGEHIGJGI\n-@HWI-ST132:678:C1LFKACXX:6:2104:10515:36849\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@CCFFFDFHHFHHJIJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:6101:64627\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-@@@FFFFFHHD:C<@@@CGHIIII\n-@HWI-ST132:678:C1LFKACXX:6:2105:18687:69886\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-BCCFFFFEHHFFH@FHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:16747:90974\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-B@@F?DBDHHHCC<EGIJJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:2108:1476:22607\n-TAATAGTCAGGGCGCGAATTTTTA\n-+\n-CCCFFFFFHHHHFGHJHHHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:4401:62600\n-TAATAGTCAGGGCGCGAATTTTTAA\n-+\n-@@@FFFDEHHBCFGGIEHGHIJJGH\n-@HWI-ST132:678:C1LFKACXX:6:1103:11719:61615\n-TAATAGTCAGGGCGCGAATTTTTAA\n-+\n-@CCFFFFFDHFFHIJFEGHIIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1104:5727:21771\n-TAATAGTCAGGGCGCGAATTTTTAA\n-+\n-CCCFFFFFHHHDFIIFHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:18599:5567\n-TAATAGTCAGGGCGCGAATTTTTAA\n-+\n-CCCFFFEEHHHHHCGIIIIJJJJJJ\n-@HWI-ST'..b':678:C1LFKACXX:6:1304:10404:89803\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJIIGE?CGHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1305:13291:74216\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJIHGC?1:E@HHHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1305:14099:91760\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-GIGIIIEHFC?EHGHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1306:4852:79972\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJIIIGFC:?FJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1306:14526:93144\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIIIIIHFC8EHHF<HFFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1306:12830:100458\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJIIGIGHEE:CHHHFHFFFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1307:3341:79302\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIIIHG<HEGHIHFFHHDDD=D@@@\n-@HWI-ST132:678:C1LFKACXX:6:1309:20666:8951\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIHCBD?C:C?EDDHHGFFFDF@@@\n @HWI-ST132:678:C1LFKACXX:6:1310:20517:19080\n TTCGATCGCCGACGTGTGAAGACGT\n +\n FHGGGF?GGFEHHHFHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1310:19552:89269\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJIJJIHFCCHHGHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1310:11672:92080\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IIJIHFGHHGHJHHHHHFFFDFCCC\n @HWI-ST132:678:C1LFKACXX:6:1312:14124:76448\n TTCGATCGCCGACGTGTGAAGACGT\n +\n@@ -2458,111 +250,7 @@\n TTCGATCGCCGACGTGTGAAGACGT\n +\n AIIJJJIHFFGDHHHHHFFFDFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1315:9373:25299\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-G>FDCC4;;EEIFDFDFDD=+D?@@\n-@HWI-ST132:678:C1LFKACXX:6:1315:12968:32460\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-BD9FGFFBF?GGF<FFFDDDB=1@@\n-@HWI-ST132:678:C1LFKACXX:6:2101:18316:34316\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJJJJIHHEIHHFHHFFEDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2101:18438:36839\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJJJJHGG?HHHDHHFFDDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2101:14608:56807\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJJIHHHFIIHHHHHFFFDDBCB\n-@HWI-ST132:678:C1LFKACXX:6:2103:7602:64596\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-GHIIHFBC??:@FCCDF@+A;D??=\n @HWI-ST132:678:C1LFKACXX:6:2103:17863:69050\n TTCGATCGCCGACGTGTGAAGACGT\n +\n GIJJJJIIHFGIHFHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2104:5137:4251\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJIJJIHEHHJHHDHGFFEFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2104:20272:16658\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJIHHJIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2104:8336:35547\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJIHHDC?C@F@@HGFFFFD@B=\n-@HWI-ST132:678:C1LFKACXX:6:2104:17454:68818\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-IJJJIIHFEIIIHHHHHFFFBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-DIGJIFD?1@@C<0@HHDFFDD??:\n-@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-?HEGHC4HFHG@HFDHHDDD=D@@@\n-@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIIHIHFHHHFFFFF@CC\n-@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-HJJJJJJHIHIJHHHHHFFFFFBCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-FJJIIIGD?FCGHHHHHDDB?FCBB\n-@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n-TTCGATCGCCGACGTGTGAAGACGT\n-+\n-JJJJIHF?114C@@CHHFFFFFBB=\n-@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n-TTCGATCGCCGACGTGTGAAGACG\n-+\n-IIIGC<HGGFGHHHHHFFEBFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n-ATTCGATCGCCGACGTGTGAAGACG\n-+\n-JJIHGGCGIGJJGHHHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n-TTCGATCGCCGACGTGTGAAGAC\n-+\n-JJHIGHEGFIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n-TGCAAGCTAAGAATTCCGAAACGCC\n-+\n-JJIJJJJJJIHFCAC:HDA==D?B:\n-@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n-GTAACACTTTGTAACGGATCGCAAA\n-+\n-@@@DFFFFHHHGHIJJJEIIIIDII\n-@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n-TTTCCGTCGACTAACAATAAGCCGT\n-+\n-B@CFFFDDFHHHHJJIJJDHIIIJG\n-@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n-AAAATGTCAGTCACTCAGCCAAAGG\n-+\n-BBCFFFDF?FHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n-TCCTTTGGCTGAGTGACTGACATTT\n-+\n-HEHCFHFFHCA2<<CHFDBDDF@@?\n-@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n-CAAGGAGTCGGCAGCTGAAGTAGCA\n-+\n-=@@DD?DDFF?)@FAH>FEFHHEHE\n-@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n-TCGTACCGATCTAGACATCTCTTC\n-+\n-GIJJJJJJIGJHHHGHD<FFD@@@\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,311 +1,27 @@\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n-TTAAACTGTGAATTAAGCGCG\n-+\n-JGHJJJJJHHHFCFFFFF@CB\n-@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n-TGTGGAGTCCTGTTGATCATT\n-+\n-IJIJJJJIHDHHHDFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n-ACAGCGAATTGATCGGATTGC\n-+\n-CCIHIJJIHHHDHDDAFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHGHHHHFIIJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHHFFHIJHHIJJH\n-@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n-TTCCGAATTGTCTGCACTGGT\n-+\n-:=?DDF:22<<DFGIBEGHIC\n-@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n-CCCCTGATCAAACATCGTCTG\n-+\n-B@BDFFDFHHHHHJJJJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n-TAATACAATACATCAGACGAT\n-+\n-EEHFBIHIGHHDHDDB=4+??\n-@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n-AAGACTTCGGAGTTAAGTATC\n-+\n-IHHHJIHE>DHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n-TACATACCTGGGAAGACTTCG\n-+\n-JJIIIHEHHBFHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n-TTCTGGGAATTCCGAAGATGG\n-+\n-JJJHHGEAHHHHHFFFFFCCC\n @HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n ATAAACTGTCTGACAGGGACC\n +\n CCCFFFFFHHHBHIIGHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n-TACCTATGTCGATTGCCACCT\n-+\n-GIIIHGHGF?A??DDDDD?@?\n-@HWI-ST132:678:C1LFKACXX:6:2106:14268:13093\n-AAGGCAATGATTGTTGAGGGC\n-+\n-4==DBD+42>CFHHJGIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1205:15169:28150\n-TGACTTGGCCTCTGTGCGCAC\n-+\n-CCCFFFEFHHHHHJHHHHIIJ\n-@HWI-ST132:678:C1LFKACXX:6:2109:6872:55506\n-CAATGACTTGGCCTCTGTGCG\n-+\n-BB@DDEFFHHHGHJJJIGEHH\n-@HWI-ST132:678:C1LFKACXX:6:2108:12752:15836\n-CAGAGGCCAAGTCATTGAGCG\n-+\n-FA+IIIIIHHHHHFDFFFC@@\n @HWI-ST132:678:C1LFKACXX:6:1115:4388:39138\n CGGCGCTCAATGACTTGGCCT\n +\n @CCAFFFFHDHHHIIIIIIIH\n-@HWI-ST132:678:C1LFKACXX:6:2107:13841:82210\n-AGCGGCGCTCAATGACTTGGC\n-+\n-CCCFDFFFHHHHHEGHJJCC?\n-@HWI-ST132:678:C1LFKACXX:6:2103:11417:67112\n-CAAGTCATTGAGCGCCGCTTC\n-+\n-JJIIHFB2ACHHHFFFDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1205:15296:60784\n-GTCATTGAGCGCCGCTTCCAG\n-+\n-JIIJIJIJHHFHHEBFFFB@B\n-@HWI-ST132:678:C1LFKACXX:6:2106:12781:78894\n-TCATTGAGCGCCGCTTCCAGG\n-+\n-JJJJJJJIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1213:6801:56774\n-TAAGAGCGACCTGGAAGCGGC\n-+\n-CCCFFFFFDHHHHIIJJJJIH\n-@HWI-ST132:678:C1LFKACXX:6:2109:11200:65312\n-TCCAGGTCGCTCTTAAACTTG\n-+\n-IIIGC,IIHHHD@DDDDD@@@\n @HWI-ST132:678:C1LFKACXX:6:1201:10525:92672\n GTCGCTCTTAAACTTGGGAAC\n +\n HFJIHDHHHHFBHFFFFDBBB\n-@HWI-ST132:678:C1LFKACXX:6:1204:20435:17195\n-GGGGAAAGTTTCGGAAAGCGT\n-+\n-BCCFFFFFFHHGHJIIJJJJG\n-@HWI-ST132:678:C1LFKACXX:6:2109:17802:67038\n-TAGAACTCAGCAAGGTGAGCT\n-+\n-CCCFFFFFGHHHHFHCGIEHI\n-@HWI-ST132:678:C1LFKACXX:6:1301:15212:7880\n-TTTTGCGTACGTGGCTGCCCA\n-+\n-JJJHGJIHDCFHHDFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1203:17614:29016\n-TTTGCGTACGTGGCTGCCCAG\n-+\n-JIJJJJIHHFCHHDDFFDC@@\n-@HWI-ST132:678:C1LFKACXX:6:1312:6743:61160\n-GCTAAGATCGGACACGAGCCT\n-+\n-@@BDDDFFFHHHHJIJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:10877:43166\n-CTCGTGTCCGATCTTAGCTTC\n-+\n-IIHGGJJJHHFFHFDDDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1114:20246:58873\n-CAGATGCGTAGCTGCCTGGCT\n-+\n-GIHEGIIIHGGHGFFDB=1<?\n-@HWI-ST132:678:C1LFKACXX:6:1210:1131:47701\n-CAGATGCGTAGCTGCCTGGCT\n-+\n-BFAHEGH>HD>FHDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1205:8301:45085\n-ACATTCGAGACTCAACGGCGC\n-+\n-??@DFFFFH;CAC<FFHGB@F\n-@HWI-ST132:678:C1LFKACXX:6:1114:18437:39882\n-CTTTAGGTCCTCATTCTGGAG\n-+\n-E?<CEFA4?FC=222244114\n-@HWI-ST132:678:C1LFKACXX:6:2103:20767:66007\n-TTCTGACTTGTCGCGGTGGTA\n-+\n-E:C@2@FJHHDGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:6048:16581\n-TTCTGACTTGTCGCGGTGGTA\n-+\n-C:<<2<AGHHFHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2109:18810:55523\n-TTGACTAGCGACTGCAGTGCT\n-+\n-CCCFFFFFGFHHHJEGHHCHH\n-@HWI-ST132:678:C1LFKACXX:6:1212:19203:63197\n-CCTGAACGGGTCGTTGCGATC\n-+\n-JJHGEEIHHFDHGFEDDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1311:7177:19732\n-CCCCTGATCGCAACGACCCGT\n-+\n-@@@DDDD>FAFDDH1ACAGG:\n-@HWI-ST132:678:C1LFKACXX:6:1101:11100:95584\n-TCGAACGGTTGATCTGGCAAC\n-+\n-JJJJJJJIHF?HFFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1103:11021:88518'..b'-IJJJHFG@GHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:9456:8227\n-TGACGAGGCAGAGCGGGCTGC\n-+\n-JIHIHF@IHHHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:6680:6448\n-TGACGAGGCAGAGCGGGCTGC\n-+\n-IHGB:2@GHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2109:16435:34131\n-TGACGAGGCAGAGCGGGCTGC\n-+\n-HGH@:@JIHHHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1307:1328:76760\n-GACGAGGCAGAGCGGGCTGCC\n-+\n-GHF@<:IHHGGHHFFDDFC@@\n @HWI-ST132:678:C1LFKACXX:6:2105:10714:3663\n CAGAGCGGGCTGCCGGTCCCT\n +\n JJJIIHJJHHHHHFFFFD@@B\n-@HWI-ST132:678:C1LFKACXX:6:2106:6452:10486\n-CAGAGCGGGCTGCCGGTCCCT\n-+\n-IIIHHDIHHDD@)FFFFFC@@\n-@HWI-ST132:678:C1LFKACXX:6:2107:13837:84657\n-CAGAGCGGGCTGCCGGTCCCT\n-+\n-JJIHFIHIHHHHHFFFFF@CB\n-@HWI-ST132:678:C1LFKACXX:6:1104:19315:94114\n-AGAGCGGGCTGCCGGTCCCTC\n-+\n-JJJJIHGJGHHHGFFDBF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1104:7430:21922\n-GCGGGCTGCCGGTCCCTCTCC\n-+\n-JIJIIIHC<<DFHAFDFFC@@\n-@HWI-ST132:678:C1LFKACXX:6:1307:14679:35813\n-GCGGGCTGCCGGTCCCTCTCC\n-+\n-JIJJJIHF@@FHHFFFFFC@B\n @HWI-ST132:678:C1LFKACXX:6:1313:2242:53030\n GCGGGCTGCCGGTCCCTCTCC\n +\n HIHGGHHGCHDFGDDDFD@?=\n-@HWI-ST132:678:C1LFKACXX:6:2108:20023:78881\n-ACAACAGCTGGAGAGGGACCG\n-+\n-BCCFFFFFHHDFFHGGCEGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:19637:62229\n-CCTCTCCAGCTGTTGTTGTTG\n-+\n-FHJIJJJIHGHHHFFDBA11+\n @HWI-ST132:678:C1LFKACXX:6:1304:17194:95501\n TACCTCCAACAACAACAGCTG\n +\n BCCFFFFFFHHFHJFIJIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:5151:98200\n-TGTTGTTGTTGGAGGTAGCGG\n-+\n-<<GFA<IGDFCHHFFFFFBBB\n-@HWI-ST132:678:C1LFKACXX:6:1209:9824:17749\n-TGTTGTTGTTGGAGGTAGCGG\n-+\n-IHFE<3HFAFCHFFFFFFB@?\n-@HWI-ST132:678:C1LFKACXX:6:1111:15377:25850\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-IIIGFA222FCFFFFEFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1215:3469:66547\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-GGGIIIHE<GHHHFDD=D@C@\n-@HWI-ST132:678:C1LFKACXX:6:1215:3511:69906\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-GGJGHGC?<FFFFDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1302:9816:51867\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-JJJIHGGACDHHHEDBDFCB@\n-@HWI-ST132:678:C1LFKACXX:6:1111:14307:12122\n-TAGCGGGGCTTCTGTCGGAGC\n-+\n-IHGGHFBHFD?HHFDFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1212:7672:92273\n-TAGCGGGGCTTCTGTCGGAGC\n-+\n-GBIGHD?GFBFFAD?DDD@@@\n @HWI-ST132:678:C1LFKACXX:6:1315:17800:56780\n TCTGTCGGAGCCAATAGAGCG\n +\n BEHCGEDFFDF?@==A4D8@?\n-@HWI-ST132:678:C1LFKACXX:6:1211:8820:25669\n-TCGGAGCCAATAGAGCGGGAG\n-+\n-C?AIGC24FFCACDD@AB@@=\n-@HWI-ST132:678:C1LFKACXX:6:1107:4152:41817\n-CAACAAATCAAGAAAGAGCCC\n-+\n-CCCFFFFFHHHHHHHIJIIIJ\n @HWI-ST132:678:C1LFKACXX:6:1107:13749:41003\n TGATTTGTTGGTAGAAGAAGG\n +\n JJJIJJIGFFFHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1112:7021:46842\n-TGATTTGTTGGTAGAAGAAGG\n-+\n-JIGHHFGGHFHHFDFFFF@@B\n @HWI-ST132:678:C1LFKACXX:6:2106:12928:28648\n TGATTTGTTGGTAGAAGAAGG\n +\n@@ -9010,59 +910,11 @@\n TGATTTGTTGGTAGAAGAAGG\n +\n JIHE<,A<23<HHFFFDD=:1\n-@HWI-ST132:678:C1LFKACXX:6:1104:18932:34578\n-GCTATGGGTTATTGACCGCTC\n-+\n-JJJIHFE?GHFFFFFEDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1202:4878:86481\n-TGCGTTTGGGATTGTCGGTGA\n-+\n-IHDJIHFHHGHHDFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1115:14400:83897\n-TTTGGGATTGTCGGTGAGACG\n-+\n-IHHFGGEGDFAFFBFDFD@?@\n-@HWI-ST132:678:C1LFKACXX:6:1213:16820:54984\n-TTGTCGGTGAGACGTAGGAGA\n-+\n-IJIIGBFHFDFFFDFFFFCCB\n @HWI-ST132:678:C1LFKACXX:6:1106:4136:80459\n TAGGAGAAGTACGCGTTGTTG\n +\n CDEE<<)EDDDDDD?A4D???\n-@HWI-ST132:678:C1LFKACXX:6:1108:12282:61422\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JIIJJIJJHHFAFFDEDFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1111:13707:90938\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JJIHF@@JHFC<CFDDAF@@?\n-@HWI-ST132:678:C1LFKACXX:6:1314:12461:28557\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JJHIHGHJGHFDHFDFFFC@B\n-@HWI-ST132:678:C1LFKACXX:6:2106:10137:48564\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JJJJHHIIHHFFHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2109:19752:91497\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-GCHIIIEGHFFFHDDBD?@@@\n-@HWI-ST132:678:C1LFKACXX:6:1215:19556:9898\n-GAAGTACGCGTTGTTGCGCTG\n-+\n-IIIIIIIIHFHHFDA2441+:\n-@HWI-ST132:678:C1LFKACXX:6:1208:16914:37703\n-TGTTGCGCTGAATTGAGAGTC\n-+\n-HEGHFF<GFF6GHFFFFFC@@\n @HWI-ST132:678:C1LFKACXX:6:2103:12622:49391\n TGTTGCGCTGAATTGAGAGTC\n +\n HAHJJJJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1104:12986:68120\n-TTGCGCTGAATTGAGAGTCGG\n-+\n-IGHEGC2+FFF<FDDDDD@@@\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,311 +1,27 @@\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n-TTAAACTGTGAATTAAGCGCG\n-+\n-JGHJJJJJHHHFCFFFFF@CB\n-@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n-TGTGGAGTCCTGTTGATCATT\n-+\n-IJIJJJJIHDHHHDFFFF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n-ACAGCGAATTGATCGGATTGC\n-+\n-CCIHIJJIHHHDHDDAFD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHGHHHHFIIJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHHFFHIJHHIJJH\n-@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n-TTCCGAATTGTCTGCACTGGT\n-+\n-:=?DDF:22<<DFGIBEGHIC\n-@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n-CCCCTGATCAAACATCGTCTG\n-+\n-B@BDFFDFHHHHHJJJJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n-TAATACAATACATCAGACGAT\n-+\n-EEHFBIHIGHHDHDDB=4+??\n-@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n-AAGACTTCGGAGTTAAGTATC\n-+\n-IHHHJIHE>DHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n-TACATACCTGGGAAGACTTCG\n-+\n-JJIIIHEHHBFHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n-TTCTGGGAATTCCGAAGATGG\n-+\n-JJJHHGEAHHHHHFFFFFCCC\n @HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n ATAAACTGTCTGACAGGGACC\n +\n CCCFFFFFHHHBHIIGHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n-TACCTATGTCGATTGCCACCT\n-+\n-GIIIHGHGF?A??DDDDD?@?\n-@HWI-ST132:678:C1LFKACXX:6:2106:14268:13093\n-AAGGCAATGATTGTTGAGGGC\n-+\n-4==DBD+42>CFHHJGIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1205:15169:28150\n-TGACTTGGCCTCTGTGCGCAC\n-+\n-CCCFFFEFHHHHHJHHHHIIJ\n-@HWI-ST132:678:C1LFKACXX:6:2109:6872:55506\n-CAATGACTTGGCCTCTGTGCG\n-+\n-BB@DDEFFHHHGHJJJIGEHH\n-@HWI-ST132:678:C1LFKACXX:6:2108:12752:15836\n-CAGAGGCCAAGTCATTGAGCG\n-+\n-FA+IIIIIHHHHHFDFFFC@@\n @HWI-ST132:678:C1LFKACXX:6:1115:4388:39138\n CGGCGCTCAATGACTTGGCCT\n +\n @CCAFFFFHDHHHIIIIIIIH\n-@HWI-ST132:678:C1LFKACXX:6:2107:13841:82210\n-AGCGGCGCTCAATGACTTGGC\n-+\n-CCCFDFFFHHHHHEGHJJCC?\n-@HWI-ST132:678:C1LFKACXX:6:2103:11417:67112\n-CAAGTCATTGAGCGCCGCTTC\n-+\n-JJIIHFB2ACHHHFFFDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1205:15296:60784\n-GTCATTGAGCGCCGCTTCCAG\n-+\n-JIIJIJIJHHFHHEBFFFB@B\n-@HWI-ST132:678:C1LFKACXX:6:2106:12781:78894\n-TCATTGAGCGCCGCTTCCAGG\n-+\n-JJJJJJJIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1213:6801:56774\n-TAAGAGCGACCTGGAAGCGGC\n-+\n-CCCFFFFFDHHHHIIJJJJIH\n-@HWI-ST132:678:C1LFKACXX:6:2109:11200:65312\n-TCCAGGTCGCTCTTAAACTTG\n-+\n-IIIGC,IIHHHD@DDDDD@@@\n @HWI-ST132:678:C1LFKACXX:6:1201:10525:92672\n GTCGCTCTTAAACTTGGGAAC\n +\n HFJIHDHHHHFBHFFFFDBBB\n-@HWI-ST132:678:C1LFKACXX:6:1204:20435:17195\n-GGGGAAAGTTTCGGAAAGCGT\n-+\n-BCCFFFFFFHHGHJIIJJJJG\n-@HWI-ST132:678:C1LFKACXX:6:2109:17802:67038\n-TAGAACTCAGCAAGGTGAGCT\n-+\n-CCCFFFFFGHHHHFHCGIEHI\n-@HWI-ST132:678:C1LFKACXX:6:1301:15212:7880\n-TTTTGCGTACGTGGCTGCCCA\n-+\n-JJJHGJIHDCFHHDFFFFCC@\n-@HWI-ST132:678:C1LFKACXX:6:1203:17614:29016\n-TTTGCGTACGTGGCTGCCCAG\n-+\n-JIJJJJIHHFCHHDDFFDC@@\n-@HWI-ST132:678:C1LFKACXX:6:1312:6743:61160\n-GCTAAGATCGGACACGAGCCT\n-+\n-@@BDDDFFFHHHHJIJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:10877:43166\n-CTCGTGTCCGATCTTAGCTTC\n-+\n-IIHGGJJJHHFFHFDDDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1114:20246:58873\n-CAGATGCGTAGCTGCCTGGCT\n-+\n-GIHEGIIIHGGHGFFDB=1<?\n-@HWI-ST132:678:C1LFKACXX:6:1210:1131:47701\n-CAGATGCGTAGCTGCCTGGCT\n-+\n-BFAHEGH>HD>FHDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1205:8301:45085\n-ACATTCGAGACTCAACGGCGC\n-+\n-??@DFFFFH;CAC<FFHGB@F\n-@HWI-ST132:678:C1LFKACXX:6:1114:18437:39882\n-CTTTAGGTCCTCATTCTGGAG\n-+\n-E?<CEFA4?FC=222244114\n-@HWI-ST132:678:C1LFKACXX:6:2103:20767:66007\n-TTCTGACTTGTCGCGGTGGTA\n-+\n-E:C@2@FJHHDGHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:6048:16581\n-TTCTGACTTGTCGCGGTGGTA\n-+\n-C:<<2<AGHHFHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2109:18810:55523\n-TTGACTAGCGACTGCAGTGCT\n-+\n-CCCFFFFFGFHHHJEGHHCHH\n-@HWI-ST132:678:C1LFKACXX:6:1212:19203:63197\n-CCTGAACGGGTCGTTGCGATC\n-+\n-JJHGEEIHHFDHGFEDDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1311:7177:19732\n-CCCCTGATCGCAACGACCCGT\n-+\n-@@@DDDD>FAFDDH1ACAGG:\n-@HWI-ST132:678:C1LFKACXX:6:1101:11100:95584\n-TCGAACGGTTGATCTGGCAAC\n-+\n-JJJJJJJIHF?HFFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1103:11021:88518'..b'-IJJJHFG@GHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:9456:8227\n-TGACGAGGCAGAGCGGGCTGC\n-+\n-JIHIHF@IHHHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:6680:6448\n-TGACGAGGCAGAGCGGGCTGC\n-+\n-IHGB:2@GHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2109:16435:34131\n-TGACGAGGCAGAGCGGGCTGC\n-+\n-HGH@:@JIHHHHGFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1307:1328:76760\n-GACGAGGCAGAGCGGGCTGCC\n-+\n-GHF@<:IHHGGHHFFDDFC@@\n @HWI-ST132:678:C1LFKACXX:6:2105:10714:3663\n CAGAGCGGGCTGCCGGTCCCT\n +\n JJJIIHJJHHHHHFFFFD@@B\n-@HWI-ST132:678:C1LFKACXX:6:2106:6452:10486\n-CAGAGCGGGCTGCCGGTCCCT\n-+\n-IIIHHDIHHDD@)FFFFFC@@\n-@HWI-ST132:678:C1LFKACXX:6:2107:13837:84657\n-CAGAGCGGGCTGCCGGTCCCT\n-+\n-JJIHFIHIHHHHHFFFFF@CB\n-@HWI-ST132:678:C1LFKACXX:6:1104:19315:94114\n-AGAGCGGGCTGCCGGTCCCTC\n-+\n-JJJJIHGJGHHHGFFDBF@C@\n-@HWI-ST132:678:C1LFKACXX:6:1104:7430:21922\n-GCGGGCTGCCGGTCCCTCTCC\n-+\n-JIJIIIHC<<DFHAFDFFC@@\n-@HWI-ST132:678:C1LFKACXX:6:1307:14679:35813\n-GCGGGCTGCCGGTCCCTCTCC\n-+\n-JIJJJIHF@@FHHFFFFFC@B\n @HWI-ST132:678:C1LFKACXX:6:1313:2242:53030\n GCGGGCTGCCGGTCCCTCTCC\n +\n HIHGGHHGCHDFGDDDFD@?=\n-@HWI-ST132:678:C1LFKACXX:6:2108:20023:78881\n-ACAACAGCTGGAGAGGGACCG\n-+\n-BCCFFFFFHHDFFHGGCEGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:19637:62229\n-CCTCTCCAGCTGTTGTTGTTG\n-+\n-FHJIJJJIHGHHHFFDBA11+\n @HWI-ST132:678:C1LFKACXX:6:1304:17194:95501\n TACCTCCAACAACAACAGCTG\n +\n BCCFFFFFFHHFHJFIJIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:5151:98200\n-TGTTGTTGTTGGAGGTAGCGG\n-+\n-<<GFA<IGDFCHHFFFFFBBB\n-@HWI-ST132:678:C1LFKACXX:6:1209:9824:17749\n-TGTTGTTGTTGGAGGTAGCGG\n-+\n-IHFE<3HFAFCHFFFFFFB@?\n-@HWI-ST132:678:C1LFKACXX:6:1111:15377:25850\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-IIIGFA222FCFFFFEFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1215:3469:66547\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-GGGIIIHE<GHHHFDD=D@C@\n-@HWI-ST132:678:C1LFKACXX:6:1215:3511:69906\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-GGJGHGC?<FFFFDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:1302:9816:51867\n-TGTTGTTGGAGGTAGCGGGGC\n-+\n-JJJIHGGACDHHHEDBDFCB@\n-@HWI-ST132:678:C1LFKACXX:6:1111:14307:12122\n-TAGCGGGGCTTCTGTCGGAGC\n-+\n-IHGGHFBHFD?HHFDFFF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1212:7672:92273\n-TAGCGGGGCTTCTGTCGGAGC\n-+\n-GBIGHD?GFBFFAD?DDD@@@\n @HWI-ST132:678:C1LFKACXX:6:1315:17800:56780\n TCTGTCGGAGCCAATAGAGCG\n +\n BEHCGEDFFDF?@==A4D8@?\n-@HWI-ST132:678:C1LFKACXX:6:1211:8820:25669\n-TCGGAGCCAATAGAGCGGGAG\n-+\n-C?AIGC24FFCACDD@AB@@=\n-@HWI-ST132:678:C1LFKACXX:6:1107:4152:41817\n-CAACAAATCAAGAAAGAGCCC\n-+\n-CCCFFFFFHHHHHHHIJIIIJ\n @HWI-ST132:678:C1LFKACXX:6:1107:13749:41003\n TGATTTGTTGGTAGAAGAAGG\n +\n JJJIJJIGFFFHHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1112:7021:46842\n-TGATTTGTTGGTAGAAGAAGG\n-+\n-JIGHHFGGHFHHFDFFFF@@B\n @HWI-ST132:678:C1LFKACXX:6:2106:12928:28648\n TGATTTGTTGGTAGAAGAAGG\n +\n@@ -9010,59 +910,11 @@\n TGATTTGTTGGTAGAAGAAGG\n +\n JIHE<,A<23<HHFFFDD=:1\n-@HWI-ST132:678:C1LFKACXX:6:1104:18932:34578\n-GCTATGGGTTATTGACCGCTC\n-+\n-JJJIHFE?GHFFFFFEDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1202:4878:86481\n-TGCGTTTGGGATTGTCGGTGA\n-+\n-IHDJIHFHHGHHDFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1115:14400:83897\n-TTTGGGATTGTCGGTGAGACG\n-+\n-IHHFGGEGDFAFFBFDFD@?@\n-@HWI-ST132:678:C1LFKACXX:6:1213:16820:54984\n-TTGTCGGTGAGACGTAGGAGA\n-+\n-IJIIGBFHFDFFFDFFFFCCB\n @HWI-ST132:678:C1LFKACXX:6:1106:4136:80459\n TAGGAGAAGTACGCGTTGTTG\n +\n CDEE<<)EDDDDDD?A4D???\n-@HWI-ST132:678:C1LFKACXX:6:1108:12282:61422\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JIIJJIJJHHFAFFDEDFCBB\n-@HWI-ST132:678:C1LFKACXX:6:1111:13707:90938\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JJIHF@@JHFC<CFDDAF@@?\n-@HWI-ST132:678:C1LFKACXX:6:1314:12461:28557\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JJHIHGHJGHFDHFDFFFC@B\n-@HWI-ST132:678:C1LFKACXX:6:2106:10137:48564\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-JJJJHHIIHHFFHFFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2109:19752:91497\n-TAGGAGAAGTACGCGTTGTTG\n-+\n-GCHIIIEGHFFFHDDBD?@@@\n-@HWI-ST132:678:C1LFKACXX:6:1215:19556:9898\n-GAAGTACGCGTTGTTGCGCTG\n-+\n-IIIIIIIIHFHHFDA2441+:\n-@HWI-ST132:678:C1LFKACXX:6:1208:16914:37703\n-TGTTGCGCTGAATTGAGAGTC\n-+\n-HEGHFF<GFF6GHFFFFFC@@\n @HWI-ST132:678:C1LFKACXX:6:2103:12622:49391\n TGTTGCGCTGAATTGAGAGTC\n +\n HAHJJJJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1104:12986:68120\n-TTGCGCTGAATTGAGAGTCGG\n-+\n-IGHEGC2+FFF<FDDDDD@@@\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,235 +1,19 @@\n-@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n-GTACTCGATCGCCTGAAGAAC\n-+\n-@@CFFFFFHHCFHI+AEHHII\n-@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n-TTACAAAGTCAGTGGGGATGC\n-+\n-@@@FFFFFFFHFCGGE<F@A<\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n-TTAAACTGTGAATTAAGCGCG\n-+\n-BC@FFFFFCFHHHJJJJJHGJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n-TGTGGAGTCCTGTTGATCATT\n-+\n-@C@FFFFDHHHDHIJJJJIJI\n-@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n-ACAGCGAATTGATCGGATTGC\n-+\n-@@@DFADDHDHHHIJJIHICC\n-@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHGHHHHFIIJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHHFFHIJHHIJJH\n-@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n-TTCCGAATTGTCTGCACTGGT\n-+\n-:=?DDF:22<<DFGIBEGHIC\n-@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n-CCCCTGATCAAACATCGTCTG\n-+\n-B@BDFFDFHHHHHJJJJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n-TAATACAATACATCAGACGAT\n-+\n-??+4=BDDHDHHGIHIBFHEE\n-@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n-AAGACTTCGGAGTTAAGTATC\n-+\n-CCCFFFFFHHHD>EHIJHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n-TACATACCTGGGAAGACTTCG\n-+\n-CCCFFFFFHHFBHHEHIIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n-TTCTGGGAATTCCGAAGATGG\n-+\n-CCCFFFFFHHHHHAEGHHJJJ\n @HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n ATAAACTGTCTGACAGGGACC\n +\n CCCFFFFFHHHBHIIGHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n-TACCTATGTCGATTGCCACCT\n-+\n-?@?DDDDD??A?FGHGHIIIG\n @HWI-ST132:678:C1LFKACXX:6:2105:13825:18518\n TGTCCAGTCTGACGATATCAG\n +\n CCCFFFFFGHHHH:FHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1111:12949:86137\n-TGATGCCAGACCGGGCTTCAG\n-+\n-CCCFFFFFHHHHHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:14660:78489\n-CCGGGCTTCAGTCTGGGCGCC\n-+\n-B@@FFFFFHGDAFGEGGHJGJ\n-@HWI-ST132:678:C1LFKACXX:6:1301:9997:96604\n-CCGGGCTTCAGTCTGGGCGCC\n-+\n-@CCFFFFDHHHHHGHIHH<?G\n-@HWI-ST132:678:C1LFKACXX:6:2103:4365:12003\n-CGGGCTTCAGTCTGGGCGCCA\n-+\n-BCCFFFFFHHFHHIGDABCGI\n-@HWI-ST132:678:C1LFKACXX:6:1315:14025:50396\n-TAGAGTCTGGACTGTGGCGCC\n-+\n-@@@DFDFDFH?DBH<EFGGBE\n-@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:BBDA2=A=CCFHIJJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?@BDD=BDADHHHHJ3CFGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BDDFFFHHHHFGIJJIIGI\n-@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@BDDEFFFFHHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B?BDFDFFCFHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:?BDDDFFCF<<<<EGIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDDDDFCFHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BFFDFFDHFHHJJFIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@BBDFDFFCFHHGHIJIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDDDDFADHHHIJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?:?DADDD=?::DEEB:<+<:\n-@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCBFFFFFFHHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@CFFFFFFHGHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@@DFFFFF?FHGGIIEHEHG\n-@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBCFFDDFA;DFHIJIIIGII\n-@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFDFFFFFHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBFFFFFHH;DHIJJJJJGJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n-TCT'..b'ACXX:6:1204:8915:42482\n-ACACCCACTTCATGTCGACAG\n-+\n-@@@FBDDDHHFGHH<EGFHGG\n-@HWI-ST132:678:C1LFKACXX:6:1109:5525:6504\n-TAATTTATTGTCGACTCCTGA\n-+\n-C@CFFFDFHHHHH3EHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16003:74425\n-GAGGACAACCACTCCGGCAGC\n-+\n-CC@FDFDFHHGHHJJJJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1103:16164:28590\n-ATTGCGGCTGCACACAGAGAA\n-+\n-BCBDDFFFHHHHHJIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:17496:94074\n-ATACGACAAATGATACTGAGT\n-+\n-CCCFFFFFHHHDHIJJJIFA<\n-@HWI-ST132:678:C1LFKACXX:6:1310:11295:14789\n-CCAGACGACTTTGTCCGCCTC\n-+\n-CCCFFFFFHHHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:16743:60430\n-TGCAGGATCAGAACTCAGAAT\n-+\n-CCCFFFFFHHHHHIJJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1108:9976:99924\n-GTTCCTCTTCTTTATCGGGTG\n-+\n-C@@FFFFFHHHHHGHIII<AF\n-@HWI-ST132:678:C1LFKACXX:6:1311:17281:3877\n-CCACGACGTTCAACATTGACT\n-+\n-@@BFFDDFHDHFH@EHIIHIG\n @HWI-ST132:678:C1LFKACXX:6:1209:13387:2204\n ACTTCATATCCTTTTCGGGTG\n +\n @BBDFFFFHHHHHJJJJJJFG\n-@HWI-ST132:678:C1LFKACXX:6:1201:10388:40542\n-GCAACTCTGCCACTTGAACCC\n-+\n-CCCFFFFFHHHHHJJGIJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1207:6411:98409\n GCAACTCTGCCACTTGAACCC\n +\n @@@FFFED8CFHDGIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:6060:56314\n-CGAGATGACGCTGGCTGACTG\n-+\n-@C@DDFFFGHHFHHGIIIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1110:13887:78568\n CAACTGCGCTCTGGAATAAAC\n +\n CCCFFFFFHHHHHIJJIIJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:1449:44316\n-CGCTGTTCAGCTCCTCTCAGT\n-+\n-B@CFDDDDHHHHHJJJJJIIH\n-@HWI-ST132:678:C1LFKACXX:6:2103:8728:29903\n-TAGACGCCAGCAAGGATTGCT\n-+\n-CCCFFFFFHHFHG2AGFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:10389:44836\n-TCTCCAGCTGTAAATACAACT\n-+\n-BBBFFFFFHHCFH<FHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1208:2325:6974\n-AAAACAAAATTCGGCGGCATC\n-+\n-CCCFFFFFDHHHHIIJJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:1312:11197:31549\n AAAACAAAATTCGGCGGCATC\n +\n @@@FFDFF@FFFHCFFHHIGG\n-@HWI-ST132:678:C1LFKACXX:6:1314:11236:21715\n-ATCAGGGGCTTTGCTGACGCC\n-+\n-CCBFFFFFHHHHHIJIIJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:7857:86148\n-AACATACTTGTGGCCTGGCCT\n-+\n-C@CFFFFFHHHBFIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:17527:21097\n-AGATGTTGACATTGAATGGCC\n-+\n-BC@DFFFFFHHGHIIIJIJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:8227:45651\n-CGCACTCAGTCACTCGGTTTG\n-+\n-@CCFFFFFDFHFHHIJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:16767:67452\n-GCAGCTCTAGTTGGTCGCGGC\n-+\n-@C@FFFFF>FCFHEGGGIGHI\n-@HWI-ST132:678:C1LFKACXX:6:1114:13156:95650\n-AATTATTTACAAGCGGCGAGC\n-+\n-@@@=BDFFHDFHFIFH<GIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:18254:36868\n-GTCGATCGATCGAACGGGCGT\n-+\n-BBCDFFFFHHHHHGIGHIJIH\n-@HWI-ST132:678:C1LFKACXX:6:1101:2206:66004\n-AACCAGCGGACATCGGACATC\n-+\n-:?@D?DBDH@@CCFHIIJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:3454:76338\n-TTTACACATAACTCTTCGCAT\n-+\n-@@@D?DDDHFHBFBGHIIIIG\n-@HWI-ST132:678:C1LFKACXX:6:2108:18053:41000\n-TCTGCAGCGATTCCGAACTCC\n-+\n-CC@FFFFFHGHHHI3<EHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n-CTTTCGATGGCAGAGTTGGTC\n-+\n-@BBFFFDDHHHHHJJGIIGHI\n-@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n-CCACTGTGGAATTATGAGAGC\n-+\n-B@BFFFDDFDHHH4CAEEGII\n-@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n-AAGCAGCCAAAGCTCCAGGGC\n-+\n-CCBFFFFFHHHDFIJJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n-GCAACCAGTTGATTGGGGACT\n-+\n-@CCFFFFFFHHHHJIJEHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n-TTCCAAAGTTGTGAGGCACTC\n-+\n-@@@F?DDEDFHHHJIHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n-TTAATTTCGCGTTTTTTCTCG\n-+\n-:?BDDF?DFH@00BFHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n-ACCGGACAGCACGGTCGTGTT\n-+\n-@CCFFFFFFHHHGEEGIFGHG\n-@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n-TTAACAATCAGTGCGGTGTAC\n-+\n-CCCFFFFEHHHDFGIIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n-GCATATCGCAGTCCATGCTGT\n-+\n-CCCFFFFFHHHHHJJJJJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n @HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n ATACTAGATTCGTTGAAAAGT\n +\n @@@F7DDDFA<CC?;FAEBH?\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,235 +1,19 @@\n-@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n-GTACTCGATCGCCTGAAGAAC\n-+\n-@@CFFFFFHHCFHI+AEHHII\n-@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n-TTACAAAGTCAGTGGGGATGC\n-+\n-@@@FFFFFFFHFCGGE<F@A<\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n-TTAAACTGTGAATTAAGCGCG\n-+\n-BC@FFFFFCFHHHJJJJJHGJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n-TGTGGAGTCCTGTTGATCATT\n-+\n-@C@FFFFDHHHDHIJJJJIJI\n-@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n-ACAGCGAATTGATCGGATTGC\n-+\n-@@@DFADDHDHHHIJJIHICC\n-@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHGHHHHFIIJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n-TTCCGAATTGTCTGCACTGGT\n-+\n-CCCFFFFFHHFFHIJHHIJJH\n-@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n-TTCCGAATTGTCTGCACTGGT\n-+\n-:=?DDF:22<<DFGIBEGHIC\n-@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n-CCCCTGATCAAACATCGTCTG\n-+\n-B@BDFFDFHHHHHJJJJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n-TAATACAATACATCAGACGAT\n-+\n-??+4=BDDHDHHGIHIBFHEE\n-@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n-AAGACTTCGGAGTTAAGTATC\n-+\n-CCCFFFFFHHHD>EHIJHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n-TACATACCTGGGAAGACTTCG\n-+\n-CCCFFFFFHHFBHHEHIIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n-TTCTGGGAATTCCGAAGATGG\n-+\n-CCCFFFFFHHHHHAEGHHJJJ\n @HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n ATAAACTGTCTGACAGGGACC\n +\n CCCFFFFFHHHBHIIGHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n-TACCTATGTCGATTGCCACCT\n-+\n-?@?DDDDD??A?FGHGHIIIG\n @HWI-ST132:678:C1LFKACXX:6:2105:13825:18518\n TGTCCAGTCTGACGATATCAG\n +\n CCCFFFFFGHHHH:FHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1111:12949:86137\n-TGATGCCAGACCGGGCTTCAG\n-+\n-CCCFFFFFHHHHHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:14660:78489\n-CCGGGCTTCAGTCTGGGCGCC\n-+\n-B@@FFFFFHGDAFGEGGHJGJ\n-@HWI-ST132:678:C1LFKACXX:6:1301:9997:96604\n-CCGGGCTTCAGTCTGGGCGCC\n-+\n-@CCFFFFDHHHHHGHIHH<?G\n-@HWI-ST132:678:C1LFKACXX:6:2103:4365:12003\n-CGGGCTTCAGTCTGGGCGCCA\n-+\n-BCCFFFFFHHFHHIGDABCGI\n-@HWI-ST132:678:C1LFKACXX:6:1315:14025:50396\n-TAGAGTCTGGACTGTGGCGCC\n-+\n-@@@DFDFDFH?DBH<EFGGBE\n-@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:BBDA2=A=CCFHIJJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?@BDD=BDADHHHHJ3CFGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BDDFFFHHHHFGIJJIIGI\n-@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@BDDEFFFFHHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B?BDFDFFCFHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:?BDDDFFCF<<<<EGIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDDDDFCFHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BFFDFFDHFHHJJFIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@BBDFDFFCFHHGHIJIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDDDDFADHHHIJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?:?DADDD=?::DEEB:<+<:\n-@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCBFFFFFFHHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@CFFFFFFHGHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@@DFFFFF?FHGGIIEHEHG\n-@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBCFFDDFA;DFHIJIIIGII\n-@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFDFFFFFHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBFFFFFHH;DHIJJJJJGJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n-TCT'..b'ACXX:6:1204:8915:42482\n-ACACCCACTTCATGTCGACAG\n-+\n-@@@FBDDDHHFGHH<EGFHGG\n-@HWI-ST132:678:C1LFKACXX:6:1109:5525:6504\n-TAATTTATTGTCGACTCCTGA\n-+\n-C@CFFFDFHHHHH3EHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16003:74425\n-GAGGACAACCACTCCGGCAGC\n-+\n-CC@FDFDFHHGHHJJJJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1103:16164:28590\n-ATTGCGGCTGCACACAGAGAA\n-+\n-BCBDDFFFHHHHHJIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:17496:94074\n-ATACGACAAATGATACTGAGT\n-+\n-CCCFFFFFHHHDHIJJJIFA<\n-@HWI-ST132:678:C1LFKACXX:6:1310:11295:14789\n-CCAGACGACTTTGTCCGCCTC\n-+\n-CCCFFFFFHHHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:16743:60430\n-TGCAGGATCAGAACTCAGAAT\n-+\n-CCCFFFFFHHHHHIJJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1108:9976:99924\n-GTTCCTCTTCTTTATCGGGTG\n-+\n-C@@FFFFFHHHHHGHIII<AF\n-@HWI-ST132:678:C1LFKACXX:6:1311:17281:3877\n-CCACGACGTTCAACATTGACT\n-+\n-@@BFFDDFHDHFH@EHIIHIG\n @HWI-ST132:678:C1LFKACXX:6:1209:13387:2204\n ACTTCATATCCTTTTCGGGTG\n +\n @BBDFFFFHHHHHJJJJJJFG\n-@HWI-ST132:678:C1LFKACXX:6:1201:10388:40542\n-GCAACTCTGCCACTTGAACCC\n-+\n-CCCFFFFFHHHHHJJGIJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1207:6411:98409\n GCAACTCTGCCACTTGAACCC\n +\n @@@FFFED8CFHDGIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:6060:56314\n-CGAGATGACGCTGGCTGACTG\n-+\n-@C@DDFFFGHHFHHGIIIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1110:13887:78568\n CAACTGCGCTCTGGAATAAAC\n +\n CCCFFFFFHHHHHIJJIIJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:1449:44316\n-CGCTGTTCAGCTCCTCTCAGT\n-+\n-B@CFDDDDHHHHHJJJJJIIH\n-@HWI-ST132:678:C1LFKACXX:6:2103:8728:29903\n-TAGACGCCAGCAAGGATTGCT\n-+\n-CCCFFFFFHHFHG2AGFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:10389:44836\n-TCTCCAGCTGTAAATACAACT\n-+\n-BBBFFFFFHHCFH<FHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1208:2325:6974\n-AAAACAAAATTCGGCGGCATC\n-+\n-CCCFFFFFDHHHHIIJJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:1312:11197:31549\n AAAACAAAATTCGGCGGCATC\n +\n @@@FFDFF@FFFHCFFHHIGG\n-@HWI-ST132:678:C1LFKACXX:6:1314:11236:21715\n-ATCAGGGGCTTTGCTGACGCC\n-+\n-CCBFFFFFHHHHHIJIIJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:7857:86148\n-AACATACTTGTGGCCTGGCCT\n-+\n-C@CFFFFFHHHBFIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:17527:21097\n-AGATGTTGACATTGAATGGCC\n-+\n-BC@DFFFFFHHGHIIIJIJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:8227:45651\n-CGCACTCAGTCACTCGGTTTG\n-+\n-@CCFFFFFDFHFHHIJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:16767:67452\n-GCAGCTCTAGTTGGTCGCGGC\n-+\n-@C@FFFFF>FCFHEGGGIGHI\n-@HWI-ST132:678:C1LFKACXX:6:1114:13156:95650\n-AATTATTTACAAGCGGCGAGC\n-+\n-@@@=BDFFHDFHFIFH<GIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:18254:36868\n-GTCGATCGATCGAACGGGCGT\n-+\n-BBCDFFFFHHHHHGIGHIJIH\n-@HWI-ST132:678:C1LFKACXX:6:1101:2206:66004\n-AACCAGCGGACATCGGACATC\n-+\n-:?@D?DBDH@@CCFHIIJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:3454:76338\n-TTTACACATAACTCTTCGCAT\n-+\n-@@@D?DDDHFHBFBGHIIIIG\n-@HWI-ST132:678:C1LFKACXX:6:2108:18053:41000\n-TCTGCAGCGATTCCGAACTCC\n-+\n-CC@FFFFFHGHHHI3<EHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n-CTTTCGATGGCAGAGTTGGTC\n-+\n-@BBFFFDDHHHHHJJGIIGHI\n-@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n-CCACTGTGGAATTATGAGAGC\n-+\n-B@BFFFDDFDHHH4CAEEGII\n-@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n-AAGCAGCCAAAGCTCCAGGGC\n-+\n-CCBFFFFFHHHDFIJJJJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n-GCAACCAGTTGATTGGGGACT\n-+\n-@CCFFFFFFHHHHJIJEHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n-TTCCAAAGTTGTGAGGCACTC\n-+\n-@@@F?DDEDFHHHJIHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n-TTAATTTCGCGTTTTTTCTCG\n-+\n-:?BDDF?DFH@00BFHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n-ACCGGACAGCACGGTCGTGTT\n-+\n-@CCFFFFFFHHHGEEGIFGHG\n-@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n-TTAACAATCAGTGCGGTGTAC\n-+\n-CCCFFFFEHHHDFGIIIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n-GCATATCGCAGTCCATGCTGT\n-+\n-CCCFFFFFHHHHHJJJJJJIH\n-@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n @HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n ATACTAGATTCGTTGAAAAGT\n +\n @@@F7DDDFA<CC?;FAEBH?\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,395 +1,51 @@\n-@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:BBDA2=A=CCFHIJJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?@BDD=BDADHHHHJ3CFGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BDDFFFHHHHFGIJJIIGI\n-@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJJJJJJIHHHFFFFEDDB@@\n-@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B?BDFDFFCFHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:?BDDDFFCF<<<<EGIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJJJJJJJHHHFCFDDDDBBB\n-@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-B@BFFDFFDHFHHJJFIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@BBDFDFFCFHHGHIJIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJJIJJJIHHHDAFDDDDBBB\n-@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-?:?DADDD=?::DEEB:<+<:\n-@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCBFFFFFFHHHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFHHHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@CFFFFFFHGHHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@@DFFFFF?FHGGIIEHEHG\n-@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBCFFDDFA;DFHIJIIIGII\n-@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFDFFFFFHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JGJJJJJIHD;HHFFFFFBBB\n-@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-IGIIGGIHDCA<44224AB:1\n-@HWI-ST132:678:C1LFKACXX:6:2103:10548:14756\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-:B@DFDFFFH<<AEGHHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:2103:3737:60160\n TCTAGAGGTGGCTCCAGGCTC\n +\n B@BDDDEFDFHHHJJJJGIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:8921:19194\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBDFFFFAFDFHIJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:2104:15981:63048\n TCTAGAGGTGGCTCCAGGCTC\n +\n B@BDDFFFFHHHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:11258:78941\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BBBFFFFFHH?FHHIJIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:17344:88675\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-BCCFFFFFFFFHHJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:1224:28968\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-CGCFFGFEC<DAADA2A4=:=\n-@HWI-ST132:678:C1LFKACXX:6:2107:13563:38548\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-@@@FF?DFHH?HHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:9652:62249\n-TCTAGAGGTGGCTCCAGGCTC\n-+\n-JJIIJIHGHHFHFFFFFDBB@\n-@HWI-ST132:678:C1LFKACXX:6:2103:10593:14771\n-CTAGAGGTGGCTCCAGGCTCT\n-+\n-@BCFDFFAFFHHHJJJGIIJG\n-@HWI-ST132:678:C1LFKACXX:6:1303:18356:53287\n-TAGAGGTGGCTCCAGGCTCTC\n-+\n-@@@AA?DDDDDD?F<+AAF??\n-@HWI-ST132:678:C1LFKACXX:6:1116:9986:43842\n-TTTTGTCAAATTTACAATGCA\n-+\n-:;?4A+2A:2=CDEE4E@FC4\n-@HWI-ST132:678:C1LFKACXX:6:1204:5313:61167\n-TATTATTTTTGATCAATTGGC\n-+\n-GC<GIGEA22<HHFDD7D@==\n-@HWI-ST132:678:C1LFKACXX:6:1303:7540:74272\n-TTTTTGATCAATTGGCACCAT\n-+\n-<GGEBEE<CC<>HDD@DD@@@\n @HWI-ST132:678:C1LFKACXX:6:1306:18477:89522\n TTTTTGATCAATTGGCACCAT\n +\n-HFBIIIHFHHHDHFDABFC@@\n+@@CFBADFHDHHHFHIIIBFH\n @HWI-ST132:678:C1LFKACXX:6:1105:15526:35511\n TTTTGATCAATTGGCACCATG\n +\n JJIJIHC:HHHFHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1209:1090:70698\n-TTTTGATCAATTGGCACCATG\n-+\n-H<?EA<A+HHFFFB?D7D@@@\n @HWI-ST132:678:C1LFKACXX:6:1313:1351:74638\n TTTTGATCAATTGGCACCATG\n +\n IIIJIIIJGHFDFFDDDBB@@\n-@HWI-ST132:678:C1LFKACXX:6:1104:10085:14672\n-TGATCAATTGGCACCATGCGA\n-+\n-CCCFFFFFHHHHHJJJJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1105:15364:57523\n TGATCAATTGGCACCATGCGA\n +\n JIHIJJIGDABHHFED?D@@B\n-@HWI-ST132:678:C1LFKACXX:6:1308:14142:6756\n-TGATCAATTGGCACCATGCGA\n-+\n-JJJIJJJIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2'..b'465:39807\n-TTTATTTCTTCGTTGTCGGCT\n-+\n-GC)JIJJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1305:18383:99803\n-TTTATTTCTTCGTTGTCGGCT\n-+\n-JJIGC>2>3AHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2102:14700:71462\n-TTTATTTCTTCGTTGTCGGCT\n-+\n-FGGHE<+IHHHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:2105:13617:68367\n-TTTATTTCTTCGTTGTCGGCT\n-+\n-GC1HE<+IHHHHHDDDDD@@@\n-@HWI-ST132:678:C1LFKACXX:6:2105:19074:82706\n-TTTATTTCTTCGTTGTCGGCT\n-+\n-HE1IIIIGF?HHHDDDDD@@@\n @HWI-ST132:678:C1LFKACXX:6:2105:12588:90115\n TTTATTTCTTCGTTGTCGGCT\n +\n JJJJJHJIHFHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2107:6251:60107\n-TTTATTTCTTCGTTGTCGGCT\n-+\n-HB@JJHJIHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2109:11439:45695\n-TTTATTTCTTCGTTGTCGGCT\n-+\n-JJJIHGHIFHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1211:17814:64440\n-CTTTATTTCTTCGTTGTCGGC\n-+\n-IIIIIIIHHHHHHFDB=4?@@\n-@HWI-ST132:678:C1LFKACXX:6:1307:19394:48868\n-CTTTATTTCTTCGTTGTCGGC\n-+\n-GF<IHHIJHHHHHFFDDF@@@\n-@HWI-ST132:678:C1LFKACXX:6:1316:17264:85131\n-CTTTATTTCTTCGTTGTCGGC\n-+\n-IIIIIIIIHHHHHFDD=4?::\n @HWI-ST132:678:C1LFKACXX:6:1115:13122:92533\n GATCTTTATTTCTTCGTTGTC\n +\n JIIJJJJJHHGHHAFFFD@@;\n-@HWI-ST132:678:C1LFKACXX:6:1116:15851:89973\n-GATCTTTATTTCTTCGTTGTC\n-+\n-HFGHFEGGHDHFDFFFFFC@@\n-@HWI-ST132:678:C1LFKACXX:6:1303:3205:5702\n-CTTTTATTTATTGAATCTTCT\n-+\n-BCCFFFFFHHHHHHEHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1311:7780:75331\n-TATTATTTTTCCAACTGTTCT\n-+\n-@@@FFFEAHHDHHHBGH<IHH\n-@HWI-ST132:678:C1LFKACXX:6:1312:5511:15085\n-TATTATTTTTCCAACTGTTCT\n-+\n-@CCFFFFFHHHHH@GIJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:17724:13368\n-ATTGAGAGTCGGCGTTCGTCA\n-+\n-B@BFFFDFFHH:DHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1307:8604:58747\n-TTGAGAGTCGGCGTTCGTCAT\n-+\n-BBCFDDFDFHFHHGIJJFHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1215:11848:43824\n-TGAGAGTCGGCGTTCGTCATG\n-+\n-CCCFFFFFHHHHFHJHGHGII\n-@HWI-ST132:678:C1LFKACXX:6:2109:18960:100005\n-TGAGAGTCGGCGTTCGTCATG\n-+\n-=BBF:=2AFCF@0BE?FGHJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:18683:51205\n-GTCGGCGTTCGTCATGCTCGC\n-+\n-BBBFFFFFHFHFHHHHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:4432:47194\n-GTCGGCGTTCGTCATGCTCGC\n-+\n-@??DDD:DHHDACEAGIEH;G\n @HWI-ST132:678:C1LFKACXX:6:1309:20184:93600\n GTCGGCGTTCGTCATGCTCGC\n +\n @@@D?DDDHHHBAH;FFGGG<\n-@HWI-ST132:678:C1LFKACXX:6:1314:14515:11013\n-AGCGCGAGCATGACGAACGCC\n-+\n-JIJIGIHGHDHHGFFFFF@B@\n-@HWI-ST132:678:C1LFKACXX:6:1310:19583:64029\n-CAGCGCGAGCATGACGAACGC\n-+\n-JJIHHECBHGHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:2108:10695:38989\n-ACCGATTTTGTGCGGAGCACG\n-+\n-@CCFFFFFHHFHHCF@EGIGJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674\n-TCTTCACACGTCGGCGATCGA\n-+\n-@@@DDFFFFHFFDHJGIDD@G\n-@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725\n-TAAGAATTCCGAAACGCCATC\n-+\n-IHEGAG@ED8FDDBBDDD=+?\n-@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937\n-CGATGTGTTTGTTCGCCCGTC\n-+\n-@@CFFBDBFHHDFHAFHI)@F\n @HWI-ST132:678:C1LFKACXX:6:1209:11809:98806\n AACCTCCTAGTCGCTGTGACT\n +\n JJIJIJIGGHHHHFFFFFBCB\n-@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841\n-CAGGTTAACCTCCTAGTCGCT\n-+\n-JIJJJJJJHHHHHFFFDFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084\n-CAGGTTAACCTCCTAGTCGCT\n-+\n-IIIJIJJIHHHHHFFFDFC@@\n-@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864\n-TTCTTGAACTTGCGAGCACCG\n-+\n-CCCFFFFFHHHAAFC3BEHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094\n-TTCTTGAACTTGCGAGCACCG\n-+\n-CCCFFFFFHHHDHCCFFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705\n-TTGCATTAATCTGAAAGTTGC\n-+\n-IHIGIJJJHHHHHFFFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870\n-CAAATTGGCTTTCCGTCGACT\n-+\n-@@@DFFFFHHGHFHJJEIGHH\n-@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164\n-CCAAGGAGTCGGCAGCTGAAG\n-+\n-@@@DDDDDCD?FF1)AEGGII\n-@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805\n-AGTGGGGCCAGAGGGGCTGCT\n-+\n->?:C?:@BFFFCHDADDD@?<\n-@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042\n-CGGCTTTGTCACTGTTTGATC\n-+\n-@CBFFFFFHHHHHIGHHIGJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204\n-TATTGAACTGAAGCCCCCGGC\n-+\n-CCCFFFFFHHHHGJJJJJ@GG\n @HWI-ST132:678:C1LFKACXX:6:2102:9712:32185\n ATTGAACTGAAGCCCCCGGCC\n +\n ?@@BBDBDDFFADHIIIH)?F\n-@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925\n-GAGCGGGTTTGGCCGGGGGCT\n-+\n-JJJJJJJJHGHHHDFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120\n-TGCACGATTCCAATAGTGCTG\n-+\n-IJIGCJIJHHHHHFFFFFCCC\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,83 +1,15 @@ -@HWI-ST132:678:C1LFKACXX:6:1215:7425:70721 -TTTAAAAATTCGCGCCCTGAC -+ -GGGBGIIHADHHHFDDFFCC@ -@HWI-ST132:678:C1LFKACXX:6:1107:4740:59863 -CATGTCGTGGCTATACAGGCA -+ -@CCFFFFDDFFHHJJJJJGIJ -@HWI-ST132:678:C1LFKACXX:6:1110:13407:81154 -TATACAGGCAGTAGAGCAGGG -+ -@CCFFFFFGHHHHGIHIJHII @HWI-ST132:678:C1LFKACXX:6:1208:19446:35829 TATACAGGCAGTAGAGCAGGG + BCCDDFDFHHHFFHGEFFGIJ -@HWI-ST132:678:C1LFKACXX:6:1311:4516:46469 -TATACAGGCAGTAGAGCAGGG -+ -@@@DFDFF@FHBHIGGGBBGH -@HWI-ST132:678:C1LFKACXX:6:2102:18209:60973 -GTAGTGTCCTCGGCCCCCTGC -+ -IGJJJIHGF@HHFFFFDDBCB -@HWI-ST132:678:C1LFKACXX:6:2107:16133:23528 -CAAGGTAGTGTCCTCGGCCCC -+ -JJIJJIJJHHFFFFFEFFCC@ -@HWI-ST132:678:C1LFKACXX:6:1105:9134:90339 -CCACAAGGTAGTGTCCTCGGC -+ -3<JJJJJHHFFDADDB?FB@@ -@HWI-ST132:678:C1LFKACXX:6:1214:4589:21667 -CCACAAGGTAGTGTCCTCGGC -+ -IGIIHEHGHFFFAFFFFFC@B -@HWI-ST132:678:C1LFKACXX:6:1113:8038:50061 -ATTGTAAGGATTATGGAAGCC -+ -JIIJJJJJHHHHHEDDDDBBB -@HWI-ST132:678:C1LFKACXX:6:1313:3092:45831 -ATTGTAAGGATTATGGAAGCC -+ -JGJHGGGEBFHFHDFDDFC@@ -@HWI-ST132:678:C1LFKACXX:6:1315:9832:44147 -ATTGTAAGGATTATGGAAGCC -+ -IFIGF>E<3FDADDB==A?=1 @HWI-ST132:678:C1LFKACXX:6:2107:18504:90825 ATTGTAAGGATTATGGAAGCC + HFFA>2<JHHHFFFFFDFBBB -@HWI-ST132:678:C1LFKACXX:6:1305:2494:20888 -CTTCGTTGTCGGCTTAAGACT -+ -HF9IHDGBHFCFFFEDFFC@@ -@HWI-ST132:678:C1LFKACXX:6:1308:7696:86834 -CTTCGTTGTCGGCTTAAGACT -+ -HJJIIIIHF@DHHFDBFFB@@ @HWI-ST132:678:C1LFKACXX:6:2103:15073:18548 CTTCGTTGTCGGCTTAAGACT + JIGGEA<20@0A32224B=14 -@HWI-ST132:678:C1LFKACXX:6:2105:19555:27066 -CTTCGTTGTCGGCTTAAGACT -+ -JJIJJIJIHAHHHFFDFFBCB -@HWI-ST132:678:C1LFKACXX:6:2108:8901:73378 -CTTCGTTGTCGGCTTAAGACT -+ -JJJJJJJJHGHHHFFFFFCBB -@HWI-ST132:678:C1LFKACXX:6:1313:16120:41247 -TCTTCGTTGTCGGCTTAAGAC -+ -F??DE@A@1FFFFDDDDD?8@ -@HWI-ST132:678:C1LFKACXX:6:1314:16626:18588 -TCTTCGTTGTCGGCTTAAGAC -+ -C9FIHHGGAFHHFDBADD@@? @HWI-ST132:678:C1LFKACXX:6:2108:9483:4135 TCTTCGTTGTCGGCTTAAGAC + @@ -86,231 +18,27 @@ TTTCTTCGTTGTCGGCTTAAG + IIGHE@1IHHHHDFDEFF@@@ -@HWI-ST132:678:C1LFKACXX:6:2108:8693:52625 -TTTCTTCGTTGTCGGCTTAAG -+ -HGIIHIHGHHHHHFFFFFBCB -@HWI-ST132:678:C1LFKACXX:6:1102:14940:58653 -TTATTTCTTCGTTGTCGGCTT -+ -JJJJIHGHDCFHHFFFFFCCB -@HWI-ST132:678:C1LFKACXX:6:1205:17717:14363 -TTATTTCTTCGTTGTCGGCTT -+ -JJJJHGCFHHHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1209:4476:91514 -TTATTTCTTCGTTGTCGGCTT -+ -JIJJJIJJHHHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:2105:20298:47029 -TTATTTCTTCGTTGTCGGCTT -+ -JJJJIGFAHGHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1108:9462:85509 -TTTATTTCTTCGTTGTCGGCT -+ -IGFIIFIJHGHHHEFFFFCC@ -@HWI-ST132:678:C1LFKACXX:6:1110:11726:92535 -TTTATTTCTTCGTTGTCGGCT -+ -JIGIHG@IHGHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1115:13091:61553 -TTTATTTCTTCGTTGTCGGCT -+ -FFE:FECA?DFFFDDB4+=@? -@HWI-ST132:678:C1LFKACXX:6:1205:13792:13310 -TTTATTTCTTCGTTGTCGGCT -+ -GGHGHGHFAFHHHFFFFFCC@ -@HWI-ST132:678:C1LFKACXX:6:1206:8454:66983 -TTTATTTCTTCGTTGTCGGCT -+ -JJIHGC:IHBHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1207:14397:31782 -TTTATTTCTTCGTTGTCGGCT -+ -IG@IHGHIHGHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1212:12155:21211 -TTTATTTCTTCGTTGTCGGCT -+ -HGFHHEHHFHHHHFFFFDCCB @HWI-ST132:678:C1LFKACXX:6:1215:9718:26126 TTTATTTCTTCGTTGTCGGCT + EHAD@HGGDDDHHDDFFD@@@ -@HWI-ST132:678:C1LFKACXX:6:1303:16630:18638 -TTTATTTCTTCGTTGTCGGCT -+ -HHJJJHIIFHHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1305:4465:39807 -TTTATTTCTTCGTTGTCGGCT -+ -GC)JIJJJHHHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1305:18383:99803 -TTTATTTCTTCGTTGTCGGCT -+ -JJIGC>2>3AHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:2102:14700:71462 -TTTATTTCTTCGTTGTCGGCT -+ -FGGHE<+IHHHHHFFFFFBCB -@HWI-ST132:678:C1LFKACXX:6:2105:13617:68367 -TTTATTTCTTCGTTGTCGGCT -+ -GC1HE<+IHHHHHDDDDD@@@ -@HWI-ST132:678:C1LFKACXX:6:2105:19074:82706 -TTTATTTCTTCGTTGTCGGCT -+ -HE1IIIIGF?HHHDDDDD@@@ @HWI-ST132:678:C1LFKACXX:6:2105:12588:90115 TTTATTTCTTCGTTGTCGGCT + JJJJJHJIHFHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:2107:6251:60107 -TTTATTTCTTCGTTGTCGGCT -+ -HB@JJHJIHHHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:2109:11439:45695 -TTTATTTCTTCGTTGTCGGCT -+ -JJJIHGHIFHHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1211:17814:64440 -CTTTATTTCTTCGTTGTCGGC -+ -IIIIIIIHHHHHHFDB=4?@@ -@HWI-ST132:678:C1LFKACXX:6:1307:19394:48868 -CTTTATTTCTTCGTTGTCGGC -+ -GF<IHHIJHHHHHFFDDF@@@ -@HWI-ST132:678:C1LFKACXX:6:1316:17264:85131 -CTTTATTTCTTCGTTGTCGGC -+ -IIIIIIIIHHHHHFDD=4?:: @HWI-ST132:678:C1LFKACXX:6:1115:13122:92533 GATCTTTATTTCTTCGTTGTC + JIIJJJJJHHGHHAFFFD@@; -@HWI-ST132:678:C1LFKACXX:6:1116:15851:89973 -GATCTTTATTTCTTCGTTGTC -+ -HFGHFEGGHDHFDFFFFFC@@ -@HWI-ST132:678:C1LFKACXX:6:1303:3205:5702 -CTTTTATTTATTGAATCTTCT -+ -BCCFFFFFHHHHHHEHIJJJJ -@HWI-ST132:678:C1LFKACXX:6:1311:7780:75331 -TATTATTTTTCCAACTGTTCT -+ -@@@FFFEAHHDHHHBGH<IHH -@HWI-ST132:678:C1LFKACXX:6:1312:5511:15085 -TATTATTTTTCCAACTGTTCT -+ -@CCFFFFFHHHHH@GIJIIJJ -@HWI-ST132:678:C1LFKACXX:6:2107:17724:13368 -ATTGAGAGTCGGCGTTCGTCA -+ -B@BFFFDFFHH:DHIJJJJJJ -@HWI-ST132:678:C1LFKACXX:6:1307:8604:58747 -TTGAGAGTCGGCGTTCGTCAT -+ -BBCFDDFDFHFHHGIJJFHIJ -@HWI-ST132:678:C1LFKACXX:6:1215:11848:43824 -TGAGAGTCGGCGTTCGTCATG -+ -CCCFFFFFHHHHFHJHGHGII -@HWI-ST132:678:C1LFKACXX:6:2109:18960:100005 -TGAGAGTCGGCGTTCGTCATG -+ -=BBF:=2AFCF@0BE?FGHJJ -@HWI-ST132:678:C1LFKACXX:6:1209:18683:51205 -GTCGGCGTTCGTCATGCTCGC -+ -BBBFFFFFHFHFHHHHIIJJJ -@HWI-ST132:678:C1LFKACXX:6:1213:4432:47194 -GTCGGCGTTCGTCATGCTCGC -+ -@??DDD:DHHDACEAGIEH;G @HWI-ST132:678:C1LFKACXX:6:1309:20184:93600 GTCGGCGTTCGTCATGCTCGC + @@@D?DDDHHHBAH;FFGGG< -@HWI-ST132:678:C1LFKACXX:6:1314:14515:11013 -AGCGCGAGCATGACGAACGCC -+ -JIJIGIHGHDHHGFFFFF@B@ -@HWI-ST132:678:C1LFKACXX:6:1310:19583:64029 -CAGCGCGAGCATGACGAACGC -+ -JJIHHECBHGHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:2108:10695:38989 -ACCGATTTTGTGCGGAGCACG -+ -@CCFFFFFHHFHHCF@EGIGJ -@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674 -TCTTCACACGTCGGCGATCGA -+ -@@@DDFFFFHFFDHJGIDD@G -@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725 -TAAGAATTCCGAAACGCCATC -+ -IHEGAG@ED8FDDBBDDD=+? -@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937 -CGATGTGTTTGTTCGCCCGTC -+ -@@CFFBDBFHHDFHAFHI)@F @HWI-ST132:678:C1LFKACXX:6:1209:11809:98806 AACCTCCTAGTCGCTGTGACT + JJIJIJIGGHHHHFFFFFBCB -@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841 -CAGGTTAACCTCCTAGTCGCT -+ -JIJJJJJJHHHHHFFFDFCCB -@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084 -CAGGTTAACCTCCTAGTCGCT -+ -IIIJIJJIHHHHHFFFDFC@@ -@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864 -TTCTTGAACTTGCGAGCACCG -+ -CCCFFFFFHHHAAFC3BEHIJ -@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094 -TTCTTGAACTTGCGAGCACCG -+ -CCCFFFFFHHHDHCCFFHIJJ -@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705 -TTGCATTAATCTGAAAGTTGC -+ -IHIGIJJJHHHHHFFFFFCCC -@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870 -CAAATTGGCTTTCCGTCGACT -+ -@@@DFFFFHHGHFHJJEIGHH -@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164 -CCAAGGAGTCGGCAGCTGAAG -+ -@@@DDDDDCD?FF1)AEGGII -@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805 -AGTGGGGCCAGAGGGGCTGCT -+ ->?:C?:@BFFFCHDADDD@?< -@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042 -CGGCTTTGTCACTGTTTGATC -+ -@CBFFFFFHHHHHIGHHIGJJ -@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204 -TATTGAACTGAAGCCCCCGGC -+ -CCCFFFFFHHHHGJJJJJ@GG @HWI-ST132:678:C1LFKACXX:6:2102:9712:32185 ATTGAACTGAAGCCCCCGGCC + ?@@BBDBDDFFADHIIIH)?F -@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925 -GAGCGGGTTTGGCCGGGGGCT -+ -JJJJJJJJHGHHHDFFFFCCB -@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120 -TGCACGATTCCAATAGTGCTG -+ -IJIGCJIJHHHHHFFFFFCCC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq_all_mappers.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq_all_mappers.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq_all_mappers.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,735 +1,67 @@\n-@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n-TTTTTAACGAATCTAGTATACCCT\n-+\n-B@BDFFFFF?<ADFHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n-TAATCGAATGCTAATTGTAATT\n-+\n-=??AAD?B:<CD>,AFAGF9FA\n @HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n TTAACCGTTTTGAGCTCGGCGACCT\n +\n 1=14BDDDHHHFFIIIIFEA??@FH\n-@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n-TCTTTATATTCGTTGGTATTTGGC\n-+\n-CCCFFFFFHHH<2><C<CJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n-CCGGGACTGCACAGACGAAGCGG\n-+\n-@C@FFFFFHHHHHJJJIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n-AGATTCATGTTCGGATCGTCGATAC\n-+\n-@C@FFFFFHHHHHIJBHIJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n-CGCTTCTTTTGAATGCGTCGTGGTG\n-+\n-CCCFFFFFHHHHHJ,AGHI@<?HCG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n-GCTGCCGCGATTCCCAAACCGTCCTG\n-+\n-B@BDDFFFF?@DFEH<EGIGIJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n TCCTGAGAGTCTGGTCACCGTAGAG\n +\n CCCF?EFFHHHFHJHJJJJ3343<A\n-@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n-ACCGTAGAGAATCTGAGCGTCAGAA\n-+\n-@CCFDFFFGFHHHJGDGHGGHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n CACCAGTCGGCAATATAGATCTCCT\n +\n BCBFFFDFHHHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n-TCTATATTGCCGACTGGTGGCTCAGT\n-+\n-BCBFDFFFHHHHHJJHFCFGGGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n-TCCTTGGCGGAGGTATCGTAGTGAG\n-+\n-CCCFFFFFHHFHH?FHJJJJJHJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n-GTACTCGATCGCCTGAAGAAC\n-+\n-@@CFFFFFHHCFHI+AEHHII\n-@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n-TTCCGGATTGGCAATACCCGCCTC\n-+\n-CCCFFFFFHHHHHGI<GHIJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n-TTACAAAGTCAGTGGGGATGC\n-+\n-@@@FFFFFFFHFCGGE<F@A<\n-@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n-TTTGGCAAGAGGCGGCTCCTCCTG\n-+\n-@@BFFFFFHHDFHEHGIJIIIJII\n-@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n-TCTGTTGGCAGCTAGATCAGGGGC\n-+\n-BCCFDFFFHHFHHGIIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n-TCTGTTGGCAGCTAGATCAGGGG\n-+\n-BBCFDEDFHA<DFHFFHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n-TACTTGAGGACATAGACAAACATTG\n-+\n-BBCFFFFFD=CFHH+AEHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n-TCCAGAACAGGTCTGTGGGACTGATC\n-+\n-CCCFFFFFHHHDHI3<EGIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n-TATCCAGAACAGGTCTGTGGGAC\n-+\n-CCCFFFFFHHH?FFHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n-TCCATAATCCTGACCATCCGGGCAG\n-+\n-CC@FFFFFHHHHGIJIJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n-CCCGGATGGTCAGGATTATGGAAGC\n-+\n-CCCFFFFFHFHHHGHIIIIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n-TACGGTAGAACAACTACACCGAGTGGT\n-+\n-@CCFFDDDGBHHHJIIIJJJJJJFHGI\n-@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n-TTTGCTCGACCACTCGGTGTAGTTGT\n-+\n-CCCFFFFFHHHHHJJEE<ACGIIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n-TTTGCTCGACCACTCGGTGTAGT\n-+\n-@C@FFFFFHHHFHIJFEA+@CFH\n @HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n AAAAACACGACCGTTCGCTTTGAAA\n +\n @CCFBDDFHFHHHHIJJJJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-@@@D;;DDABF,AA?:ECEFE<<\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGC'..b'HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n @HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n ATACTAGATTCGTTGAAAAGT\n +\n@@ -155998,163 +15854,19 @@\n TGTTGCGGCAACTTCTTTAAGTTG\n +\n CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n-TGGCCTAATGGATAAGGCGTCGGACT\n-+\n-@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:9014:81599\n-TTCGGATCCGAAGATTGCAGG\n-+\n-@CCFFDFFHGGGGDCEGIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:11875:25254\n-CGAAGATTGCAGGTTCGAGTC\n-+\n-CC@FFFFFHHHFCAFHIJ+AH\n-@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n-ACCGTTCTATGCTTTTTTTT\n-+\n-:BBDDDDFHH<2<CFHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n-AAGTAGCAGTCGTGGCCGAGTG\n-+\n-??+4=B?DDHHF<EGHGGGIDG\n-@HWI-ST132:678:C1LFKACXX:6:1205:9493:45438\n-GCAGTCGTGGCCGAGTGG\n-+\n-BCCFDFFFHHHHHIDCFH\n-@HWI-ST132:678:C1LFKACXX:6:1207:2720:86231\n-GCAGTCGTGGCCGAGTGG\n-+\n-@@@FFFFDHHHGFIG2AF\n-@HWI-ST132:678:C1LFKACXX:6:1214:18091:41339\n-GCAGTCGTGGCCGAGTGGTTAAGG\n-+\n-?@:4ABDDHHFHFDGCGDFHFGIG\n-@HWI-ST132:678:C1LFKACXX:6:1309:18921:24185\n-GCAGTCGTGGCCGAGTGGTTAAGG\n-+\n-@CCFDFFFHHHHHI@ACGFHIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:1391:88663\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@@@FDEDDAFHHHJH+AFFHIJEHG\n-@HWI-ST132:678:C1LFKACXX:6:1310:15410:68712\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@@@DDFFFHHHHH?EEGHIJHIEEH\n-@HWI-ST132:678:C1LFKACXX:6:1202:15769:84946\n-AGCGTAGGTTCGAATCCT\n-+\n-?@@D=ADDHHFDHFGGIG\n-@HWI-ST132:678:C1LFKACXX:6:2105:13686:25294\n-AGCGTAGGTTCGAATCCT\n-+\n-BCCFFFFFFHHDDHHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n-ATCCTACCGGCTGCGAATGA\n-+\n-@CCFFFFFDFFHHJGEHGBG\n-@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n-ACCGGCTGCGAATGAGAA\n-+\n-B@BFFFFFGHDFCFHEGI\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n-@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n-AATGAGAATGTATATTTT\n-+\n-BCBDDFFFHHFHHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:10954:88904\n-GCAGTCGTGGCCGAGTGG\n-+\n-B@CFFFFFFHGFHGIFHI\n-@HWI-ST132:678:C1LFKACXX:6:1301:8478:85932\n-GCAGTCGTGGCCGAGTGG\n-+\n-@CCFDFFDFHHHHGHAFG\n @HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n GCAGTCGTGGCCGAGTGG\n +\n @@CFFDFFHHGHH>GAGH\n-@HWI-ST132:678:C1LFKACXX:6:2107:20194:63182\n-GCAGTCGTGGCCGAGTGG\n-+\n-BCCFFFFFHGHHHBH<EH\n-@HWI-ST132:678:C1LFKACXX:6:1116:13015:74545\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-B@:BDDFDFHFFFBG2CDHGGGFHI\n-@HWI-ST132:678:C1LFKACXX:6:1209:1463:48119\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-BCCFDFDDHHHHHJJFHIIJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:4928:7411\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@C@FFDFFHHFHHJJAEGGHGIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1113:20573:45425\n-AGTCGTGGCCGAGTGGTTAAGGC\n-+\n-CCCFFFFFFHHHH?EHHHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2109:6492:70002\n-GTCGTGGCCGAGTGGTTAAGGC\n-+\n-CCCFFFFFGHG@2<EAFHGGJI\n-@HWI-ST132:678:C1LFKACXX:6:1104:13333:89311\n-TTAAGGCGTCTGACTCGAAATCAGA\n-+\n-CCCFFFFFHHHHHIIJJGGIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:7606:88539\n-TGACTCGAAATCAGATTCCCTCTG\n-+\n-CCCFFFFFHHHHHJJJIJGIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n-ATATAGCCTGAGCTTCGACC\n-+\n-CCCFFFDFHHH?FHIJJJJJ\n @HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n TCGGATCCGAAGATTGCAGG\n +\n @@CFFFFFDHHGHEHEFFHI\n-@HWI-ST132:678:C1LFKACXX:6:1203:8956:45599\n-AGATTGCAGGTTCGAGTCCT\n-+\n-@@@DFFFFHHFHH<A<AEHH\n-@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n-GTAACTGACCGTGTGGCCCAATGGA\n-+\n-??@DFFFFGHDHGG?GGIEH3<FGH\n @HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n AAGATTGCAGGTTCGAGTC\n +\n @@@:BDDDAFHHFIIGHFA\n-@HWI-ST132:678:C1LFKACXX:6:1306:9972:7484\n-AAGATTGCAGGTTCGAGTCCT\n-+\n-@@CFFFFAFFHHHG@GEBGHH\n-@HWI-ST132:678:C1LFKACXX:6:1303:16006:44426\n-AGATTGCAGGTTCGAGTCCT\n-+\n-@@@FFFFFDHDFHCE<AEHI\n @HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n AATGGATAAGGCGTCGGA\n +\n 818A:3ADHHFBFC1@FB\n-@HWI-ST132:678:C1LFKACXX:6:1214:1663:16969\n-ATTGCAGGTTCGAGTCCTG\n-+\n-@@@FDFFFCFFHHIGHIIJ\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq_unique_mappers.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq_unique_mappers.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq_unique_mappers.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,735 +1,67 @@\n-@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n-TTTTTAACGAATCTAGTATACCCT\n-+\n-B@BDFFFFF?<ADFHHIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n-TAATCGAATGCTAATTGTAATT\n-+\n-=??AAD?B:<CD>,AFAGF9FA\n @HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n TTAACCGTTTTGAGCTCGGCGACCT\n +\n 1=14BDDDHHHFFIIIIFEA??@FH\n-@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n-TCTTTATATTCGTTGGTATTTGGC\n-+\n-CCCFFFFFHHH<2><C<CJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n-CCGGGACTGCACAGACGAAGCGG\n-+\n-@C@FFFFFHHHHHJJJIHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n-AGATTCATGTTCGGATCGTCGATAC\n-+\n-@C@FFFFFHHHHHIJBHIJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n-CGCTTCTTTTGAATGCGTCGTGGTG\n-+\n-CCCFFFFFHHHHHJ,AGHI@<?HCG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n-GCTGCCGCGATTCCCAAACCGTCCTG\n-+\n-B@BDDFFFF?@DFEH<EGIGIJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n TCCTGAGAGTCTGGTCACCGTAGAG\n +\n CCCF?EFFHHHFHJHJJJJ3343<A\n-@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n-ACCGTAGAGAATCTGAGCGTCAGAA\n-+\n-@CCFDFFFGFHHHJGDGHGGHIJIJ\n @HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n CACCAGTCGGCAATATAGATCTCCT\n +\n BCBFFFDFHHHHHJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n-TCTATATTGCCGACTGGTGGCTCAGT\n-+\n-BCBFDFFFHHHHHJJHFCFGGGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n-TCCTTGGCGGAGGTATCGTAGTGAG\n-+\n-CCCFFFFFHHFHH?FHJJJJJHJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n-GTACTCGATCGCCTGAAGAAC\n-+\n-@@CFFFFFHHCFHI+AEHHII\n-@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n-TTCCGGATTGGCAATACCCGCCTC\n-+\n-CCCFFFFFHHHHHGI<GHIJIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n-TTACAAAGTCAGTGGGGATGC\n-+\n-@@@FFFFFFFHFCGGE<F@A<\n-@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n-TTTGGCAAGAGGCGGCTCCTCCTG\n-+\n-@@BFFFFFHHDFHEHGIJIIIJII\n-@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n-TCTGTTGGCAGCTAGATCAGGGGC\n-+\n-BCCFDFFFHHFHHGIIJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n-TCTGTTGGCAGCTAGATCAGGGG\n-+\n-BBCFDEDFHA<DFHFFHIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n-TACTTGAGGACATAGACAAACATTG\n-+\n-BBCFFFFFD=CFHH+AEHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n-TCCAGAACAGGTCTGTGGGACTGATC\n-+\n-CCCFFFFFHHHDHI3<EGIIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n-TATCCAGAACAGGTCTGTGGGAC\n-+\n-CCCFFFFFHHH?FFHJJIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n-TCCATAATCCTGACCATCCGGGCAG\n-+\n-CC@FFFFFHHHHGIJIJJJJIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n-CCCGGATGGTCAGGATTATGGAAGC\n-+\n-CCCFFFFFHFHHHGHIIIIIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n-TACGGTAGAACAACTACACCGAGTGGT\n-+\n-@CCFFDDDGBHHHJIIIJJJJJJFHGI\n-@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n-TTTGCTCGACCACTCGGTGTAGTTGT\n-+\n-CCCFFFFFHHHHHJJEE<ACGIIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n-TTTGCTCGACCACTCGGTGTAGT\n-+\n-@C@FFFFFHHHFHIJFEA+@CFH\n @HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n AAAAACACGACCGTTCGCTTTGAAA\n +\n @CCFBDDFHFHHHHIJJJJJJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n-TTCAAAGCGAACGGTCGTGTTTTT\n-+\n-CCCFFFFFHHHHHJFEGEC?HHII\n-@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n-AAGATTATTAAAAACCACTGCTG\n-+\n-@@@D;;DDABF,AA?:ECEFE<<\n-@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n-CTTTAATTATCATATATTGTA\n-+\n-BBBD;=ABFHHHHJJJJJDJI\n-@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n-TTATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CC@FFFFFHFHHHJHIJIJJJGGGIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-B@@FBDDFHHHHHIIJIJJIJJJJIG\n-@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n-TATTAAAGATCCGTTCGCTTCGCGAG\n-+\n-@@@DDDDDH8FHHGDHII:CHHIIBF\n-@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFDFDDHHHBBGC@FHFFDEGF\n-@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-CCCFFFDFHHHHHIHIJIIJJHHI\n-@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n-TTAAAGATCCGTTCGCTTCGCGAG\n-+\n-???DDDBDDDDDDI1CEEIIII)C\n-@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n-TTAAAGATCCGTTCGCTTCGCGAGTG\n-+\n-BCCFFFFFHHFDFH)CGIJJIJIIDH\n-@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n-TGATTTGTGCAGTAGTTTAAACAA\n-+\n-BC@FFFFDHHHHHIJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n-ACCGCACGAGAGCAGTCTGC'..b'LFKACXX:6:1210:13319:91815\n-TAAGATCAAAGTGTAGTATCT\n-+\n-???>B,ADAADDDAB4<4AFB\n-@HWI-ST132:678:C1LFKACXX:6:2109:9914:52085\n-TACTACACTTTGATCTTAGCC\n-+\n-@C@FBDDFHHHCFIJJIIIII\n-@HWI-ST132:678:C1LFKACXX:6:2102:1701:35741\n-GGCTAAGATCAAAGTGTAGTA\n-+\n-BB?DDDEBFDFHFHIIJHIJG\n-@HWI-ST132:678:C1LFKACXX:6:1202:8828:29937\n-ATCGCTTCTCGGCCTTATGGC\n-+\n-@@@DDDDDFF:+<@EGEI4AE\n-@HWI-ST132:678:C1LFKACXX:6:2104:17481:85616\n-ATCGCTTCTCGGCCTTATGGC\n-+\n-CCCFFFFFHHHAFHJJJJHGG\n-@HWI-ST132:678:C1LFKACXX:6:1212:17759:93921\n-TCTGGTTTCTCTTCAATTGTCGAA\n-+\n-CCCFFDFFHHHHHJIIJJJJJIIH\n-@HWI-ST132:678:C1LFKACXX:6:2104:8345:10717\n-TCTGGTTTCTCTTCAATTGTCGAA\n-+\n-BCBFFDFFHHHHHJHGGIHJJIJJ\n @HWI-ST132:678:C1LFKACXX:6:2101:6634:31854\n TCTGGTTTCTCTTCAATTGTCGAATA\n +\n B@BDDBDFHHHHHIIJJJJHHIIJJI\n-@HWI-ST132:678:C1LFKACXX:6:1209:12786:26644\n-TTCAATTGTCGAATAAATC\n-+\n-=?BDDDFFHH<>ACDHIIH\n-@HWI-ST132:678:C1LFKACXX:6:1209:18048:62736\n-TCAATTGTCGAATAAATCTTTCGCCT\n-+\n-BBCFFFFDHCFFHGHDGEHIGIIIII\n-@HWI-ST132:678:C1LFKACXX:6:1105:18208:78501\n-TACTAAAGATTTCCGTGGAGA\n-+\n-CC@FFFFFHHHHGIIIBEGGI\n-@HWI-ST132:678:C1LFKACXX:6:1304:17498:41952\n-TAAAGATTTCCGTGGAGAGGAACAC\n-+\n-@CCFFFFFH?HA2AFFEBGGIJIGI\n @HWI-ST132:678:C1LFKACXX:6:1111:20383:95318\n ATTTCCGTGGAGAGGAACACTCTAA\n +\n ?BBFFFFDF@BFBHGHJJIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1308:3875:44175\n-TTTCCGTGGAGAGGAACACTCTAAT\n-+\n-?@@=DD;D>CAADB9GGBHGHHEHH\n-@HWI-ST132:678:C1LFKACXX:6:1106:2389:76347\n-TCCGTGGAGAGGAACACTCTAATGAGTC\n-+\n-@@@D??DDHF?=FGB?FGE4CHHBC<CE\n-@HWI-ST132:678:C1LFKACXX:6:1115:16622:79776\n-TTTTATTGAGGCCTGATAAC\n-+\n-??B=BDFADCFHHJJGIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1116:4776:14732\n-TTTTATTGAGGCCTGATAAC\n-+\n-:=?BBAD?FCFF1CF9F@FH\n-@HWI-ST132:678:C1LFKACXX:6:1309:10904:34703\n-TTTTATTGAGGCCTGATAAC\n-+\n-@@@DDDDDF?FFBGGECFHF\n-@HWI-ST132:678:C1LFKACXX:6:2104:17165:61168\n-TTTTATTGAGGCCTGATAACTTA\n-+\n-B@CFDFFFHHFHHJGHHJJJIH@\n-@HWI-ST132:678:C1LFKACXX:6:1110:7504:42025\n-TTTTATTGAGGCCTGATAACTTATG\n-+\n-@CCFFDFEHDHHGJJIFHJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1105:3736:74280\n-TTTATTGAGGCCTGATAAC\n-+\n-?;@BDD4B+=CF<ECEC<F\n-@HWI-ST132:678:C1LFKACXX:6:1114:8935:54596\n-TTTATTGAGGCCTGATAAC\n-+\n-?@@DD?DBFF7FHIIIIGI\n-@HWI-ST132:678:C1LFKACXX:6:1208:18583:40303\n-TTTATTGAGGCCTGATAAC\n-+\n-BCBDFFFFHHHHHHIIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1209:18835:53497\n-TTTATTGAGGCCTGATAAC\n-+\n-@BCDFFDEFHFHHJIJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:9714:54959\n-TTTATTGAGGCCTGATAAC\n-+\n-BBBDDFFFFFHHHJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1315:9439:5750\n-TTTATTGAGGCCTGATAAC\n-+\n-BCBDDFEFHHHHHJIJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:7718:72736\n-TTTATTGAGGCCTGATAAC\n-+\n-B@BDDFDDFDFHHFGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1304:3050:15239\n-TTATTGAGGCCTGATAAC\n-+\n-@@@FFF<DFHHHH3CGHI\n-@HWI-ST132:678:C1LFKACXX:6:1305:10473:68713\n-TTATTGAGGCCTGATAAC\n-+\n-@CCFFFDAFHHHHJJFIJ\n-@HWI-ST132:678:C1LFKACXX:6:1314:14439:63568\n-TTATTGAGGCCTGATAAC\n-+\n-@@@FFFFFGHGGHGI4CF\n-@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n @HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n ATACTAGATTCGTTGAAAAGT\n +\n@@ -155922,43 +15850,3 @@\n TGTTGCGGCAACTTCTTTAAGTTG\n +\n CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n-TGGCCTAATGGATAAGGCGTCGGACT\n-+\n-@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n-ACCGTTCTATGCTTTTTTTT\n-+\n-:BBDDDDFHH<2<CFHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n-AAGTAGCAGTCGTGGCCGAGTG\n-+\n-??+4=B?DDHHF<EGHGGGIDG\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n-ATCCTACCGGCTGCGAATGA\n-+\n-@CCFFFFFDFFHHJGEHGBG\n-@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n-ACCGGCTGCGAATGAGAA\n-+\n-B@BFFFFFGHDFCFHEGI\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n-@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n-AATGAGAATGTATATTTT\n-+\n-BCBDDFFFHHFHHJJJJJ\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/fastq_dir/reads-sample-small.fastq_unmapped.fastq --- a/test-data/fastq_dir/reads-sample-small.fastq_unmapped.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/fastq_dir/reads-sample-small.fastq_unmapped.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,579 +1,63 @@\n-@HWI-ST132:678:C1LFKACXX:6:1103:5043:24327\n-TCTGTCGTGCATTGTCGG\n-+\n-IHFC<HHHHHDFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1101:19372:1918\n-AGAATTGTGACCTGAATC\n-+\n-BCCFFFFDFFHHHFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:18439:2762\n-CGCGCGCTACACTGACGG\n-+\n-@@@D?DD@FFFDDEEFGI\n @HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\n TAACTGAGTACCTGGCTC\n +\n :??DDD2222ADDE<CGG\n-@HWI-ST132:678:C1LFKACXX:6:1101:20172:4409\n-TTCTACAGTCCGACGATC\n-+\n-=@BF:====DFFHBGGIJ\n @HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\n TTCGAGACAGTAACCACA\n +\n =@@D;D?D>C<DFIIHGG\n-@HWI-ST132:678:C1LFKACXX:6:1101:9335:5110\n-AAGTAACGAAAGGATTAC\n-+\n-:?@B4=2=CFHHHJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\n AGATTTACAATTTTGGGC\n +\n BC@DFFFFHDFFHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:4811:6756\n-TGTACTACTCTACTTGTT\n-+\n-CCCFFFADHHHHHJJCGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7299:9245\n-CATTGGAACTAAATGACC\n-+\n-=BBDA4=BFHHHHJIIHJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:13600:10898\n-ATCCCGGACGAGCCCCCA\n-+\n-@CCFFFFFHHH@FHIJJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:9047:12024\n-ACGACAACCGTCATCCCG\n-+\n-@CCFFFFFHHHHFJJIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7548:13223\n-ATAGACCTGACAGCGTGC\n-+\n-?@@FDDFFH:ADAFHCGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7552:14739\n-GGAGGAAGTAGCTTTTTT\n-+\n-BBBDDDFFH2AADFHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:19574:14871\n-TTCCCCGTCGGGGAGCCA\n-+\n-BBBFFFFDF?FHF:??FH\n-@HWI-ST132:678:C1LFKACXX:6:1101:9689:16020\n-TGCTGGTCGACTATACTC\n-+\n-B?@DAAADFFHHHJJ@FG\n-@HWI-ST132:678:C1LFKACXX:6:1101:10332:16559\n-GCCCGGCTAGCTCAACCC\n-+\n-=B@FA=@DHFHHHIJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:16598:17271\n-TCCACCACGTTCCCGTGG\n-+\n-BBBFFF:AA<CFHIHCGH\n-@HWI-ST132:678:C1LFKACXX:6:1101:16473:17908\n-TTCTACAGTCCGACGATC\n-+\n-BBBFFF>AADHFHGHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:17076:19365\n-TCCCCGGCATCTCCACCA\n-+\n-CC@FFFFFHHHHHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:2970:20077\n-TCCCGGATGGAACCACCA\n-+\n-B@BFDBAD@DFHHHHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:19292:22029\n-TACAGAGGGCTGCGAGAC\n-+\n-CCCFFFFFHHHHG@FDHH\n-@HWI-ST132:678:C1LFKACXX:6:1101:7403:22551\n-GCAGTCGTGGCCGCGCGG\n-+\n-@@@DDDDDHDHHF12?FH\n-@HWI-ST132:678:C1LFKACXX:6:1101:6550:24420\n-TCTTTGGTATTCTCGCTG\n-+\n-@@@DDDDAFHHHF<+AEG\n-@HWI-ST132:678:C1LFKACXX:6:1101:15312:25043\n-ATGACACCGTTGGAAGAA\n-+\n-@BCFFFFFHHHHFGHEEF\n-@HWI-ST132:678:C1LFKACXX:6:1101:10841:25468\n-TCTTTGGTATTCTCGCTG\n-+\n-BCCFFFFBFHHHHEIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:6460:26533\n-TCCCGGGTTTCGGCACCA\n-+\n-CCCFFFFDHHH<DGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:8169:26973\n-ATCCTGGTCACGGCACCA\n-+\n-@CCFFFFEHBH@FHIJJJ\n @HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\n TCCCGGATGGAACCACCA\n +\n BBCFFFDD?FDFHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:11670:30039\n-TTCTACAGTCCGACGATC\n-+\n-CCCFFFFFHHHHGJJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:5395:30961\n-TACGGACCAATGGCAAAA\n-+\n-@B@FDDDDH=FHDHIGIG\n-@HWI-ST132:678:C1LFKACXX:6:1101:8747:33935\n-CGCATGAATGGATTAAAA\n-+\n-@@@DDF<DHH>FHGGBHG\n @HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\n ATCCCATCCTCGTCGCCA\n +\n BCBDFFFFHHHHHH@FHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:14543:34442\n-TCCACCACGTTCCCGTGG\n-+\n-@C@FFFADFFHGHJJEHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:5887:34986\n-AAACTTTCAACAACGGAT\n-+\n-@@@DFFFFH<FHHIICGI\n @HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\n AAGAGTCTTGTCTGGTAC\n +\n BCCFFBDFHHHHHJFHHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:10051:35463\n-TCTTGATCGAAGCCCCGG\n-+\n-B@BFFFFFHFFHGJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:4680:35647\n-CGGGATGTAGCGCAGCTT\n-+\n-BB@FADFDFHGFHEIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:14569:35583\n-AAGATAGAGTAGTTTTTT\n-+\n-BBCDFFFFHCHHHHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:13960:37817\n-AAAGTTCGGAAAACTGGC\n-+\n-@CCFDFDFHHHHHBGFGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:16007:38099\n-GATGACTGGGGTGAAGTC\n-+\n-B@BDDFFFHG?CFBGIEG\n-@HWI-ST132:678:C1LFKACXX:6:1101:8213:39438\n-TAATGATTCCTGTACTGA\n-+\n-BBBFFFFFHHHHFHIJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:15318:43042\n-CCGCTGCTGATCACACTG\n-+\n-CCCFFFFFHDHHHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:16708:44453\n-TGCTAGAGGGTCTCGGTA\n-+\n-?BBF;A=DFH<DHIE<<C\n-@HWI-ST132:678:C1LFKACXX:6:1101:8544:45645\n-TGCGGCTGGATCACCTCC\n-+\n-@CCFFFFF:FHHHIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:16382:46217\n-ATCC'..b'\n-TTCTTGTTGGCCATCCGCGACATGCGA\n-+\n-@CCFFFFFBFHGHJJIIJ<@FHIJFII\n-@HWI-ST132:678:C1LFKACXX:6:1103:4015:38357\n-CCAACGCTGGACGCATTGACCAAAGCT\n-+\n-CCCFFFFFHHHHH)CGHIFHJJGHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1103:10731:44106\n-TCCCGTGACATATTATCGATCGTTCGC\n-+\n-BBBFFDDF+AFHHJJJJJJJJIIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1103:13696:44351\n-AAGGATAGCTCTTGAGCCCGTGGCGTT\n-+\n-@BCFFFDDFHHHHCF2CGHJHIJJJHJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:20448:46278\n-CTTATCTGGTTCTGTCGCCCTATGGCC\n-+\n-=:=:BB4?4ACDD+2,CDED@FBFFIC\n-@HWI-ST132:678:C1LFKACXX:6:1103:13957:53937\n-TTCCCGAACTCAGAATTGAAACCTCTT\n-+\n-CCCFFFFFHHHHHJIJJIJIJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:13988:55183\n-AATTGGCCAACATTAATTCGGACGGCC\n-+\n-@CCFFFFFHHHHHJJJJJJJJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:10971:57682\n-GAGGACTGGATGCACATTTTGTGCGAA\n-+\n-@@@DDDDD?FFHHIIGHIGIGHI@@GF\n-@HWI-ST132:678:C1LFKACXX:6:1103:4202:58320\n-TTTAACGGACTAGCATACCATTTGCCC\n-+\n-BCCFFFFFHHGGHJIJJJHHIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:19968:60340\n-TTCAATTAGGGACCCCGACAAAACACC\n-+\n-@@@DDDDDFFFFF;F?FGIIIIAGGII\n-@HWI-ST132:678:C1LFKACXX:6:1103:10844:68056\n-TCATAGACTTCGGCTTCTCGGCCGCGT\n-+\n-CCCFFFFFHHHHHJIJJJIJIIJJDHG\n-@HWI-ST132:678:C1LFKACXX:6:1101:5856:40000\n-TGTAGCGGCGGCGCTTATATAGTGGCCG\n-+\n-@@CFFFFFHHFFDGHIIJJJHFEHHFFD\n-@HWI-ST132:678:C1LFKACXX:6:1101:13547:49997\n-CCCGAAAGATGGTGAACTATGCCTGAAT\n-+\n-@CCDDFDFHHHHAFHHIIJIJJJJJJII\n-@HWI-ST132:678:C1LFKACXX:6:1101:20671:76457\n-TGTTGGGACAGCTACCTCTCGATGGCAC\n-+\n-@@CFFFFDD?C?FGGIIJJIJGGIBCHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:16663:80406\n-TTTGACCAGTCGGTCAGCCTCTTGACCC\n-+\n-@@BFBDFFHFHHHHIGIJJJIJJGHHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:8314:83490\n-TGTTAAGTTGGATGTGAAAGCCCCGGGC\n-+\n-CCCFFFFFHHGDHHEEFGIGGIJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:20297:6808\n-TTCTAAGGTGAGCGAGCGAACTCTCGTT\n-+\n-BCBFFFFFFHHAFHIHIJHGIJJJJJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:9536:12163\n-ATGAGGATTGACAGATTGAGAGCTCTTT\n-+\n-11144=+222AF>B@FBF?IDF3A:FEB\n-@HWI-ST132:678:C1LFKACXX:6:1102:15554:36142\n-TGACCTCGTGTGGCCATACTCTTGGCAT\n-+\n-BCCFFFFFHHH3DGHJJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:4674:57784\n-CGTGTCTCTCCCTGAACCTTGGCCACCC\n-+\n-CCCFFFFFHHHHHJJJJJJJHIJIHHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:5627:63941\n-AACCTAAACCTGAACCAATTCGAACTTA\n-+\n-@C@FFFFDBHHHGJIJEEGHHIIIIJII\n-@HWI-ST132:678:C1LFKACXX:6:1102:4255:84044\n-TACTGATATCGACGTGACAATCGTCAAT\n-+\n-@CCFFFFFHHCDHIHCAFHJIJJGIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:9732:91789\n-TCTGCTTCGGCGCCTGGACTTTGGCACC\n-+\n-@BBDDFFFHFF)@CGHGFHGIEIJFHJJ\n @HWI-ST132:678:C1LFKACXX:6:1102:6869:95396\n TGGTGGGGCAACCCCCTTAGCGAGGGAC\n +\n BC@DDFFFHHHHH)CGIJGGIGIIIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1103:9280:32811\n-CGGCCCGCGTCTGATTAGCTAGTTGGTG\n-+\n-BCCFFFFFHFHHHGIJIJJJJJIJJJFH\n-@HWI-ST132:678:C1LFKACXX:6:1103:10425:50137\n-CGCAACCGGAACTAAAAATTCAATTAAT\n-+\n-CCCFFFFFHHHHHIIJJJJJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:7067:58224\n-TAAGTCAGAATCCGGGCCAGAAGCGACG\n-+\n-:BBFDD22=:=AFHEGHIIIIJJIJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:8620:61880\n-TGACATCGATCGTTCTTTGGAAGATGCC\n-+\n-CCCFFFFFHHHHHIJJJJEFHIGIIHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1103:13352:72268\n-CGTCAGCTTGACGTCGCCGTCGCGGCAC\n-+\n-?@@FBDDD+2CFHGIJJIGGIIJJJIII\n-@HWI-ST132:678:C1LFKACXX:6:1103:20658:95716\n-TGCGGGATCGTCTAATGGTAGGACGCTC\n-+\n-BB@FFDDDH8DHHJIJJJHHIIIJJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1104:9884:16062\n-TCAACCGCGGTCTGGGCCAGGAGGCTCT\n-+\n-@@@D?DDFFHCCFGB?EHIGHIHIIIII\n-@HWI-ST132:678:C1LFKACXX:6:1104:15610:16782\n-TACGGACTCCAACCTTGTTTTGAAGCGA\n-+\n-@@@DFDDDFDHDH>EHIFHIGGDBF?C?\n-@HWI-ST132:678:C1LFKACXX:6:1102:3401:22303\n-AAACCAAGGCAAACTCCGAATACCGAAGA\n-+\n-@@@FFFAEFFHHHJJJJJJJIJIIJIJJI\n-@HWI-ST132:678:C1LFKACXX:6:1102:10848:27205\n-GCGGGCGGCCCGGGTTCGTTTCCCGGCCG\n-+\n-@@@FDDDDDHHFFI7C@<EHIEHH=??A8\n-@HWI-ST132:678:C1LFKACXX:6:1102:7363:42223\n-TCCCGTGGTCAGTATGTCCCAGATAAATG\n-+\n-:@BFA=@@AFFHDEHAAEJHJJJJJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1102:7577:49564\n-TAGGTAGTGCCTCAAGTATCACCATCGGG\n-+\n-@CCFDDFDHHGGHJJJHJHIJJIJIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1102:16100:98436\n-AAGAGCTCAAGGAGTTCCTTAAGAGGGAC\n-+\n-=?@FFFFFHF<CCEAEHHJJJJIJJIIHI\n @HWI-ST132:678:C1LFKACXX:6:1104:6554:5377\n ACCTTATCGGATTGGTTGTGCTTTGAAGA\n +\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/reads-sample-small.fastq --- a/test-data/reads-sample-small.fastq Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/reads-sample-small.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,579 +1,63 @@\n-@HWI-ST132:678:C1LFKACXX:6:1103:5043:24327\n-TCTGTCGTGCATTGTCGG\n-+\n-IHFC<HHHHHDFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1101:19372:1918\n-AGAATTGTGACCTGAATC\n-+\n-BCCFFFFDFFHHHFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:18439:2762\n-CGCGCGCTACACTGACGG\n-+\n-@@@D?DD@FFFDDEEFGI\n @HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\n TAACTGAGTACCTGGCTC\n +\n :??DDD2222ADDE<CGG\n-@HWI-ST132:678:C1LFKACXX:6:1101:20172:4409\n-TTCTACAGTCCGACGATC\n-+\n-=@BF:====DFFHBGGIJ\n @HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\n TTCGAGACAGTAACCACA\n +\n =@@D;D?D>C<DFIIHGG\n-@HWI-ST132:678:C1LFKACXX:6:1101:9335:5110\n-AAGTAACGAAAGGATTAC\n-+\n-:?@B4=2=CFHHHJIJJJ\n @HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\n AGATTTACAATTTTGGGC\n +\n BC@DFFFFHDFFHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:4811:6756\n-TGTACTACTCTACTTGTT\n-+\n-CCCFFFADHHHHHJJCGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7299:9245\n-CATTGGAACTAAATGACC\n-+\n-=BBDA4=BFHHHHJIIHJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:13600:10898\n-ATCCCGGACGAGCCCCCA\n-+\n-@CCFFFFFHHH@FHIJJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:9047:12024\n-ACGACAACCGTCATCCCG\n-+\n-@CCFFFFFHHHHFJJIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7548:13223\n-ATAGACCTGACAGCGTGC\n-+\n-?@@FDDFFH:ADAFHCGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7552:14739\n-GGAGGAAGTAGCTTTTTT\n-+\n-BBBDDDFFH2AADFHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:19574:14871\n-TTCCCCGTCGGGGAGCCA\n-+\n-BBBFFFFDF?FHF:??FH\n-@HWI-ST132:678:C1LFKACXX:6:1101:9689:16020\n-TGCTGGTCGACTATACTC\n-+\n-B?@DAAADFFHHHJJ@FG\n-@HWI-ST132:678:C1LFKACXX:6:1101:10332:16559\n-GCCCGGCTAGCTCAACCC\n-+\n-=B@FA=@DHFHHHIJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:16598:17271\n-TCCACCACGTTCCCGTGG\n-+\n-BBBFFF:AA<CFHIHCGH\n-@HWI-ST132:678:C1LFKACXX:6:1101:16473:17908\n-TTCTACAGTCCGACGATC\n-+\n-BBBFFF>AADHFHGHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:17076:19365\n-TCCCCGGCATCTCCACCA\n-+\n-CC@FFFFFHHHHHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:2970:20077\n-TCCCGGATGGAACCACCA\n-+\n-B@BFDBAD@DFHHHHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:19292:22029\n-TACAGAGGGCTGCGAGAC\n-+\n-CCCFFFFFHHHHG@FDHH\n-@HWI-ST132:678:C1LFKACXX:6:1101:7403:22551\n-GCAGTCGTGGCCGCGCGG\n-+\n-@@@DDDDDHDHHF12?FH\n-@HWI-ST132:678:C1LFKACXX:6:1101:6550:24420\n-TCTTTGGTATTCTCGCTG\n-+\n-@@@DDDDAFHHHF<+AEG\n-@HWI-ST132:678:C1LFKACXX:6:1101:15312:25043\n-ATGACACCGTTGGAAGAA\n-+\n-@BCFFFFFHHHHFGHEEF\n-@HWI-ST132:678:C1LFKACXX:6:1101:10841:25468\n-TCTTTGGTATTCTCGCTG\n-+\n-BCCFFFFBFHHHHEIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:6460:26533\n-TCCCGGGTTTCGGCACCA\n-+\n-CCCFFFFDHHH<DGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:8169:26973\n-ATCCTGGTCACGGCACCA\n-+\n-@CCFFFFEHBH@FHIJJJ\n @HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\n TCCCGGATGGAACCACCA\n +\n BBCFFFDD?FDFHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:11670:30039\n-TTCTACAGTCCGACGATC\n-+\n-CCCFFFFFHHHHGJJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:5395:30961\n-TACGGACCAATGGCAAAA\n-+\n-@B@FDDDDH=FHDHIGIG\n-@HWI-ST132:678:C1LFKACXX:6:1101:8747:33935\n-CGCATGAATGGATTAAAA\n-+\n-@@@DDF<DHH>FHGGBHG\n @HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\n ATCCCATCCTCGTCGCCA\n +\n BCBDFFFFHHHHHH@FHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:14543:34442\n-TCCACCACGTTCCCGTGG\n-+\n-@C@FFFADFFHGHJJEHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:5887:34986\n-AAACTTTCAACAACGGAT\n-+\n-@@@DFFFFH<FHHIICGI\n @HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\n AAGAGTCTTGTCTGGTAC\n +\n BCCFFBDFHHHHHJFHHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:10051:35463\n-TCTTGATCGAAGCCCCGG\n-+\n-B@BFFFFFHFFHGJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:4680:35647\n-CGGGATGTAGCGCAGCTT\n-+\n-BB@FADFDFHGFHEIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:14569:35583\n-AAGATAGAGTAGTTTTTT\n-+\n-BBCDFFFFHCHHHHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:13960:37817\n-AAAGTTCGGAAAACTGGC\n-+\n-@CCFDFDFHHHHHBGFGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:16007:38099\n-GATGACTGGGGTGAAGTC\n-+\n-B@BDDFFFHG?CFBGIEG\n-@HWI-ST132:678:C1LFKACXX:6:1101:8213:39438\n-TAATGATTCCTGTACTGA\n-+\n-BBBFFFFFHHHHFHIJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:15318:43042\n-CCGCTGCTGATCACACTG\n-+\n-CCCFFFFFHDHHHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:16708:44453\n-TGCTAGAGGGTCTCGGTA\n-+\n-?BBF;A=DFH<DHIE<<C\n-@HWI-ST132:678:C1LFKACXX:6:1101:8544:45645\n-TGCGGCTGGATCACCTCC\n-+\n-@CCFFFFF:FHHHIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:16382:46217\n-ATCC'..b'HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n @HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n ATACTAGATTCGTTGAAAAGT\n +\n@@ -182118,163 +18422,19 @@\n TGTTGCGGCAACTTCTTTAAGTTG\n +\n CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n-TGGCCTAATGGATAAGGCGTCGGACT\n-+\n-@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:9014:81599\n-TTCGGATCCGAAGATTGCAGG\n-+\n-@CCFFDFFHGGGGDCEGIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:11875:25254\n-CGAAGATTGCAGGTTCGAGTC\n-+\n-CC@FFFFFHHHFCAFHIJ+AH\n-@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n-ACCGTTCTATGCTTTTTTTT\n-+\n-:BBDDDDFHH<2<CFHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n-AAGTAGCAGTCGTGGCCGAGTG\n-+\n-??+4=B?DDHHF<EGHGGGIDG\n-@HWI-ST132:678:C1LFKACXX:6:1205:9493:45438\n-GCAGTCGTGGCCGAGTGG\n-+\n-BCCFDFFFHHHHHIDCFH\n-@HWI-ST132:678:C1LFKACXX:6:1207:2720:86231\n-GCAGTCGTGGCCGAGTGG\n-+\n-@@@FFFFDHHHGFIG2AF\n-@HWI-ST132:678:C1LFKACXX:6:1214:18091:41339\n-GCAGTCGTGGCCGAGTGGTTAAGG\n-+\n-?@:4ABDDHHFHFDGCGDFHFGIG\n-@HWI-ST132:678:C1LFKACXX:6:1309:18921:24185\n-GCAGTCGTGGCCGAGTGGTTAAGG\n-+\n-@CCFDFFFHHHHHI@ACGFHIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:1391:88663\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@@@FDEDDAFHHHJH+AFFHIJEHG\n-@HWI-ST132:678:C1LFKACXX:6:1310:15410:68712\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@@@DDFFFHHHHH?EEGHIJHIEEH\n-@HWI-ST132:678:C1LFKACXX:6:1202:15769:84946\n-AGCGTAGGTTCGAATCCT\n-+\n-?@@D=ADDHHFDHFGGIG\n-@HWI-ST132:678:C1LFKACXX:6:2105:13686:25294\n-AGCGTAGGTTCGAATCCT\n-+\n-BCCFFFFFFHHDDHHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n-ATCCTACCGGCTGCGAATGA\n-+\n-@CCFFFFFDFFHHJGEHGBG\n-@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n-ACCGGCTGCGAATGAGAA\n-+\n-B@BFFFFFGHDFCFHEGI\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n-@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n-AATGAGAATGTATATTTT\n-+\n-BCBDDFFFHHFHHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:10954:88904\n-GCAGTCGTGGCCGAGTGG\n-+\n-B@CFFFFFFHGFHGIFHI\n-@HWI-ST132:678:C1LFKACXX:6:1301:8478:85932\n-GCAGTCGTGGCCGAGTGG\n-+\n-@CCFDFFDFHHHHGHAFG\n @HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n GCAGTCGTGGCCGAGTGG\n +\n @@CFFDFFHHGHH>GAGH\n-@HWI-ST132:678:C1LFKACXX:6:2107:20194:63182\n-GCAGTCGTGGCCGAGTGG\n-+\n-BCCFFFFFHGHHHBH<EH\n-@HWI-ST132:678:C1LFKACXX:6:1116:13015:74545\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-B@:BDDFDFHFFFBG2CDHGGGFHI\n-@HWI-ST132:678:C1LFKACXX:6:1209:1463:48119\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-BCCFDFDDHHHHHJJFHIIJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:4928:7411\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@C@FFDFFHHFHHJJAEGGHGIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1113:20573:45425\n-AGTCGTGGCCGAGTGGTTAAGGC\n-+\n-CCCFFFFFFHHHH?EHHHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2109:6492:70002\n-GTCGTGGCCGAGTGGTTAAGGC\n-+\n-CCCFFFFFGHG@2<EAFHGGJI\n-@HWI-ST132:678:C1LFKACXX:6:1104:13333:89311\n-TTAAGGCGTCTGACTCGAAATCAGA\n-+\n-CCCFFFFFHHHHHIIJJGGIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:7606:88539\n-TGACTCGAAATCAGATTCCCTCTG\n-+\n-CCCFFFFFHHHHHJJJIJGIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n-ATATAGCCTGAGCTTCGACC\n-+\n-JJJJJIHF?HHHFDFFFCCC\n @HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n TCGGATCCGAAGATTGCAGG\n +\n @@CFFFFFDHHGHEHEFFHI\n-@HWI-ST132:678:C1LFKACXX:6:1203:8956:45599\n-AGATTGCAGGTTCGAGTCCT\n-+\n-@@@DFFFFHHFHH<A<AEHH\n-@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n-GTAACTGACCGTGTGGCCCAATGGA\n-+\n-??@DFFFFGHDHGG?GGIEH3<FGH\n @HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n AAGATTGCAGGTTCGAGTC\n +\n @@@:BDDDAFHHFIIGHFA\n-@HWI-ST132:678:C1LFKACXX:6:1306:9972:7484\n-AAGATTGCAGGTTCGAGTCCT\n-+\n-@@CFFFFAFFHHHG@GEBGHH\n-@HWI-ST132:678:C1LFKACXX:6:1303:16006:44426\n-AGATTGCAGGTTCGAGTCCT\n-+\n-@@@FFFFFDHDFHCE<AEHI\n @HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n AATGGATAAGGCGTCGGA\n +\n 818A:3ADHHFBFC1@FB\n-@HWI-ST132:678:C1LFKACXX:6:1214:1663:16969\n-ATTGCAGGTTCGAGTCCTG\n-+\n-@@@FDFFFCFFHHIGHIIJ\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/reads-sample.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads-sample.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -0,0 +1,182280 @@\n+@HWI-ST132:678:C1LFKACXX:6:1103:5043:24327\n+TCTGTCGTGCATTGTCGG\n++\n+IHFC<HHHHHDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1101:19372:1918\n+AGAATTGTGACCTGAATC\n++\n+BCCFFFFDFFHHHFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:18439:2762\n+CGCGCGCTACACTGACGG\n++\n+@@@D?DD@FFFDDEEFGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\n+TAACTGAGTACCTGGCTC\n++\n+:??DDD2222ADDE<CGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:20172:4409\n+TTCTACAGTCCGACGATC\n++\n+=@BF:====DFFHBGGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\n+TTCGAGACAGTAACCACA\n++\n+=@@D;D?D>C<DFIIHGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:9335:5110\n+AAGTAACGAAAGGATTAC\n++\n+:?@B4=2=CFHHHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\n+AGATTTACAATTTTGGGC\n++\n+BC@DFFFFHDFFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4811:6756\n+TGTACTACTCTACTTGTT\n++\n+CCCFFFADHHHHHJJCGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7299:9245\n+CATTGGAACTAAATGACC\n++\n+=BBDA4=BFHHHHJIIHJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:13600:10898\n+ATCCCGGACGAGCCCCCA\n++\n+@CCFFFFFHHH@FHIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:9047:12024\n+ACGACAACCGTCATCCCG\n++\n+@CCFFFFFHHHHFJJIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7548:13223\n+ATAGACCTGACAGCGTGC\n++\n+?@@FDDFFH:ADAFHCGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7552:14739\n+GGAGGAAGTAGCTTTTTT\n++\n+BBBDDDFFH2AADFHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:19574:14871\n+TTCCCCGTCGGGGAGCCA\n++\n+BBBFFFFDF?FHF:??FH\n+@HWI-ST132:678:C1LFKACXX:6:1101:9689:16020\n+TGCTGGTCGACTATACTC\n++\n+B?@DAAADFFHHHJJ@FG\n+@HWI-ST132:678:C1LFKACXX:6:1101:10332:16559\n+GCCCGGCTAGCTCAACCC\n++\n+=B@FA=@DHFHHHIJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16598:17271\n+TCCACCACGTTCCCGTGG\n++\n+BBBFFF:AA<CFHIHCGH\n+@HWI-ST132:678:C1LFKACXX:6:1101:16473:17908\n+TTCTACAGTCCGACGATC\n++\n+BBBFFF>AADHFHGHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:17076:19365\n+TCCCCGGCATCTCCACCA\n++\n+CC@FFFFFHHHHHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:2970:20077\n+TCCCGGATGGAACCACCA\n++\n+B@BFDBAD@DFHHHHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:19292:22029\n+TACAGAGGGCTGCGAGAC\n++\n+CCCFFFFFHHHHG@FDHH\n+@HWI-ST132:678:C1LFKACXX:6:1101:7403:22551\n+GCAGTCGTGGCCGCGCGG\n++\n+@@@DDDDDHDHHF12?FH\n+@HWI-ST132:678:C1LFKACXX:6:1101:6550:24420\n+TCTTTGGTATTCTCGCTG\n++\n+@@@DDDDAFHHHF<+AEG\n+@HWI-ST132:678:C1LFKACXX:6:1101:15312:25043\n+ATGACACCGTTGGAAGAA\n++\n+@BCFFFFFHHHHFGHEEF\n+@HWI-ST132:678:C1LFKACXX:6:1101:10841:25468\n+TCTTTGGTATTCTCGCTG\n++\n+BCCFFFFBFHHHHEIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:6460:26533\n+TCCCGGGTTTCGGCACCA\n++\n+CCCFFFFDHHH<DGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:8169:26973\n+ATCCTGGTCACGGCACCA\n++\n+@CCFFFFEHBH@FHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\n+TCCCGGATGGAACCACCA\n++\n+BBCFFFDD?FDFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:11670:30039\n+TTCTACAGTCCGACGATC\n++\n+CCCFFFFFHHHHGJJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:5395:30961\n+TACGGACCAATGGCAAAA\n++\n+@B@FDDDDH=FHDHIGIG\n+@HWI-ST132:678:C1LFKACXX:6:1101:8747:33935\n+CGCATGAATGGATTAAAA\n++\n+@@@DDF<DHH>FHGGBHG\n+@HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\n+ATCCCATCCTCGTCGCCA\n++\n+BCBDFFFFHHHHHH@FHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:14543:34442\n+TCCACCACGTTCCCGTGG\n++\n+@C@FFFADFFHGHJJEHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:5887:34986\n+AAACTTTCAACAACGGAT\n++\n+@@@DFFFFH<FHHIICGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\n+AAGAGTCTTGTCTGGTAC\n++\n+BCCFFBDFHHHHHJFHHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:10051:35463\n+TCTTGATCGAAGCCCCGG\n++\n+B@BFFFFFHFFHGJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4680:35647\n+CGGGATGTAGCGCAGCTT\n++\n+BB@FADFDFHGFHEIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:14569:35583\n+AAGATAGAGTAGTTTTTT\n++\n+BBCDFFFFHCHHHHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:13960:37817\n+AAAGTTCGGAAAACTGGC\n++\n+@CCFDFDFHHHHHBGFGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:16007:38099\n+GATGACTGGGGTGAAGTC\n++\n+B@BDDFFFHG?CFBGIEG\n+@HWI-ST132:678:C1LFKACXX:6:1101:8213:39438\n+TAATGATTCCTGTACTGA\n++\n+BBBFFFFFHHHHFHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:15318:43042\n+CCGCTGCTGATCACACTG\n++\n+CCCFFFFFHDHHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16708:44453\n+TGCTAGAGGGTCTCGGTA\n++\n+?BBF;A=DFH<DHIE<<C\n+@HWI-ST132:678:C1LFKACXX:6:1101:8544:45645\n+TGCGGCTGGATCACCTCC\n++\n+@CCFFFFF:FHHHIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:16382:46217\n+AT'..b'276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n+TGGCCTAATGGATAAGGCGTCGGACT\n++\n+@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:9014:81599\n+TTCGGATCCGAAGATTGCAGG\n++\n+@CCFFDFFHGGGGDCEGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:11875:25254\n+CGAAGATTGCAGGTTCGAGTC\n++\n+CC@FFFFFHHHFCAFHIJ+AH\n+@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n+ACCGTTCTATGCTTTTTTTT\n++\n+:BBDDDDFHH<2<CFHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n+AAGTAGCAGTCGTGGCCGAGTG\n++\n+??+4=B?DDHHF<EGHGGGIDG\n+@HWI-ST132:678:C1LFKACXX:6:1205:9493:45438\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFDFFFHHHHHIDCFH\n+@HWI-ST132:678:C1LFKACXX:6:1207:2720:86231\n+GCAGTCGTGGCCGAGTGG\n++\n+@@@FFFFDHHHGFIG2AF\n+@HWI-ST132:678:C1LFKACXX:6:1214:18091:41339\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+?@:4ABDDHHFHFDGCGDFHFGIG\n+@HWI-ST132:678:C1LFKACXX:6:1309:18921:24185\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+@CCFDFFFHHHHHI@ACGFHIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:1391:88663\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@FDEDDAFHHHJH+AFFHIJEHG\n+@HWI-ST132:678:C1LFKACXX:6:1310:15410:68712\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@DDFFFHHHHH?EEGHIJHIEEH\n+@HWI-ST132:678:C1LFKACXX:6:1202:15769:84946\n+AGCGTAGGTTCGAATCCT\n++\n+?@@D=ADDHHFDHFGGIG\n+@HWI-ST132:678:C1LFKACXX:6:2105:13686:25294\n+AGCGTAGGTTCGAATCCT\n++\n+BCCFFFFFFHHDDHHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n+ATCCTACCGGCTGCGAATGA\n++\n+@CCFFFFFDFFHHJGEHGBG\n+@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n+ACCGGCTGCGAATGAGAA\n++\n+B@BFFFFFGHDFCFHEGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n+AATGAGAATGTATATTTT\n++\n+BCBDDFFFHHFHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:10954:88904\n+GCAGTCGTGGCCGAGTGG\n++\n+B@CFFFFFFHGFHGIFHI\n+@HWI-ST132:678:C1LFKACXX:6:1301:8478:85932\n+GCAGTCGTGGCCGAGTGG\n++\n+@CCFDFFDFHHHHGHAFG\n+@HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n+GCAGTCGTGGCCGAGTGG\n++\n+@@CFFDFFHHGHH>GAGH\n+@HWI-ST132:678:C1LFKACXX:6:2107:20194:63182\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFFFFFHGHHHBH<EH\n+@HWI-ST132:678:C1LFKACXX:6:1116:13015:74545\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+B@:BDDFDFHFFFBG2CDHGGGFHI\n+@HWI-ST132:678:C1LFKACXX:6:1209:1463:48119\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+BCCFDFDDHHHHHJJFHIIJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:4928:7411\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@C@FFDFFHHFHHJJAEGGHGIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1113:20573:45425\n+AGTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFFHHHH?EHHHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2109:6492:70002\n+GTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFGHG@2<EAFHGGJI\n+@HWI-ST132:678:C1LFKACXX:6:1104:13333:89311\n+TTAAGGCGTCTGACTCGAAATCAGA\n++\n+CCCFFFFFHHHHHIIJJGGIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:7606:88539\n+TGACTCGAAATCAGATTCCCTCTG\n++\n+CCCFFFFFHHHHHJJJIJGIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n+ATATAGCCTGAGCTTCGACC\n++\n+JJJJJIHF?HHHFDFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n+TCGGATCCGAAGATTGCAGG\n++\n+@@CFFFFFDHHGHEHEFFHI\n+@HWI-ST132:678:C1LFKACXX:6:1203:8956:45599\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@DFFFFHHFHH<A<AEHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n+GTAACTGACCGTGTGGCCCAATGGA\n++\n+??@DFFFFGHDHGG?GGIEH3<FGH\n+@HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n+AAGATTGCAGGTTCGAGTC\n++\n+@@@:BDDDAFHHFIIGHFA\n+@HWI-ST132:678:C1LFKACXX:6:1306:9972:7484\n+AAGATTGCAGGTTCGAGTCCT\n++\n+@@CFFFFAFFHHHG@GEBGHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:16006:44426\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@FFFFFDHDFHCE<AEHI\n+@HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n+AATGGATAAGGCGTCGGA\n++\n+818A:3ADHHFBFC1@FB\n+@HWI-ST132:678:C1LFKACXX:6:1214:1663:16969\n+ATTGCAGGTTCGAGTCCTG\n++\n+@@@FDFFFCFFHHIGHIIJ\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res.html --- a/test-data/res.html Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res.html Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -244,7 +244,7 @@ </p><img class="featurette-image" src="reads-sample-small.fastq/genome//distribution.png"/><br /> </div> </div> - <div class="container"><h2>mappers #: 39040</h2><h2>unique mappers #: 38991</h2> </div> + <div class="container"><h2>mappers #: 3968</h2><h2>unique mappers #: 3963</h2> </div> <div id="page"> <div id="container"> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq-bonafide_reads-genome.html --- a/test-data/res_files/reads-sample-small.fastq-bonafide_reads-genome.html Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq-bonafide_reads-genome.html Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -260,10 +260,6 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/unique/chrom_2.png" title="chrom_2">chrom_2</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/unique/chrom_4.png" title="chrom_4">chrom_4</a> </li> @@ -298,10 +294,6 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/rand/chrom_2.png" title="chrom_2">chrom_2</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/rand/chrom_4.png" title="chrom_4">chrom_4</a> </li> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq-piRNAs-PPP.html --- a/test-data/res_files/reads-sample-small.fastq-piRNAs-PPP.html Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq-piRNAs-PPP.html Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -236,24 +236,27 @@ <th data-sortable="true">p-value</th> </tr> </thead> - <tbody><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I.html">BATUMI_I</a> </td><td> 92 </td><td> 22 </td><td> 4 </td><td> 6.26931797136554 </td><td> 2.87112570812537 </td><td> 0.00204506417965455 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR.html">BATUMI_LTR</a> </td><td> 13 </td><td> 1 </td><td> 0.565217391304348 </td><td> 0.824941998304795 </td><td> 0.52704627669473 </td><td> 0.299080726341764 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/BS2.html">BS2</a> </td><td> 4418 </td><td> 610 </td><td> 192.086956521739 </td><td> 94.6508058457982 </td><td> 4.41531416181612 </td><td> 5.04316992888665e-06 </td> + <tbody><tr><td> BATUMI_I </td> +<td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td> +</tr><tr><td> BATUMI_LTR </td> +<td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/BS2.html">BS2</a> </td><td> 185 </td><td> 51 </td><td> 8.04347826086956 </td><td> 9.6028902391509 </td><td> 4.47329092276793 </td><td> 3.85124343149634e-06 </td> </tr><tr><td> COPIA_DM_I </td> <td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td> </tr><tr><td> COPIA_DM_LTR </td> <td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/DMCR1A.html">DMCR1A</a> </td><td> 109 </td><td> 30 </td><td> 4.73913043478261 </td><td> 6.40799359023961 </td><td> 3.94208720865353 </td><td> 4.03877968415678e-05 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/DMRT1B.html">DMRT1B</a> </td><td> 299 </td><td> 13 </td><td> 13 </td><td> 10.8266980794861 </td><td> 0 </td><td> 0.5 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/FW.html">FW</a> </td><td> 9995 </td><td> 1042 </td><td> 434.565217391304 </td><td> 141.421610207381 </td><td> 4.29520482561295 </td><td> 8.7266059448643e-06 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/G6_DM.html">G6_DM</a> </td><td> 1084 </td><td> 129 </td><td> 47.1304347826087 </td><td> 28.7512636362392 </td><td> 2.84751189558847 </td><td> 0.0022031223713177 </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/DMCR1A.html">DMCR1A</a> </td><td> 8 </td><td> 1 </td><td> 0.347826086956522 </td><td> 0.560178205509788 </td><td> 1.1642257885595 </td><td> 0.122166260952844 </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/DMRT1B.html">DMRT1B</a> </td><td> 13 </td><td> 1 </td><td> 0.565217391304348 </td><td> 0.711769806249778 </td><td> 0.610847221781526 </td><td> 0.270650364023612 </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/FW.html">FW</a> </td><td> 369 </td><td> 54 </td><td> 16.0434782608696 </td><td> 9.77342564156839 </td><td> 3.88364562551062 </td><td> 5.14509267872665e-05 </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/G6_DM.html">G6_DM</a> </td><td> 58 </td><td> 9 </td><td> 2.52173913043478 </td><td> 3.95484914478846 </td><td> 1.63805511471961 </td><td> 0.0507050985511251 </td> </tr><tr><td> Gypsy2-I_DM </td> <td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM.html">Gypsy2-LTR_DM</a> </td><td> 170 </td><td> 20 </td><td> 7.39130434782609 </td><td> 4.341299449171 </td><td> 2.90435981203315 </td><td> 0.00184002483108026 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/I_DM.html">I_DM</a> </td><td> 2 </td><td> 1 </td><td> 0.0869565217391304 </td><td> 0.281771334713385 </td><td> 3.24037034920393 </td><td> 0.000596872722436026 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/MAX_I.html">MAX_I</a> </td><td> 54 </td><td> 11 </td><td> 2.34782608695652 </td><td> 2.44253424438055 </td><td> 3.5422938011818 </td><td> 0.00019833170283523 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR.html">MAX_LTR</a> </td><td> 16 </td><td> 0 </td><td> 0.695652173913043 </td><td> 1.75535906419012 </td><td> -0.396301923694456 </td><td> 0.654058845865745 </td> -</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/PROTOP.html">PROTOP</a> </td><td> 49 </td><td> 11 </td><td> 2.1304347826087 </td><td> 2.30885531258291 </td><td> 3.84154224348902 </td><td> 6.11318444337927e-05 </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM.html">Gypsy2-LTR_DM</a> </td><td> 3 </td><td> 0 </td><td> 0.130434782608696 </td><td> 0.336781160539775 </td><td> -0.387298334620742 </td><td> 0.650732320848331 </td> +</tr><tr><td> I_DM </td> +<td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/MAX_I.html">MAX_I</a> </td><td> 1 </td><td> 0 </td><td> 0.0434782608695652 </td><td> 0.203931119992323 </td><td> -0.21320071635561 </td><td> 0.584414795229119 </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR.html">MAX_LTR</a> </td><td> 1 </td><td> 0 </td><td> 0.0434782608695652 </td><td> 0.203931119992323 </td><td> -0.21320071635561 </td><td> 0.584414795229119 </td> +</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/PROTOP.html">PROTOP</a> </td><td> 3 </td><td> 2 </td><td> 0.130434782608696 </td><td> 0.447636093086391 </td><td> 4.17652920813624 </td><td> 1.47995375637811e-05 </td> </tr><tr><td> ZAM_I </td> <td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td> </tr><tr><td> ZAM_LTR </td> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq-piRNAs-genome.html --- a/test-data/res_files/reads-sample-small.fastq-piRNAs-genome.html Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq-piRNAs-genome.html Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -260,14 +260,6 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/unique/chrom_2.png" title="chrom_2">chrom_2</a> - </li> - - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/unique/chrom_4.png" title="chrom_4">chrom_4</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/unique/chrom_6.png" title="chrom_6">chrom_6</a> </li> @@ -294,14 +286,6 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/rand/chrom_2.png" title="chrom_2">chrom_2</a> - </li> - - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/rand/chrom_4.png" title="chrom_4">chrom_4</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/rand/chrom_6.png" title="chrom_6">chrom_6</a> </li> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq-siRNAs-TEs.html --- a/test-data/res_files/reads-sample-small.fastq-siRNAs-TEs.html Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq-siRNAs-TEs.html Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -261,10 +261,6 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/BATUMI_LTR.png" title="BATUMI_LTR">BATUMI_LTR</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/BS2.png" title="BS2">BS2</a> </li> @@ -289,21 +285,9 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/I_DM.png" title="I_DM">I_DM</a> - </li> - - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/MAX_I.png" title="MAX_I">MAX_I</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/MAX_LTR.png" title="MAX_LTR">MAX_LTR</a> </li> - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/PROTOP.png" title="PROTOP">PROTOP</a> - </li> - </ul> </div> <div style="clear: both;"></div></div> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq-siRNAs-genome.html --- a/test-data/res_files/reads-sample-small.fastq-siRNAs-genome.html Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq-siRNAs-genome.html Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -260,21 +260,9 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/unique/chrom_2.png" title="chrom_2">chrom_2</a> - </li> - - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/unique/chrom_4.png" title="chrom_4">chrom_4</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/unique/chrom_5.png" title="chrom_5">chrom_5</a> </li> - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/unique/chrom_6.png" title="chrom_6">chrom_6</a> - </li> - </ul> </div> </div> @@ -298,21 +286,9 @@ </li> <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_2.png" title="chrom_2">chrom_2</a> - </li> - - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_4.png" title="chrom_4">chrom_4</a> - </li> - - <li> <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_5.png" title="chrom_5">chrom_5</a> </li> - <li> - <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_6.png" title="chrom_6">chrom_6</a> - </li> - </ul> </div> <div style="clear: both;"></div></div> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq.html --- a/test-data/res_files/reads-sample-small.fastq.html Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq.html Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -244,7 +244,7 @@ </p><img class="featurette-image" src="reads-sample-small.fastq/genome//distribution.png"/><br /> </div> </div> - <div class="container"><h2>mappers #: 39040</h2><h2>unique mappers #: 38991</h2> </div> + <div class="container"><h2>mappers #: 3968</h2><h2>unique mappers #: 3963</h2> </div> <div id="page"> <div id="container"> |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/dataset_35117_18-29.fastq --- a/test-data/res_files/reads-sample-small.fastq/dataset_35117_18-29.fastq Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,182280 +0,0 @@\n-@HWI-ST132:678:C1LFKACXX:6:1103:5043:24327\n-TCTGTCGTGCATTGTCGG\n-+\n-IHFC<HHHHHDFFFFCCB\n-@HWI-ST132:678:C1LFKACXX:6:1101:19372:1918\n-AGAATTGTGACCTGAATC\n-+\n-BCCFFFFDFFHHHFHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:18439:2762\n-CGCGCGCTACACTGACGG\n-+\n-@@@D?DD@FFFDDEEFGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\n-TAACTGAGTACCTGGCTC\n-+\n-:??DDD2222ADDE<CGG\n-@HWI-ST132:678:C1LFKACXX:6:1101:20172:4409\n-TTCTACAGTCCGACGATC\n-+\n-=@BF:====DFFHBGGIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\n-TTCGAGACAGTAACCACA\n-+\n-=@@D;D?D>C<DFIIHGG\n-@HWI-ST132:678:C1LFKACXX:6:1101:9335:5110\n-AAGTAACGAAAGGATTAC\n-+\n-:?@B4=2=CFHHHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\n-AGATTTACAATTTTGGGC\n-+\n-BC@DFFFFHDFFHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:4811:6756\n-TGTACTACTCTACTTGTT\n-+\n-CCCFFFADHHHHHJJCGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7299:9245\n-CATTGGAACTAAATGACC\n-+\n-=BBDA4=BFHHHHJIIHJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:13600:10898\n-ATCCCGGACGAGCCCCCA\n-+\n-@CCFFFFFHHH@FHIJJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:9047:12024\n-ACGACAACCGTCATCCCG\n-+\n-@CCFFFFFHHHHFJJIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7548:13223\n-ATAGACCTGACAGCGTGC\n-+\n-?@@FDDFFH:ADAFHCGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:7552:14739\n-GGAGGAAGTAGCTTTTTT\n-+\n-BBBDDDFFH2AADFHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:19574:14871\n-TTCCCCGTCGGGGAGCCA\n-+\n-BBBFFFFDF?FHF:??FH\n-@HWI-ST132:678:C1LFKACXX:6:1101:9689:16020\n-TGCTGGTCGACTATACTC\n-+\n-B?@DAAADFFHHHJJ@FG\n-@HWI-ST132:678:C1LFKACXX:6:1101:10332:16559\n-GCCCGGCTAGCTCAACCC\n-+\n-=B@FA=@DHFHHHIJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:16598:17271\n-TCCACCACGTTCCCGTGG\n-+\n-BBBFFF:AA<CFHIHCGH\n-@HWI-ST132:678:C1LFKACXX:6:1101:16473:17908\n-TTCTACAGTCCGACGATC\n-+\n-BBBFFF>AADHFHGHHHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:17076:19365\n-TCCCCGGCATCTCCACCA\n-+\n-CC@FFFFFHHHHHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:2970:20077\n-TCCCGGATGGAACCACCA\n-+\n-B@BFDBAD@DFHHHHIJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:19292:22029\n-TACAGAGGGCTGCGAGAC\n-+\n-CCCFFFFFHHHHG@FDHH\n-@HWI-ST132:678:C1LFKACXX:6:1101:7403:22551\n-GCAGTCGTGGCCGCGCGG\n-+\n-@@@DDDDDHDHHF12?FH\n-@HWI-ST132:678:C1LFKACXX:6:1101:6550:24420\n-TCTTTGGTATTCTCGCTG\n-+\n-@@@DDDDAFHHHF<+AEG\n-@HWI-ST132:678:C1LFKACXX:6:1101:15312:25043\n-ATGACACCGTTGGAAGAA\n-+\n-@BCFFFFFHHHHFGHEEF\n-@HWI-ST132:678:C1LFKACXX:6:1101:10841:25468\n-TCTTTGGTATTCTCGCTG\n-+\n-BCCFFFFBFHHHHEIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:6460:26533\n-TCCCGGGTTTCGGCACCA\n-+\n-CCCFFFFDHHH<DGHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:8169:26973\n-ATCCTGGTCACGGCACCA\n-+\n-@CCFFFFEHBH@FHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\n-TCCCGGATGGAACCACCA\n-+\n-BBCFFFDD?FDFHJIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:11670:30039\n-TTCTACAGTCCGACGATC\n-+\n-CCCFFFFFHHHHGJJIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:5395:30961\n-TACGGACCAATGGCAAAA\n-+\n-@B@FDDDDH=FHDHIGIG\n-@HWI-ST132:678:C1LFKACXX:6:1101:8747:33935\n-CGCATGAATGGATTAAAA\n-+\n-@@@DDF<DHH>FHGGBHG\n-@HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\n-ATCCCATCCTCGTCGCCA\n-+\n-BCBDFFFFHHHHHH@FHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:14543:34442\n-TCCACCACGTTCCCGTGG\n-+\n-@C@FFFADFFHGHJJEHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:5887:34986\n-AAACTTTCAACAACGGAT\n-+\n-@@@DFFFFH<FHHIICGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\n-AAGAGTCTTGTCTGGTAC\n-+\n-BCCFFBDFHHHHHJFHHI\n-@HWI-ST132:678:C1LFKACXX:6:1101:10051:35463\n-TCTTGATCGAAGCCCCGG\n-+\n-B@BFFFFFHFFHGJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:4680:35647\n-CGGGATGTAGCGCAGCTT\n-+\n-BB@FADFDFHGFHEIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:14569:35583\n-AAGATAGAGTAGTTTTTT\n-+\n-BBCDFFFFHCHHHHIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:13960:37817\n-AAAGTTCGGAAAACTGGC\n-+\n-@CCFDFDFHHHHHBGFGI\n-@HWI-ST132:678:C1LFKACXX:6:1101:16007:38099\n-GATGACTGGGGTGAAGTC\n-+\n-B@BDDFFFHG?CFBGIEG\n-@HWI-ST132:678:C1LFKACXX:6:1101:8213:39438\n-TAATGATTCCTGTACTGA\n-+\n-BBBFFFFFHHHHFHIJIJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:15318:43042\n-CCGCTGCTGATCACACTG\n-+\n-CCCFFFFFHDHHHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1101:16708:44453\n-TGCTAGAGGGTCTCGGTA\n-+\n-?BBF;A=DFH<DHIE<<C\n-@HWI-ST132:678:C1LFKACXX:6:1101:8544:45645\n-TGCGGCTGGATCACCTCC\n-+\n-@CCFFFFF:FHHHIJJJI\n-@HWI-ST132:678:C1LFKACXX:6:1101:16382:46217\n-AT'..b'276\n-GATCCCAGATCCGCTGTGTTT\n-+\n-CCCFFFFFHHHHHIJFGHHIJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n-ATACTAGATTCGTTGAAAAGT\n-+\n-@@@F7DDDFA<CC?;FAEBH?\n-@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n-TGTTGCGGCAACTTCTTTAAGTTG\n-+\n-CCCFFFFFHHHHHJJJJJJJJHIJ\n-@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n-TGGCCTAATGGATAAGGCGTCGGACT\n-+\n-@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1112:9014:81599\n-TTCGGATCCGAAGATTGCAGG\n-+\n-@CCFFDFFHGGGGDCEGIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2105:11875:25254\n-CGAAGATTGCAGGTTCGAGTC\n-+\n-CC@FFFFFHHHFCAFHIJ+AH\n-@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n-ACCGTTCTATGCTTTTTTTT\n-+\n-:BBDDDDFHH<2<CFHIIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n-ACCGTTCTATGCTTTTTTTTA\n-+\n-@@CFBDFF?FHHGIIIIGIIC\n-@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n-AAGTAGCAGTCGTGGCCGAGTG\n-+\n-??+4=B?DDHHF<EGHGGGIDG\n-@HWI-ST132:678:C1LFKACXX:6:1205:9493:45438\n-GCAGTCGTGGCCGAGTGG\n-+\n-BCCFDFFFHHHHHIDCFH\n-@HWI-ST132:678:C1LFKACXX:6:1207:2720:86231\n-GCAGTCGTGGCCGAGTGG\n-+\n-@@@FFFFDHHHGFIG2AF\n-@HWI-ST132:678:C1LFKACXX:6:1214:18091:41339\n-GCAGTCGTGGCCGAGTGGTTAAGG\n-+\n-?@:4ABDDHHFHFDGCGDFHFGIG\n-@HWI-ST132:678:C1LFKACXX:6:1309:18921:24185\n-GCAGTCGTGGCCGAGTGGTTAAGG\n-+\n-@CCFDFFFHHHHHI@ACGFHIIIJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:1391:88663\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@@@FDEDDAFHHHJH+AFFHIJEHG\n-@HWI-ST132:678:C1LFKACXX:6:1310:15410:68712\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@@@DDFFFHHHHH?EEGHIJHIEEH\n-@HWI-ST132:678:C1LFKACXX:6:1202:15769:84946\n-AGCGTAGGTTCGAATCCT\n-+\n-?@@D=ADDHHFDHFGGIG\n-@HWI-ST132:678:C1LFKACXX:6:2105:13686:25294\n-AGCGTAGGTTCGAATCCT\n-+\n-BCCFFFFFFHHDDHHIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n-AATCCTACCGGCTGCGAATGA\n-+\n-@BBFFDEFHFHHHFFFFHGHJ\n-@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n-ATCCTACCGGCTGCGAATGA\n-+\n-@CCFFFFFDFFHHJGEHGBG\n-@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n-ACCGGCTGCGAATGAGAA\n-+\n-B@BFFFFFGHDFCFHEGI\n-@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n-ACCGGCTGCGAATGAGAATGT\n-+\n-???DFFFFFHF:CCCGHHBG<\n-@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n-CGGCTGCGAATGAGAATGTATATTT\n-+\n-?BBDFFFF@<@ACAAEHHHGGIJJI\n-@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n-AATGAGAATGTATATTTT\n-+\n-BCBDDFFFHHFHHJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1213:10954:88904\n-GCAGTCGTGGCCGAGTGG\n-+\n-B@CFFFFFFHGFHGIFHI\n-@HWI-ST132:678:C1LFKACXX:6:1301:8478:85932\n-GCAGTCGTGGCCGAGTGG\n-+\n-@CCFDFFDFHHHHGHAFG\n-@HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n-GCAGTCGTGGCCGAGTGG\n-+\n-@@CFFDFFHHGHH>GAGH\n-@HWI-ST132:678:C1LFKACXX:6:2107:20194:63182\n-GCAGTCGTGGCCGAGTGG\n-+\n-BCCFFFFFHGHHHBH<EH\n-@HWI-ST132:678:C1LFKACXX:6:1116:13015:74545\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-B@:BDDFDFHFFFBG2CDHGGGFHI\n-@HWI-ST132:678:C1LFKACXX:6:1209:1463:48119\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-BCCFDFDDHHHHHJJFHIIJJJIJJ\n-@HWI-ST132:678:C1LFKACXX:6:1313:4928:7411\n-GCAGTCGTGGCCGAGTGGTTAAGGC\n-+\n-@C@FFDFFHHFHHJJAEGGHGIIJI\n-@HWI-ST132:678:C1LFKACXX:6:1113:20573:45425\n-AGTCGTGGCCGAGTGGTTAAGGC\n-+\n-CCCFFFFFFHHHH?EHHHIIJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2109:6492:70002\n-GTCGTGGCCGAGTGGTTAAGGC\n-+\n-CCCFFFFFGHG@2<EAFHGGJI\n-@HWI-ST132:678:C1LFKACXX:6:1104:13333:89311\n-TTAAGGCGTCTGACTCGAAATCAGA\n-+\n-CCCFFFFFHHHHHIIJJGGIJJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:1306:7606:88539\n-TGACTCGAAATCAGATTCCCTCTG\n-+\n-CCCFFFFFHHHHHJJJIJGIJJJJ\n-@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n-ATATAGCCTGAGCTTCGACC\n-+\n-JJJJJIHF?HHHFDFFFCCC\n-@HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n-TCGGATCCGAAGATTGCAGG\n-+\n-@@CFFFFFDHHGHEHEFFHI\n-@HWI-ST132:678:C1LFKACXX:6:1203:8956:45599\n-AGATTGCAGGTTCGAGTCCT\n-+\n-@@@DFFFFHHFHH<A<AEHH\n-@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n-GTAACTGACCGTGTGGCCCAATGGA\n-+\n-??@DFFFFGHDHGG?GGIEH3<FGH\n-@HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n-AAGATTGCAGGTTCGAGTC\n-+\n-@@@:BDDDAFHHFIIGHFA\n-@HWI-ST132:678:C1LFKACXX:6:1306:9972:7484\n-AAGATTGCAGGTTCGAGTCCT\n-+\n-@@CFFFFAFFHHHG@GEBGHH\n-@HWI-ST132:678:C1LFKACXX:6:1303:16006:44426\n-AGATTGCAGGTTCGAGTCCT\n-+\n-@@@FFFFFDHDFHCE<AEHI\n-@HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n-AATGGATAAGGCGTCGGA\n-+\n-818A:3ADHHFBFC1@FB\n-@HWI-ST132:678:C1LFKACXX:6:1214:1663:16969\n-ATTGCAGGTTCGAGTCCTG\n-+\n-@@@FDFFFCFFHHIGHIIJ\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/dataset_35773_18-29.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/dataset_35773_18-29.fastq Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -0,0 +1,18440 @@\n+@HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\n+TAACTGAGTACCTGGCTC\n++\n+:??DDD2222ADDE<CGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\n+TTCGAGACAGTAACCACA\n++\n+=@@D;D?D>C<DFIIHGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\n+AGATTTACAATTTTGGGC\n++\n+BC@DFFFFHDFFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\n+TCCCGGATGGAACCACCA\n++\n+BBCFFFDD?FDFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\n+ATCCCATCCTCGTCGCCA\n++\n+BCBDFFFFHHHHHH@FHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\n+AAGAGTCTTGTCTGGTAC\n++\n+BCCFFBDFHHHHHJFHHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:20055:55949\n+GAGAACTCGGAGACCGTT\n++\n+@CCFFFDDHHHGHJJJHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:11789:65387\n+TCCCGGGCGGAAACACCA\n++\n+CCCFFFFFHHHHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:18609:92207\n+ACCCCACACCTGGCACCA\n++\n+CCCFFFFFHHHHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4535:97115\n+GTTTGTGGGTTTGCGAGC\n++\n+@@BFFFFFHAHHDGEGIG\n+@HWI-ST132:678:C1LFKACXX:6:1101:8487:99600\n+TCCCGGGCGGAAACACCA\n++\n+1:=D400<CDCFHGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:4257:12618\n+TATGGAATGACAAATTAT\n++\n+B@CFFFFFHAFFHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:2462:19250\n+ATGGTTGAGGGTTGTATT\n++\n+@BCFDDFFHGFFHIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:10238:29482\n+TAGTAAGAAATGTCTAAT\n++\n+@CCFBDFFGHHHD4CHII\n+@HWI-ST132:678:C1LFKACXX:6:1102:2799:42198\n+TGATTCTTGGCTTGTAGC\n++\n+BBCFFFFFHHHHHJHIEI\n+@HWI-ST132:678:C1LFKACXX:6:1102:7032:48876\n+GGGGATGTAGCTCAGCTC\n++\n+@@@DDDDDBHHFHI2AGH\n+@HWI-ST132:678:C1LFKACXX:6:1102:19634:50211\n+CGGGGCGTAGCGCAGCCT\n++\n+BB@FFFFDHDHFHJDGHI\n+@HWI-ST132:678:C1LFKACXX:6:1102:14195:54189\n+ACCGCCCGTCGCTAGTAC\n++\n+?@@DDDFFHHCFHG@EGG\n+@HWI-ST132:678:C1LFKACXX:6:1102:9208:66171\n+TCCCGGGCGGAAACACCA\n++\n+?<<DDDDDD))?DEBGE@\n+@HWI-ST132:678:C1LFKACXX:6:1102:3716:71175\n+GCGGATGAACGATTTTTT\n++\n+BC@DDDFFHHDFHIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1102:13242:89800\n+GAAGGACTGAGATAAAAA\n++\n+BCCFFFFFHACFFHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:4247:19579\n+TTCTACAGTCCGACGATC\n++\n+@@@F?DDDHHHHHJJBGG\n+@HWI-ST132:678:C1LFKACXX:6:1103:5887:27290\n+GGAGGAAGTAGCTTTTTT\n++\n+?B@DFADD=CCDBGHIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:17248:29068\n+GTTCGAATCTCTCCGGGC\n++\n+<:?DD?B?FHFFFA)1<@\n+@HWI-ST132:678:C1LFKACXX:6:1101:9654:8592\n+TGTTTCATCGTTATACGGC\n++\n+?@@?ADDDDBFAF+2A<AF\n+@HWI-ST132:678:C1LFKACXX:6:1101:6530:20796\n+CTATCTTCGTTCGGCCCTG\n++\n+C@@DFFFFGHHHHJI)CFH\n+@HWI-ST132:678:C1LFKACXX:6:1101:4976:22614\n+TGTTGCGTTGTAAAGAAAA\n++\n+BCCFFFFDHHHHHGHFGGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:13617:48674\n+GAAGAACAAAGAACTTTTT\n++\n+BCCFFDFFHHHHHJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:2444:58197\n+TCATGTTGGCCTGTACAAA\n++\n+CCCFFFFFHHHHHHGIIHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:19809:90971\n+AAGTAGAACCCCTTGCACC\n++\n+?@@?=2ADFHHDHJIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7128:91314\n+CCCGTCCTGGTTCGCTGTA\n++\n+@@@DFDFFFHHHGDHGIHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:8801:92682\n+GATTGACAGATTGAGAGCT\n++\n+@@@DDDDDHBFHH>GHIII\n+@HWI-ST132:678:C1LFKACXX:6:1102:7367:9714\n+ATAGAATAATGTAGGTAAA\n++\n+@@@D?DDDHHHHHA?EGHI\n+@HWI-ST132:678:C1LFKACXX:6:1102:7865:16494\n+GAAGAACAAAGAACTTTTT\n++\n+=@?B?D:DDHDAAGFFFEH\n+@HWI-ST132:678:C1LFKACXX:6:1102:8027:18652\n+ATCTTTTCTTCAGTCCGGA\n++\n+CCCFFFFDHHHHHJJIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1102:9540:27988\n+TGCACTTGAAACGGGGGAC\n++\n+CCCFFFFFHHHHHGF2?@F\n+@HWI-ST132:678:C1LFKACXX:6:1102:12292:33778\n+ATTCCCCGTCGGGGAGCCA\n++\n+BCCDFFFFHHFHHIGFHJH\n+@HWI-ST132:678:C1LFKACXX:6:1102:8232:56039\n+ATAACGTCGTCACCACTTT\n++\n+@@CFFFEFHHHHHJJIJGH\n+@HWI-ST132:678:C1LFKACXX:6:1102:14973:56939\n+CCGGCGCTCTAATTCTGGC\n++\n+@C@@FFFFHHHHHJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:1769:92633\n+GTTCTACAGTCCGACGATC\n++\n+@@@FFAEFHHHFHBDGIGI\n+@HWI-ST132:678:C1LFKACXX:6:1103:14125:21554\n+TTTCCCGGACGAGCCCCCA\n++\n+@@BFFFFFHHHHHIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:9511:34573\n+TAGTGAATGGATTAAAACA\n++\n+@@@DDDDDFH<2ACG@FHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:14964:1940\n+GAAGAACAAAGAACTTTATT\n++\n+B@@FFDBFHHAFHIJJJGJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:17632:5371\n+AGTTCTACAGTCCGACGATC\n++\n+;@@DDDDDFF:DFGFEFIII\n+@HWI-ST132:678:C1LFKACXX:6:1101:14547:15049\n+CTTCAACGGATTGGTCGACG\n++\n+CCCFFFFFHGHHHJGIJJJJ\n+@H'..b'LFKACXX:6:2101:7620:77436\n+CATATGGTTGAGGGTTGTA\n++\n+@CCDFFFDHHH<2<2<CCH\n+@HWI-ST132:678:C1LFKACXX:6:2107:17949:20034\n+CATATGGTTGAGGGTTGTA\n++\n+@@@DFFFDHFHAF:CAGDH\n+@HWI-ST132:678:C1LFKACXX:6:1104:7140:60237\n+ATATGGTTGAGGGTTGTA\n++\n+=?BFFFBDFHC?D<CFHJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:10973:44674\n+ATATGGTTGAGGGTTGTA\n++\n+:?:BDDBDH?FDHEGEBE\n+@HWI-ST132:678:C1LFKACXX:6:2105:5598:23664\n+ATATGGTTGAGGGTTGTAA\n++\n+1=BDFFDFGH<<<3>@3<C\n+@HWI-ST132:678:C1LFKACXX:6:1308:8427:30662\n+TATGGTTGAGGGTTGTAAGAC\n++\n+@@BFFBDDHHHHDGGGFHHHH\n+@HWI-ST132:678:C1LFKACXX:6:2104:15703:97661\n+GGTTGAGGGTTGTAAGACTA\n++\n+BCCFFFFFHHHHHIJEHIHJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:13675:95493\n+TAATACTGAGAAATGTCTAGCAT\n++\n+BBBDFFFFHHHHHJJHJJIECFI\n+@HWI-ST132:678:C1LFKACXX:6:1113:19632:36057\n+TAATACTGAGAAATGTCTAGCATA\n++\n+@@CF?BBDBFFFHAE2<AII@EGG\n+@HWI-ST132:678:C1LFKACXX:6:1214:15307:74617\n+TAATACTGAGAAATGTCTAGCATAAA\n++\n+?+=A1AD8FHHHDIGAGGHHIIIHHI\n+@HWI-ST132:678:C1LFKACXX:6:1112:9429:97204\n+AATACTGAGAAATGTCTAGCATAAA\n++\n+@CCFFFFDGHHHAHGHIBHEHJ@FH\n+@HWI-ST132:678:C1LFKACXX:6:1305:14585:20867\n+ATACTGAGAAATGTCTAGCATAAA\n++\n+CCCFFFFFHGHHHHJJJJJJIIHJ\n+@HWI-ST132:678:C1LFKACXX:6:1305:12194:10648\n+ATACTGAGAAATGTCTAGCATAAAA\n++\n+CCCFFFFFHHHHHJJJJJIIJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:18613:75176\n+ATACTGAGAAATGTCTAGCATAAAA\n++\n+CCCFFFFFHHGHHHIJJJJJJJBHJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:3700:24056\n+ATACTGAGAAATGTCTAGCATAAAAA\n++\n+B@CFFFFDHFFHHJIJIIJIJIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1114:14379:22162\n+ATACTGAGAAATGTCTAGCATAAAAA\n++\n+@@@DDDDDHH;FHGIIIIIII>EHII\n+@HWI-ST132:678:C1LFKACXX:6:1310:6228:13763\n+TACTGAGAAATGTCTAGCA\n++\n+CCCFFFFFFHHDHFHGIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:11103:81599\n+TACTGAGAAATGTCTAGCAT\n++\n+@CCFFFFFFDF<42<AFHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1212:6639:72302\n+TACTGAGAAATGTCTAGCATAA\n++\n+@<@DFFFFGHHA<<CGFHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:8728:57864\n+TACTGAGAAATGTCTAGCATAAA\n++\n+@@?DBDDD?CFFHFG@FE>,CIF\n+@HWI-ST132:678:C1LFKACXX:6:1108:8352:59540\n+TACTGAGAAATGTCTAGCATAAA\n++\n+@CCFFFFF<FH?FEHIIIHIIII\n+@HWI-ST132:678:C1LFKACXX:6:1110:20279:31521\n+TACTGAGAAATGTCTAGCATAAA\n++\n+CCCFFFFFHHGHFGGJJJIHIJ:\n+@HWI-ST132:678:C1LFKACXX:6:1309:7687:62435\n+TACTGAGAAATGTCTAGCATAAA\n++\n+CCCFFFFFHHHGHGHGJJJJJJE\n+@HWI-ST132:678:C1LFKACXX:6:1316:3169:53652\n+TACTGAGAAATGTCTAGCATAAA\n++\n+@=?DDDBD<FFHHEHIJJJIGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:2125:87446\n+TACTGAGAAATGTCTAGCATAAAA\n++\n+:?@FAAADFBDACGHIJJJJJJCH\n+@HWI-ST132:678:C1LFKACXX:6:1209:6491:35753\n+TACTGAGAAATGTCTAGCATAAAAA\n++\n+CCCFFFFFHHHHHIJFIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:13161:15149\n+ACTGAGAAATGTCTAGCATAAAA\n++\n+?@@FDDDEDHHHHJIAEHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n+GCTGACATTGCGAAAGTG\n++\n+HHEE1HHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1303:7435:78857\n+TCAGACGGAGTGCTAGGGGCTTG\n++\n+EIIIGIHGIGC:DHHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1116:17429:48541\n+CAGACGGAGTGCTAGGGGC\n++\n+GGGIIGHFHBHDDDAA1++\n+@HWI-ST132:678:C1LFKACXX:6:1115:7506:56877\n+AATCAGACGGAGTGCTAGGGGC\n++\n+JJJJGHIIHFFFFHFFFD?@@@\n+@HWI-ST132:678:C1LFKACXX:6:1103:8993:16195\n+TTTGGAATCAGACGGAGTGCT\n++\n+FC?CHAHGHHDGHFFFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2107:8832:61846\n+TCTGTTCTTATCAGCTTAACATCTGA\n++\n+JJJJJJJJJJIHFHHHHHFFDDFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1109:12387:46446\n+TGATAAGAACAGATACTACACT\n++\n+@@@DADDDFHHDDHHIIHJGIJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:6634:31854\n+TCTGGTTTCTCTTCAATTGTCGAATA\n++\n+B@BDDBDFHHHHHIIJJJJHHIIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1111:20383:95318\n+ATTTCCGTGGAGAGGAACACTCTAA\n++\n+?BBFFFFDF@BFBHGHJJIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n+GCAGTCGTGGCCGAGTGG\n++\n+@@CFFDFFHHGHH>GAGH\n+@HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n+TCGGATCCGAAGATTGCAGG\n++\n+@@CFFFFFDHHGHEHEFFHI\n+@HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n+AAGATTGCAGGTTCGAGTC\n++\n+@@@:BDDDAFHHFIIGHFA\n+@HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n+AATGGATAAGGCGTCGGA\n++\n+818A:3ADHHFBFC1@FB\n' |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/distribution.txt --- a/test-data/res_files/reads-sample-small.fastq/genome/distribution.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/distribution.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,13 +1,13 @@ size number percentage -18 649 1.66 -19 688 1.76 -20 1317 3.37 -21 3221 8.25 -22 3209 8.22 -23 6730 17.24 -24 10434 26.73 -25 9153 23.45 -26 2895 7.42 -27 439 1.12 -28 283 0.72 -29 22 0.06 +18 58 1.46 +19 72 1.81 +20 141 3.55 +21 317 7.99 +22 339 8.54 +23 699 17.62 +24 1029 25.93 +25 931 23.46 +26 303 7.64 +27 49 1.23 +28 27 0.68 +29 3 0.08 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/dup_mapnum.txt --- a/test-data/res_files/reads-sample-small.fastq/genome/dup_mapnum.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/dup_mapnum.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,9998 +1,2003 @@\n sequence\tcount\tmapnum\n-TGCTTGGACTACATATGGTTGAGG\t1985\t1\n-TGCTTGGACTACATATGGTTGAGGG\t1319\t1\n-TGCTTGGACTACATATGGTTGAG\t943\t1\n-TATAGAATTGTAGAGCAAGACCT\t498\t1\n-TGCTTGGACTACATATGGTTGAGGGT\t300\t1\n-TTGATTAAGATAGCTGCTCCGCCT\t297\t1\n-TATTGGCAAGCCTTTCGTCGAACC\t267\t1\n-ATATCGCAGTCCATGCTG\t240\t1\n-TTTACGGGATAGGACGGTAGCGC\t231\t1\n-TATTGACTGGCGACGCTTTTGAGG\t229\t1\n-TGCTTGGACTACATATGGTTGAGGGTTG\t226\t1\n-TGAAAGACGCAGGATGGTCCGCCT\t226\t1\n-TGAAAGACGCAGGATGGTCCGCCTG\t223\t1\n-TATGTTTAGCGTTGTAGTCGCCT\t193\t1\n-GATTGGACAGCCTCTGTAGTTTGC\t182\t1\n-AACGCATATCGCAGTCCATGCTG\t173\t1\n-TTCGATCTGCCGCGGGCTGCCGAGA\t168\t1\n-TTTCTTCGGTTCGATATCAACGGA\t163\t1\n-GGACTACATATGGTTGAGGGTTGTA\t160\t1\n-TATAGAATTGTAGAGCAAGACCTTG\t144\t1\n-CCATATCTAGGTTCTGTAGCCGAAG\t136\t1\n-TATTTGATTGTTGGGCTACAAGCA\t130\t1\n-TCAGAATCTTTGATTGTGCTCGCT\t128\t1\n-ACTACATATGGTTGAGGGTTGTA\t125\t1\n-TTCAGATGGTGCTCGACTATGGCCT\t117\t1\n-CTGCTTGGACTACATATGGTTGAG\t115\t1\n-TAACTGCGAAGTCGATCAGGTCT\t113\t1\n-GCATATCGCAGTCCATGCTG\t107\t1\n-TTTTTGATCAATTGGCACCATGCGA\t105\t1\n-TTTTTGATCAATTGGCACCATGCGAA\t105\t1\n-TCAGATGAGAGACAAATTAGAATTA\t103\t1\n-TGTAGAGGATCGCTTGTCTGGGC\t99\t1\n-AACTCTAAGCGGTGGATCACTCGGC\t94\t1\n-TAGATGTGGCCTGAAGATGATTTTC\t91\t1\n-TTAGTGTTGAATGTAGGCCAGGGA\t90\t1\n-TGCTTGGACTACATATGGTTGA\t90\t1\n-CTGCTTGGACTACATATGGTTGAGG\t86\t1\n-TCATGAGACGTCTGCTTGTTTGGC\t83\t1\n-GACTACATATGGTTGAGGGTTGTA\t83\t1\n-TGCGTTTGGGATTGTCGGTGAGAC\t82\t1\n-TAATACATCGATTTCGTGACGTCGC\t81\t1\n-TATTTGATTGTTGGGCTACAAGCATT\t81\t1\n-GCTTGGACTACATATGGTTGAGG\t81\t1\n-TGCTTGGACTACATATGGTTG\t80\t1\n-TACATATGGTTGAGGGTTGTA\t78\t1\n-TTTCTTCGGTTCGATATCAACGGAT\t76\t1\n-TATTGGCAAGCCTTTCGTCGAAC\t76\t1\n-TCTTGTAAATACTTTGATTGGCCT\t74\t1\n-TTTTCCGGGCTGAGCTTTCGCTTT\t73\t1\n-TTCGATCGCCGACGTGTGAAGACGT\t73\t1\n-TGCGTTTGGGATTGTCGGTGAGA\t71\t1\n-ACATTTCCGTTTCTCGCGACT\t71\t1\n-AACTCTAAGCGGTGGATCACTC\t70\t1\n-TGCGTTTGGGATTGTCGGTGAGACG\t70\t1\n-CCATGTCCCGTTGCTATCGACTAGA\t69\t1\n-TATTGAAGGAATTGATATATGCC\t68\t1\n-ACATATGGTTGAGGGTTGTA\t67\t1\n-TTGGGTGTTGCAGTAAGAGCTG\t65\t1\n-TACGAGTAGGATATCGATCTGGT\t65\t1\n-TAGAAGACGATTTTCGGGCCGAAAT\t63\t1\n-TGAATGGTTGAAATCGCTCGGCGA\t63\t1\n-TAATGAGATCCCTCGGTTGCCTT\t63\t1\n-TCCGAAAACAAGGCCCGTCGCTA\t62\t1\n-TTCATCAGCGACTTGTGGGATTCC\t61\t1\n-TGTGCTAGAAGACGATTTTCGGGC\t61\t1\n-TTTTTGATCAATTGGCACCATGCG\t59\t1\n-TTTACGGGATAGGACGGTAGCGCG\t58\t1\n-CTACATATGGTTGAGGGTTGTA\t58\t1\n-TCTGATGTTACGCCCGAAGAGA\t58\t1\n-GAACGCATATCGCAGTCCATGCTG\t58\t1\n-TGTATGAACAGTGGAAGTGG\t56\t1\n-CCGTAAAGGCTTACATCTGGCT\t56\t1\n-TGCTAGAAGACGATTTTCGGGC\t54\t1\n-TTAGGACGAAACACAATTGGGGTG\t54\t1\n-TAATTTGACACTGTTTGGAG\t54\t1\n-TAAGTTGTTGGCTTTGAGTTTAAG\t53\t1\n-CAAAGTCCTGGATACCATCGGCT\t52\t1\n-TTGTAATGTAGCGGTCCATTCC\t51\t1\n-TAATAGTCAGGGCGCGAATTTTTAA\t51\t1\n-TATTGGCAAGCCTTTCGTCGAACCA\t50\t1\n-CAGTATGTAGGACTCCCGGGG\t50\t1\n-TTTGGTTAAAGCTGAATGTCTGCC\t50\t1\n-TAATGAGATCCCTCGGTTGCCT\t49\t1\n-TTTTCCGGGCTGAGCTTTCGC\t49\t1\n-TTTGACAAAATATGCCCTTCACCT\t49\t1\n-TGATTGCGTTGGTAACTGATGGGA\t48\t1\n-TTTTAAACATTAGGCCGTCGAGCCAGA\t47\t1\n-TGATTACGCATCATGTCTTGAATG\t46\t1\n-TAGGACGGTAGCGCGAATGTGCTAGT\t46\t1\n-TTTTAAACATTAGGCCGTCGAGCCAG\t45\t1\n-TATCCAGAAAGGACTTCAGCCCTC\t44\t1\n-TAGGACTCCCGGGGGAAACATGGTC\t44\t1\n-TTTCTGTTTGGGTTTGGACT\t44\t1\n-CAAGCATTCGACAAAGTCTGGC\t44\t1\n-TATTGACTGGCGACGCTTTTGAG\t43\t1\n-TACGAGTAGGATATCGATCTGGTG\t43\t1\n-TTAAGTCTCTTTGGATGTTTTCACT\t43\t1\n-TAGGACTCCCGGGGGAAACATGGT\t42\t1\n-TAAAGAGGACAGGCCTTACAGGGTA\t42\t1\n-TTGTAATGTAGCGGTCCATTCCA\t41\t1\n-CCATATCTAGGTTCTGTAGCCGAAGG\t41\t1\n-TTTAAGCTGGTAGGTGTAGAAGCCT\t41\t1\n-CGCTGATGAAATCTCCAGGCTCAG\t41\t1\n-TTCAGTATTGAGTTTTGGGCTTAGC\t41\t1\n-TATGTTTAGCGTTGTAGTCGCCTGC\t41\t1\n-TTTTTGATCAATTGGCACCATGC\t41\t1\n-TCCGGGCTGAGCTTTCGCTTT\t40\t1\n-TCTGATGTTACGCCCGAAGAGATAAC\t40\t1\n-TTTCTGTTTGGGTTTGGAC\t40\t1\n-AACTCTAAGCGGTGGATCACTCG\t40\t1\n-TCAGATGAGAGACAAATTAGAAT\t40\t1\n-TCATACTCTTCGATCTCGAGCCAG\t39\t1\n-TTATTGAATCTTCTTGTATAAGAACT\t39\t1\n-CAAATGTGGATACCGTTAAGCGAC\t38\t1\n-TATTGAAGGAATTGATATATGC\t38\t1\n-TAGAATAACAAGATGCGTAACGGCC\t38\t1\n-TCAAAGTATTTACAAGACGGCTT\t38\t1\n-TTGCGTTGGTAACTGATGGGAT\t38\t1\n-TTGTAATGTAGCGGTCCATTCCAG\t38\t1\n-TAATGAGATCCCTCGGTTGCCTTCT\t37\t1\n-CACAGAGGCCAAGTCATTGAGCGCC\t37\t1\n-TTGATTAAGATAGCTGCTCCGCC\t36\t1\n-TCATACTCTTCGATCTCGAGCCA\t35\t1\n-TAGGACGGTAGCGCGAATGTGCTAG\t35\t1\n-TCTCGGTGGGCAGTAGACCGC\t35\t1\n-AAGATTCTGAGAACCATCACTGGGG\t35\t1\n-TGAATTGAGAGTCGGCGTTCGTCA\t34\t1\n-TTTGACAAAATATGCCCTTCACC\t34\t1\n'..b'CAACAACCGCAC\t1\t1\n-TAAGCGGTGGATCACTCGGCT\t1\t1\n-GCTTGATGACTGGTACTG\t1\t1\n-AAGTTAATGATTACTTTGATTGCC\t1\t1\n-ATTTATTGAAGGAATTGATATATGC\t1\t1\n-CTTTCCGCTGTCAACGACCAG\t1\t1\n-TGAATCTGATATAGAGAGCTGCAC\t1\t1\n-AGCGCGAGCATGACGAACGCC\t1\t1\n-TGGCATTGCCCCATAACTGTGAGCC\t1\t1\n-CAATCTGGACCTATGGCTC\t1\t1\n-TACCAGAGGCAGGTGGTCGGAGCTA\t1\t1\n-CGGGAGTGGTATGCTGTTCAACAAGA\t1\t1\n-CATCATCAACGTCCTGTCCAGAG\t1\t1\n-CTCCGACAGAAGCCCCGCTACC\t1\t1\n-CAACTCGTCCACGTAAAACGTCGCT\t1\t1\n-TAACAAAGAGAGCCTGGAGCC\t1\t1\n-TAGCACTTGTAAATTAAGACTCACT\t1\t1\n-TAAAAATAAATGTTCGGGAC\t1\t1\n-TGAGCGGAGAACCAGAGTTGAT\t1\t1\n-ATCCCAAACGCAGACATCG\t1\t1\n-GATGGTGCTCGACTATGGCCT\t1\t1\n-CAAGGTAGTGTCCTCGGCCC\t1\t1\n-AATTCGATCGCCGACGTGTGAA\t1\t1\n-GCTGATCCGACTTAATCAACA\t1\t1\n-TTTTTTCTAGGAGGCTTGTTTTC\t1\t1\n-GTAAAACGTCGCTTACGCAGAG\t1\t1\n-AACTGGCCAACGCTCTGAAACAAGAAG\t1\t1\n-TAAGGCTTTACGCGGCTGACGC\t1\t1\n-CTTGTACTCAAAGCTCCTCCACGGCT\t1\t1\n-TCCTTGGCGGAGGTATCGTAGTGAG\t1\t1\n-TGCTGCGTTCGGCTGTGG\t1\t1\n-GAATCCCACAAGTCGCTGATGAAA\t1\t1\n-TATTGGCGGAGGCTTTGTTTTCTT\t1\t1\n-AACGCATATCGCAGTCCATGCTGT\t1\t1\n-CAATGACTTCGGCTACCTCGCAG\t1\t1\n-TTCTGTAGTCGTCCTCCGTTTTCGT\t1\t1\n-TATTTTTCCAACTGTTCT\t1\t1\n-TGCTTTTCCGTCGGGATG\t1\t1\n-TGGGGGCGTAGCATTACTAGTGC\t1\t1\n-GTTGTTGGCTTTGAGTTTAAG\t1\t1\n-TGCAAGTAGTCCTGAAGG\t1\t1\n-GATAAGCGTCAGCTTCTGCGGACC\t1\t1\n-CCGTTGTGGTTGTTGTTACTG\t1\t1\n-GGGATGTCGGCTGTATAGATGA\t1\t1\n-CACCGTGGTACGTTCGGAGTGAAAAC\t1\t1\n-GATCCCAGATCCGCTGTGTTT\t1\t1\n-TATCGTCGGCAAATGTGGATA\t1\t1\n-TGCCGAGATATGCTGCGAGTTG\t1\t1\n-CCGTGATTGCGTTGGTAACTGAT\t1\t1\n-TGAGGACGTATTTTGAGAGACC\t1\t1\n-TCGCTTCGCTTTCGACTCCGGT\t1\t1\n-CCGGAAATGATCATCCAGC\t1\t1\n-CAAATGATCAACAGGACTCCACAAC\t1\t1\n-TACCGCTGAGGACGTGCCGCTGG\t1\t1\n-TAGATTGGACAGCCTCTGTAGTT\t1\t1\n-CGGGTATCTTGTTGGTCCTCCTG\t1\t1\n-TCTGAGAACCATCACTGGGGCACC\t1\t1\n-CACCATCTGAAGACCCACCAG\t1\t1\n-CTACTAGCACATTCGCGCTAC\t1\t1\n-GCTCGATGCGTGGCCTGGTACAGTC\t1\t1\n-TCGGATCCGAAGATTGCAGG\t1\t5\n-TCAGAACACATGCCATAAAG\t1\t1\n-GTGTGTGAATATCGAGAACCT\t1\t1\n-TTGCCTTTTGTCGGAGAAATCCGT\t1\t1\n-TTTAAAATCAGGTATGACGCC\t1\t1\n-TTCCTTAAGTTCCGTGATTGCGTT\t1\t1\n-AACATCGCTTCTATCTGACCGGA\t1\t1\n-AAAGTCACTGTGGCGAGCCCA\t1\t1\n-TTCGCTGTGGAAGGCCACGCGCGCAAT\t1\t1\n-CTAGAGGTGGCTCCAGGCTCT\t1\t1\n-TGACCTCGTGTGGCCATACTCTT\t1\t1\n-TGTTGCGGCTGCTGCGGCT\t1\t1\n-CACTCCGTTGAGGGCGTCT\t1\t1\n-TTCAGCTCTTTGTAGATTGGACA\t1\t1\n-TTGTTTCAGAGCGTTGGCCAGTTT\t1\t1\n-AAGGAATTCATCAGGTGGCTGGGC\t1\t1\n-GTGAGTTGCTCTATGTATCGGC\t1\t1\n-CAAGCCGGAAAGGGAGCCCGCCTCCTAC\t1\t1\n-TTGATCAAGGTAGAGTTGTCGCGT\t1\t1\n-GACCTTGTGATCTAGGCTGAGCGGA\t1\t1\n-TTCTCCTACGTCTCACCG\t1\t1\n-TACACATCCTGATTCTGCCAGCGCTC\t1\t1\n-AAAACGTCGCTTACGCAGAGA\t1\t1\n-TTGCTGGTAGATACCGCTGAGGA\t1\t1\n-GAAGTACGCGTTGTTGCGCTG\t1\t1\n-ACAACAAATGTTAAACTGATTT\t1\t1\n-TGTGTCCGCACTTCGTGCCT\t1\t1\n-GTAGGATCACGGTAGAAG\t1\t1\n-GCGGAAAGAATGCAGACCTTTGGTCAGC\t1\t1\n-GGCTAGCTCAGTCGGTAGA\t1\t1\n-TGATTTGTTGGTAGAAGAAG\t1\t1\n-ATCAGACGGAGTGCTAGGGGCT\t1\t1\n-CGATAAGGAATTCATCAGGTGGCT\t1\t1\n-CAAATCGAGCAACTCGTCCACG\t1\t1\n-CCACACGGAAACTGGCCAACGCTC\t1\t1\n-GCAAAAATTGAAGTCGATCCCGG\t1\t1\n-TTCAGTCGGTGGGCGAAGA\t1\t1\n-TCCAGAAAGGACTTCAGCCCTC\t1\t1\n-TCGCCTGTACTAATTCACCT\t1\t1\n-ACCGCCGGCGCAAGTTGCACCTTGG\t1\t1\n-TATCGACTAGAGGCGCCTTCCTCGTG\t1\t1\n-TTGTAAGGATTATGGAAGCCCAG\t1\t1\n-GATGAAGCGACTGTGTGGTTCTTACCA\t1\t1\n-GACTTTTCTGTAGTCGTCCTCCGTT\t1\t1\n-TTTCAGGTCTCTGTGCAGGGTGGTG\t1\t1\n-ACCCTTCGGCTACAGAACCTAGATA\t1\t1\n-TAATAATAACGTTAAGGCA\t1\t1\n-TCTTGAAGAGTGGTTGGGGCTGCC\t1\t1\n-CAAAGATTCTGAGAACCATCACT\t1\t1\n-TTCAGGAGATCGTGCACTAATAGAT\t1\t1\n-CGGTAGAGCATGAGACTC\t1\t1\n+TTTGCCGGATGAAGATATTTATTAA\t1\t1\n+TCGATATGCTTCTCATGTAGGA\t1\t1\n+GGTTTACGGGATAGGACGGTAGCGC\t1\t1\n+CTCGGATCATTGGCAGTGTAGGCTA\t1\t1\n+CCAGCTTAAAAGCAGCAAGGGC\t1\t1\n+GATTTCATCAGCGACTTGTGGGA\t1\t1\n+TTCAGGACTACTTGCAGGCCC\t1\t1\n+TTCAAAGTTCTGGAAGATTTTCTG\t1\t1\n+TGTAGAGGATCGCTTGTCTGG\t1\t1\n+TCTATGACAGAAAGTTTGCAGT\t1\t1\n+TCTGTTCTTATCAGCTTAACATCTGA\t1\t1\n+TTCCATCATGCTCTGTTGTAAG\t1\t1\n+GTACGTTGGTCTTTTTTGAATTAA\t1\t1\n+TGATGTCAATATTGCTGTTGCTGGC\t1\t1\n+TAAAATTAAAACATCCCTACCCGAA\t1\t1\n+TCGTAACTTTTTAGCAACCTGCTCC\t1\t1\n+GTGAGTTGCTCTATGTATCGGCGCT\t1\t1\n+TCTATGTATCGGCGCTGATCGTCGT\t1\t1\n+GTCGACCTGGCAGACTGGAAT\t1\t1\n+AACATTAGCTTAAGGGATACTAT\t1\t1\n+CAGGCAGTAGAGCAGGGGGCCGAGG\t1\t1\n+TGATATTGTTGGTGAGCAGTT\t1\t1\n+CGGAAAAGCACACGGTGGCACCGC\t1\t1\n+CCTTTCGCCGGAGACGGGA\t1\t1\n+CGCACTTTTAGCTGGTCGTTGACAGC\t1\t1\n+TCCGGCTCGAAGGACCAAAAAAAT\t1\t1\n+TGTAGGTGAGCGGCAAATGTGTTG\t1\t1\n+TTCCGATGTACTATCCGTCAATCT\t1\t1\n+ACCGATGTAGATCTAGGCATC\t1\t1\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/dup_nonmapp.txt --- a/test-data/res_files/reads-sample-small.fastq/genome/dup_nonmapp.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/dup_nonmapp.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,4720 +1,550 @@\n sequence\tcount\n-TATTGCACTTGAGCCGGCCTGA\t156\n-TCTTTGGTATTCTCGCTGTAGA\t112\n-TGAGATCATTTTGCAAGCTGATT\t93\n-AAATGAGAGTCAGTAACTGCC\t80\n-TAGTTCTACAGTCCGACGATC\t50\n-TGAGATCATTTTGCAAGCTGAT\t48\n-TGGACGGAGAACTGATAAGGGCA\t47\n-TATTGCACTTGAGACGGCCTGAA\t41\n-TATTGCACTTGAGCCGGCCTG\t39\n-CTAAGGAAATAGTCGCCGTGAT\t35\n-AAAAATGAGAGTCAGTAACTGCC\t33\n-TATTGCACTTGAGACGGCCTGAAA\t30\n-AGTTCTACAGTCCGACGATC\t30\n-TATTGCACCTTCACCGGCCTGA\t22\n-TCTTTGGTATTCTCGCTGTAG\t20\n-TGACTAGATCCACACTCATTAC\t19\n-TGACCACACATTTCAAGGATTAATG\t19\n-AAAATGAGAGTCAGTAACTGCC\t18\n-TGACTAGATCCACACTCATTAAA\t17\n-TGTGATGTGACGTCGTGGAACA\t16\n-TCTTTGGTATTCTAGCTGTAGAAA\t15\n-TTCTACAGTCCGACGATC\t15\n-TGAGCTCATTTTGAAAGCTGATT\t14\n-AGAGTTCTACAGTCCGACGATC\t14\n-TAGCCCCACATGATTCGGCTT\t14\n-TATTGCACTTGAGACGGCCTGT\t13\n-TATTGCACTTGAGCCGGCCTGAAA\t13\n-TAAGATTGGACCCCGTACACTGCCT\t12\n-TATTTGATGACCGGAATTTTGAAA\t12\n-AATGAGAGTCAGTAACTGCC\t11\n-TCTTGGACTGAGCCGCTACTGTT\t11\n-TGAGATCATTTTGCAAGCTGA\t11\n-TGGACGGAGAACTGATAAGGGA\t11\n-GTTCTACAGTCCGACGATC\t11\n-TGGACGGAGAACTGATAAGGGCAA\t11\n-TGGACGGAGAACTGATAATGGC\t11\n-TGGACGGAGAACTTATAAGGGC\t11\n-TATTGCACATTCACCGGCCTGAT\t10\n-AAAAATGAGAGTCAGTAACTGCCA\t10\n-TCTTTGGTCTTCTCGCTGTAGA\t10\n-AAATGAGAGTCAGTAACTGC\t10\n-TATTGCACTTGAGCCGGCCTGAA\t10\n-AAGAGAGCTATCCGTCGACAGTCC\t10\n-TCAGGTACTTAGTGACTCTCACC\t10\n-TGAGATCATTTTGAACGCTGATT\t10\n-TAATACTGTCAGGTACAGATGTC\t10\n-GAAGAACAAAGAACTTTTT\t9\n-AAATGAGAGTCAGTAACTGCCA\t9\n-CAGAGTTCTACAGTCCGACGATC\t9\n-AATTGCACTAGTCCCGGCCTGT\t9\n-TTCTTGACAACCCGATCGGACCTCAA\t9\n-AAAAATGAGAGTCCGTAACTGCC\t8\n-NGGACGGAGAACTGATAAGGGC\t8\n-TGTTAACTGTAAGCCTGTGTCT\t8\n-TGACTAGATCCACCCTCATTAA\t8\n-AAGGGTCGGGTAGTGAGGGCC\t8\n-GAGTTCTACAGTCCGACGATC\t8\n-TATCTGTGGTCTCCCACTAAGGGACA\t8\n-TTACCGTACGATCCGGACAACCGT\t8\n-TAATCCTGTCAGGTAAAGATGTC\t8\n-NCACTGGGCTTTGTTTATCTCA\t8\n-TATTGCACATTCACCGGCCTGAC\t7\n-TTTCTGACGATCGACGACCTCCCGT\t7\n-TCAGGTACTTAGTGACTCTCAAA\t7\n-TCCCGGGTTTCGGCACCA\t7\n-TCCCGGGCGGAAACACCA\t7\n-TACAGATCGTACCTTCACTACC\t7\n-TAATACTGTCAGGTAAAGATGTCT\t7\n-TTCTTTGGATCTCCGCTTAAGACT\t7\n-CGGCACATGTTGACGTACACTC\t6\n-TCTTTGGTCTTCTAGCTGTAGA\t6\n-TGAGTATTACATCCGGTACTGGT\t6\n-TGGACGGAGAACTGATAAGGGT\t6\n-TCAATTCCCCGTCGGGGAGCCA\t6\n-CGGCACATGTTGACGTACACTCA\t6\n-TCAGGTACCTGAAGTCGCGCGC\t6\n-TGCTTCGGCGCCTGGACTTTGGCACC\t6\n-TCAATTTGGTCGTAAGGCTTGGAT\t5\n-TCAGGTACTTAGTGACTCTCAC\t5\n-TGAGATCATTTTGAAAGCTGATTA\t5\n-CGATCTTTTCTCCTCGGACC\t5\n-TCACGGGGCTTTGTTTATCTCA\t5\n-TCACTGGGCTTTGCTTATCTCA\t5\n-TCAGGTACCTGAAGTAGCGCGCGC\t5\n-TGGACGGATAACTGATAAGGGC\t5\n-TGAGATCATTTTGAAAGCTGATA\t5\n-TGAGATCATTTTGAACGCTGAT\t5\n-TACCATAGTAGCTCTGCAGCGAAA\t5\n-TGAAAGACGCAGGATAGTCCGCCTG\t5\n-TTTCTGTACGACGCCGATGATCCT\t5\n-TGAGATAATTTTGAAAGCTGATT\t5\n-ATCCAAAGAATAACGTCGTGAAAC\t4\n-GGAGGAAGTAGCTTTTTT\t4\n-TAGGCACTTCATACCGTGCTCT\t4\n-TAACATCGTAGCCGCTAATGCTGA\t4\n-TTACTGGGCTTTGTTTATCTCA\t4\n-TGAGCTCATTTTGAAAGCTGAT\t4\n-TTCTTGACCACCCGATCGGACCTC\t4\n-GTGCATTGTAGTCGCATTGTCA\t4\n-TCAGGTACCTGAAGTAGCGCGCGA\t4\n-TGAGATCATTTTGAAAGCTGAA\t4\n-TATAGAATTGTAGCGCAAGACCT\t4\n-TCTTTGGTATTCTAGCTGTAGAA\t4\n-TCACTGGGCTTTGTTTATCGCA\t4\n-GAAGAACAAAGAACTTTTTT\t4\n-AATTGCACTAGTCCCGGCCTGCT\t4\n-TGAGATCATTTTGCAAGCTGATA\t4\n-TCCCCGGCATCTCCACCA\t4\n-TGTCTTTTTCCGCTTACTTGCG\t4\n-TTCAATTCCCCGTCGGGGAGCCA\t4\n-TATTGCACATTCACCGGCCTGG\t4\n-TGACTAGATCCACCCTCATTAC\t4\n-TACATATGGTTGAGGGTTGTAT\t4\n-TCACTGGGCTGTGTTTATCTCA\t4\n-CATCTTACCGGGCCGCATTAGA\t4\n-TGTGATGTGACGTCGTGGAAC\t4\n-TCAGGTACCTGAAGTAGCGCGCC\t4\n-TCTCGAATAGCGTTGTGACTGAA\t3\n-TTATCTGTGGTCTCCCACTAAGGGACA\t3\n-TCGTTTCCCGGCCGATGCACCA\t3\n-TAATACTGTCAGGTAAAGCTGTC\t3\n-AATGAGAGTCAGTAACTGCCA\t3\n-TTCTAGTTCGTCTCGGACTGTCCT\t3\n-TCTGAATCACTTTCTACTCGGCATC\t3\n-TGCCGGCTGTTCACACATGAACAC\t3\n-TTTCACCTATCGTTCCATTTGCAGT\t3\n-TGTCTGATGATGACTCGAAAGCCCC\t3\n-TGAGATCATTTTGAACGCTGA\t3\n-TAGGAGTTTTGCGCAAATCTGCCT\t3\n-TCACTGGGCTTTGTTTATCTCG\t3\n-ATTTCCCGGACGAGCCCCCA\t3\n-TTTTCGGCAGGGTTGGTAACTCC\t3\n-TCACTGGGCTTTGTTTATCTCAC\t3\n-TGAAAGACGCAGGCTGGTCCGCCTG\t3\n-ATCCCGGACGAGCCCCCA\t3\n-TGAACACAGCTGGTGGTATCCAGTT\t3\n-TACTTGCATCGCGCCTATCTTATCG\t3\n-CAAGGGACTGACTCGTGTAGTGTG\t3\n-GTGCATTGTAGTCGCATTTTC\t3\n-ATTCCCCGTCGGGGAGCCA\t3\n-TCTTGGACTGAGCCGCTACTGTTTG\t3\n-TGGAAGGAGAACTGATAAGGGC\t3\n-AAGGGTCGGGTAGTGAGGGCCTT\t3\n-TAGGGACGGTCGGGGGCATC\t3\n-CTAAGGAAATAGTAGCCGTGG\t3\n-AATGGCACTGGAAGACTTCACGGG\t3\n-TAAGATTGGACCCCGTACACTGCC\t3\n-GCATGAATGGATTCACGAC'..b'TC\t1\n-TCTTCGGTAGAGGTACGCCTTTTAC\t1\n-TTTTGCACTTTTCTCTGCGTAAATG\t1\n-TACGCCTAAAGCAACTCCACTGGT\t1\n-GTCGGTACCTTGGCATCACGGAATT\t1\n-CAATAGTCAAATAGTAGAGTCAACCC\t1\n-TAGTCTCTGATTGGTGTAAAC\t1\n-TATCTTCGGTTTACACGGAGCCC\t1\n-TTCTCCAATTGTCGGTTGACGACCG\t1\n-TCGGAGACTCGCCAATCTATTGCT\t1\n-TATGTTGGCACTACTCTCGCATACGA\t1\n-GAAGGTGAAACTGTTCTGGACGG\t1\n-NTGTCGGACACCGAACCGGGA\t1\n-TTTGCGGCTGTCTGATCAGGC\t1\n-TTCCGCGACTTAGACTTTGTCTGT\t1\n-TTTACTATTTGCATACTCCAGTACT\t1\n-TGGCTGCGAAGGACTCTGGAGTCCC\t1\n-ATGGAGGTGGCTGGTTTGGACC\t1\n-TCCCATATGGTCTCGTGGCTAG\t1\n-TTTCTGAATGTGAACCAAGTTAATCT\t1\n-TTCCCGGCCGATGCACCA\t1\n-TATACTAGGCGTTGCAATCATGCG\t1\n-TACCCGGACGTAGGCAGTCT\t1\n-TCATGACGTCATGGACCATCA\t1\n-ATAGGAGATCTCTATCACTGGCGCC\t1\n-NGCGAAATGACTCTGTCCC\t1\n-AATATTCCTGCACGACTTGTA\t1\n-TGCACACTGTACCCTCTAAA\t1\n-ATAGCATTGGTTGGTGGGGAAACT\t1\n-GACACAAGAGACCCGACCTG\t1\n-CTCGGAGTACCTCCAACTAAACTT\t1\n-TATCGTAGAACCTGTATAGACGACA\t1\n-TACCATAGTAGCTCTGCAGCGAC\t1\n-AATAAGGACAAATTAATA\t1\n-TTGAGGAGGTGCCTGAAAGCC\t1\n-TGACCCGTTCGGCACCTTACGAGA\t1\n-CACCGAGAGCATCCACGGCCTGGCA\t1\n-CGCATCGGGACCTTNAGGTGACGCA\t1\n-CGTCATATCAGGAGGCCTGT\t1\n-TCACTCGGCTTTGTTTATCTCA\t1\n-TAATGAAACGTCTGTAATAATTCC\t1\n-GTGAGTAGAACAGCCGAGCTTCCGT\t1\n-TATAATGATGACTGGCTCTTGAACC\t1\n-CACTTAGGGCTGCTTGCAAA\t1\n-AGCGAAATGACTCTGGCCCAGC\t1\n-GATGCTGCAGATCCACCAGA\t1\n-AAGTGGTTATTTGCTTTGTAAAGGCC\t1\n-TAATGAGACGAATCGTAAGTACGT\t1\n-TAGCTGCGGAACTCGGAAAA\t1\n-AACTCAGACTGTGGGCCATCACC\t1\n-CGAATGCTTGGGATACGTCTAAC\t1\n-TCTGGTGGATCAAGAACTCTTGGGC\t1\n-ATTGGTTTTTGCGGCTGTCCG\t1\n-TTTTGAATAGTATAATCCTGGTA\t1\n-TGCAGAGACTTGAGATCTCT\t1\n-CAGTCCAAGAAGCTCTGCAGTTTT\t1\n-GAAAAGGGTACTCTAGTCTCGGCCT\t1\n-TACCCACGGACAACACGCTGACAAC\t1\n-TGGGTGGGTTGTTCGTTATCTGCT\t1\n-CGAGTATTACATCAGGTACT\t1\n-ACATTTGCTAAATTCCAAGAGGGC\t1\n-GAGGCCTGGATGCACATTTTGT\t1\n-TCAGGTACCTTAAGTAGCGCGCGT\t1\n-TTAATTTGGCCGATCGGAACA\t1\n-TCAAGGGACTGACTCGTGTAGT\t1\n-TAATGCAACTTAACGAACCGAATGTT\t1\n-ACCGGACTCCCATCAGCTTTCAATC\t1\n-TTTTGGAACTCTTCGTTTTAGCCT\t1\n-TAGCTGCTGCAGTCCTCGGATCGC\t1\n-AATGGCACTGGAAGAATTCATGGG\t1\n-AGCGCCGCGTCTTCGGATATGTCTCT\t1\n-TCGGACAAAGAAAACTTGCCAGGCAA\t1\n-TGAGCAGCTATCCCAGACTGC\t1\n-GCTGGGCGTCGCCGGGGGTGGCACAC\t1\n-TGACTAGATCCACACTCATTAAAA\t1\n-TCGAATCCCATCCTCGTCGCCA\t1\n-CTTCCTACAACTGTGTGAGTACT\t1\n-TAGTGGCCGAACACTCGATAGTGAC\t1\n-ACCACACTACAAACTTCTGGAGAACT\t1\n-TTCGGATCAGCGGCAGTTTTGCGC\t1\n-TATTTCTGAAACTAACTATGGTCCT\t1\n-TTACCTAAGAATTGTTGATATTGCA\t1\n-CGGCCCATGTTGAAGTACACTCT\t1\n-TTTAAGGCTCCGTCGATGTTTGAAC\t1\n-AGCTCCTGCGTCATCGTGTGAACT\t1\n-TTTCCTTGGCAAGATCGCGTCGCA\t1\n-ATATTCTGCGTCATCATCG\t1\n-CGGAAGGGATAACCGCTGAAAGC\t1\n-TGAGTGGATCAGGTCTAGGAGG\t1\n-TCTCAAGAGTCCCTAAAGTAGCT\t1\n-GCAAGAATTAAAGCCCCATAAGCTC\t1\n-CCTCTGAGCAGCCAACGCCCGTATT\t1\n-CTCCGAGTCTGAATCTAG\t1\n-TATTGATCCTGATCTTCTATAGAATA\t1\n-ATTCATGTTGGCAGTCAAATGC\t1\n-ATCTGTTACGGCCCTTGAGCAA\t1\n-TGTGCCGGGCTGGCACCAACACTGC\t1\n-AATTCCACCACGTTCCCGTGG\t1\n-CTTAGCAATGCTTAAAGGAGTTGGC\t1\n-TTCATACGGCTGCCATTTTAATAT\t1\n-TGGAGGAGCTGAGCTTTTTCTCT\t1\n-TCCGACCCACTGCCGCGCTGCCGCCA\t1\n-CACCGTATCCCGAGCGTCTTGGCCG\t1\n-TCGGGTGACAAATGCTGTGTACGGCT\t1\n-ACGACAACCGTCATCCCG\t1\n-AATCACGAGGGTTGCATCCCGCCTG\t1\n-TAGGAGTGACTGCACCAAGGCTTGC\t1\n-ATGAGAGTCAGTAACTGC\t1\n-TTATGAATGTCTCCTCTGATCCGG\t1\n-ACCCAAAAAGTAATCGTTGACCTGC\t1\n-AATGTAGTCTGTCTGGTCTGG\t1\n-TTTGACCAGTCGGTCAGCCTCTTGACCC\t1\n-CGTTTCGATAGCCCACTCTGGCGGGA\t1\n-TTGGAGCTCAGAGCCTCTTCTCT\t1\n-TTTTTATTCTGAAGTTAACTT\t1\n-AAGAGAGCTATCCGTCGACAGTCT\t1\n-TCGCCGATCTATGCCTAATTTGGGCT\t1\n-TTTATTAATTTAACTTAGGTCTTGGC\t1\n-AGACTTGTAGAATTAGCGCGGGCGCGT\t1\n-TGAATTCCCGCCTGCCCACAGT\t1\n-TCGTCGCGGCTGATGGCAAAC\t1\n-CGCATGAATGGATTAACGACA\t1\n-ATAGCCCTGACAGCGTGC\t1\n-TTTCGCAAAGATGCAGATGTCGGC\t1\n-ACCCTTGACTACGCCTCTGTAGGCTC\t1\n-NATGCGCATTAACCTGTAGGC\t1\n-AAACAGACTGGACCAACACTC\t1\n-TAGAGCTTTATTACCCAAAACC\t1\n-TCATGACGTTCGGCGTGCCCGAA\t1\n-AAAGGTGCTGAAAGACTATACC\t1\n-TGTGCGATCGCGCGGCAACTGCGCA\t1\n-TCCTGGATCACGCTGTCATATTGA\t1\n-GCCTCGGTGGCGCATCGGCTC\t1\n-TATCCTCTGACTTCACATTATTCCA\t1\n-TCTTTCTCTGTGACTTAATTGGCG\t1\n-AACTGCACTAGTCCCGGCCTGC\t1\n-AGAAAGAACAAAAAGAAAACT\t1\n-AAGAAGCGGGATACTTAACCAT\t1\n-GCTTGGATCGGGGACCTTGAA\t1\n-CAATCGGAGGCCGGTTGACATC\t1\n-AACTGTTCCCTTTGCAAGTGTTAGT\t1\n-CCATATATGACGGCCTCATGGCACC\t1\n+CATGGCTGGGGACCCGAAAG\t1\n+TATCTCTTAGAGGCCATGAACGGCA\t1\n+TAACGGGTATGTGCTAGTTGGGCT\t1\n+GTGATAGTTTAATGGTCAGAATG\t1\n+TGCTGCTGCGAACTCGACTCCACT\t1\n+TTTCCCGGACGAGCCCCCA\t1\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/dup_unique.txt --- a/test-data/res_files/reads-sample-small.fastq/genome/dup_unique.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/dup_unique.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,9974 +1,1998 @@\n sequence\tcount\n-TGCTTGGACTACATATGGTTGAGG\t1985\n-TGCTTGGACTACATATGGTTGAGGG\t1319\n-TGCTTGGACTACATATGGTTGAG\t943\n-TATAGAATTGTAGAGCAAGACCT\t498\n-TGCTTGGACTACATATGGTTGAGGGT\t300\n-TTGATTAAGATAGCTGCTCCGCCT\t297\n-TATTGGCAAGCCTTTCGTCGAACC\t267\n-ATATCGCAGTCCATGCTG\t240\n-TTTACGGGATAGGACGGTAGCGC\t231\n-TATTGACTGGCGACGCTTTTGAGG\t229\n-TGCTTGGACTACATATGGTTGAGGGTTG\t226\n-TGAAAGACGCAGGATGGTCCGCCT\t226\n-TGAAAGACGCAGGATGGTCCGCCTG\t223\n-TATGTTTAGCGTTGTAGTCGCCT\t193\n-GATTGGACAGCCTCTGTAGTTTGC\t182\n-AACGCATATCGCAGTCCATGCTG\t173\n-TTCGATCTGCCGCGGGCTGCCGAGA\t168\n-TTTCTTCGGTTCGATATCAACGGA\t163\n-GGACTACATATGGTTGAGGGTTGTA\t160\n-TATAGAATTGTAGAGCAAGACCTTG\t144\n-CCATATCTAGGTTCTGTAGCCGAAG\t136\n-TATTTGATTGTTGGGCTACAAGCA\t130\n-TCAGAATCTTTGATTGTGCTCGCT\t128\n-ACTACATATGGTTGAGGGTTGTA\t125\n-TTCAGATGGTGCTCGACTATGGCCT\t117\n-CTGCTTGGACTACATATGGTTGAG\t115\n-TAACTGCGAAGTCGATCAGGTCT\t113\n-GCATATCGCAGTCCATGCTG\t107\n-TTTTTGATCAATTGGCACCATGCGA\t105\n-TTTTTGATCAATTGGCACCATGCGAA\t105\n-TCAGATGAGAGACAAATTAGAATTA\t103\n-TGTAGAGGATCGCTTGTCTGGGC\t99\n-AACTCTAAGCGGTGGATCACTCGGC\t94\n-TAGATGTGGCCTGAAGATGATTTTC\t91\n-TTAGTGTTGAATGTAGGCCAGGGA\t90\n-TGCTTGGACTACATATGGTTGA\t90\n-CTGCTTGGACTACATATGGTTGAGG\t86\n-TCATGAGACGTCTGCTTGTTTGGC\t83\n-GACTACATATGGTTGAGGGTTGTA\t83\n-TGCGTTTGGGATTGTCGGTGAGAC\t82\n-TAATACATCGATTTCGTGACGTCGC\t81\n-TATTTGATTGTTGGGCTACAAGCATT\t81\n-GCTTGGACTACATATGGTTGAGG\t81\n-TGCTTGGACTACATATGGTTG\t80\n-TACATATGGTTGAGGGTTGTA\t78\n-TTTCTTCGGTTCGATATCAACGGAT\t76\n-TATTGGCAAGCCTTTCGTCGAAC\t76\n-TCTTGTAAATACTTTGATTGGCCT\t74\n-TTTTCCGGGCTGAGCTTTCGCTTT\t73\n-TTCGATCGCCGACGTGTGAAGACGT\t73\n-TGCGTTTGGGATTGTCGGTGAGA\t71\n-ACATTTCCGTTTCTCGCGACT\t71\n-AACTCTAAGCGGTGGATCACTC\t70\n-TGCGTTTGGGATTGTCGGTGAGACG\t70\n-CCATGTCCCGTTGCTATCGACTAGA\t69\n-TATTGAAGGAATTGATATATGCC\t68\n-ACATATGGTTGAGGGTTGTA\t67\n-TTGGGTGTTGCAGTAAGAGCTG\t65\n-TACGAGTAGGATATCGATCTGGT\t65\n-TAGAAGACGATTTTCGGGCCGAAAT\t63\n-TGAATGGTTGAAATCGCTCGGCGA\t63\n-TAATGAGATCCCTCGGTTGCCTT\t63\n-TCCGAAAACAAGGCCCGTCGCTA\t62\n-TTCATCAGCGACTTGTGGGATTCC\t61\n-TGTGCTAGAAGACGATTTTCGGGC\t61\n-TTTTTGATCAATTGGCACCATGCG\t59\n-TTTACGGGATAGGACGGTAGCGCG\t58\n-CTACATATGGTTGAGGGTTGTA\t58\n-TCTGATGTTACGCCCGAAGAGA\t58\n-GAACGCATATCGCAGTCCATGCTG\t58\n-TGTATGAACAGTGGAAGTGG\t56\n-CCGTAAAGGCTTACATCTGGCT\t56\n-TGCTAGAAGACGATTTTCGGGC\t54\n-TTAGGACGAAACACAATTGGGGTG\t54\n-TAATTTGACACTGTTTGGAG\t54\n-TAAGTTGTTGGCTTTGAGTTTAAG\t53\n-CAAAGTCCTGGATACCATCGGCT\t52\n-TTGTAATGTAGCGGTCCATTCC\t51\n-TAATAGTCAGGGCGCGAATTTTTAA\t51\n-TATTGGCAAGCCTTTCGTCGAACCA\t50\n-CAGTATGTAGGACTCCCGGGG\t50\n-TTTGGTTAAAGCTGAATGTCTGCC\t50\n-TAATGAGATCCCTCGGTTGCCT\t49\n-TTTTCCGGGCTGAGCTTTCGC\t49\n-TTTGACAAAATATGCCCTTCACCT\t49\n-TGATTGCGTTGGTAACTGATGGGA\t48\n-TTTTAAACATTAGGCCGTCGAGCCAGA\t47\n-TGATTACGCATCATGTCTTGAATG\t46\n-TAGGACGGTAGCGCGAATGTGCTAGT\t46\n-TTTTAAACATTAGGCCGTCGAGCCAG\t45\n-TATCCAGAAAGGACTTCAGCCCTC\t44\n-TAGGACTCCCGGGGGAAACATGGTC\t44\n-TTTCTGTTTGGGTTTGGACT\t44\n-CAAGCATTCGACAAAGTCTGGC\t44\n-TATTGACTGGCGACGCTTTTGAG\t43\n-TACGAGTAGGATATCGATCTGGTG\t43\n-TTAAGTCTCTTTGGATGTTTTCACT\t43\n-TAGGACTCCCGGGGGAAACATGGT\t42\n-TAAAGAGGACAGGCCTTACAGGGTA\t42\n-TTGTAATGTAGCGGTCCATTCCA\t41\n-CCATATCTAGGTTCTGTAGCCGAAGG\t41\n-TTTAAGCTGGTAGGTGTAGAAGCCT\t41\n-CGCTGATGAAATCTCCAGGCTCAG\t41\n-TTCAGTATTGAGTTTTGGGCTTAGC\t41\n-TATGTTTAGCGTTGTAGTCGCCTGC\t41\n-TTTTTGATCAATTGGCACCATGC\t41\n-TCCGGGCTGAGCTTTCGCTTT\t40\n-TCTGATGTTACGCCCGAAGAGATAAC\t40\n-TTTCTGTTTGGGTTTGGAC\t40\n-AACTCTAAGCGGTGGATCACTCG\t40\n-TCAGATGAGAGACAAATTAGAAT\t40\n-TCATACTCTTCGATCTCGAGCCAG\t39\n-TTATTGAATCTTCTTGTATAAGAACT\t39\n-CAAATGTGGATACCGTTAAGCGAC\t38\n-TATTGAAGGAATTGATATATGC\t38\n-TAGAATAACAAGATGCGTAACGGCC\t38\n-TCAAAGTATTTACAAGACGGCTT\t38\n-TTGCGTTGGTAACTGATGGGAT\t38\n-TTGTAATGTAGCGGTCCATTCCAG\t38\n-TAATGAGATCCCTCGGTTGCCTTCT\t37\n-CACAGAGGCCAAGTCATTGAGCGCC\t37\n-TTGATTAAGATAGCTGCTCCGCC\t36\n-TCATACTCTTCGATCTCGAGCCA\t35\n-TAGGACGGTAGCGCGAATGTGCTAG\t35\n-TCTCGGTGGGCAGTAGACCGC\t35\n-AAGATTCTGAGAACCATCACTGGGG\t35\n-TGAATTGAGAGTCGGCGTTCGTCA\t34\n-TTTGACAAAATATGCCCTTCACC\t34\n-TTATTCTAATTAGTTAGGCTCTCCC\t34\n-TATTTGATTGTTGGGCTACAAGC\t34\n-TTTGGGTGTTGCAGTAAGAGCTG\t34\n-TTAAAGAGGACAGGCCTTACAGGGTA\t34\n-TAGGACTCCCGGGGGAAACATGG\t33\n-TGTAGAGGATCGCTTGTCTGGGCAG\t33\n-TCCCTGAGACCCTAACTTGTGA\t32\n-AACTCTAAGCGGTGGATCACTCGGCT\t32\n-TGTAGAGGATCGCTTGTCTGGG\t32\n-TT'..b'TGTTCAACAAGAGCGGAGGACA\t1\n-GAAAAAACCCAAATCAACCATCGGC\t1\n-TATATGTATCTGTTTTGGCCC\t1\n-TGCTGTAGGAGCCAAGTTCTCCACCT\t1\n-TTGATTTGTTGGTAGAAGAAGGTT\t1\n-ACCACTATTATCGAAGAAACGCAG\t1\n-TCAGGTCTCTGTGCAGGGT\t1\n-CGTAAGCTTGCTGCGCGCGGAGC\t1\n-GTTATACAATGATCATGTGTT\t1\n-CTTTAATTATCATATATTGTA\t1\n-TGTGATCTAGGCTGAGCGGAG\t1\n-TCGGAGCTAAGCTCAACAACCGCAC\t1\n-TAAGCGGTGGATCACTCGGCT\t1\n-GCTTGATGACTGGTACTG\t1\n-AAGTTAATGATTACTTTGATTGCC\t1\n-ATTTATTGAAGGAATTGATATATGC\t1\n-CTTTCCGCTGTCAACGACCAG\t1\n-TGAATCTGATATAGAGAGCTGCAC\t1\n-AGCGCGAGCATGACGAACGCC\t1\n-TGGCATTGCCCCATAACTGTGAGCC\t1\n-CAATCTGGACCTATGGCTC\t1\n-TACCAGAGGCAGGTGGTCGGAGCTA\t1\n-CGGGAGTGGTATGCTGTTCAACAAGA\t1\n-CATCATCAACGTCCTGTCCAGAG\t1\n-CTCCGACAGAAGCCCCGCTACC\t1\n-CAACTCGTCCACGTAAAACGTCGCT\t1\n-TAACAAAGAGAGCCTGGAGCC\t1\n-TAGCACTTGTAAATTAAGACTCACT\t1\n-TAAAAATAAATGTTCGGGAC\t1\n-TGAGCGGAGAACCAGAGTTGAT\t1\n-ATCCCAAACGCAGACATCG\t1\n-GATGGTGCTCGACTATGGCCT\t1\n-CAAGGTAGTGTCCTCGGCCC\t1\n-AATTCGATCGCCGACGTGTGAA\t1\n-GCTGATCCGACTTAATCAACA\t1\n-TTTTTTCTAGGAGGCTTGTTTTC\t1\n-GTAAAACGTCGCTTACGCAGAG\t1\n-AACTGGCCAACGCTCTGAAACAAGAAG\t1\n-TAAGGCTTTACGCGGCTGACGC\t1\n-CTTGTACTCAAAGCTCCTCCACGGCT\t1\n-TCCTTGGCGGAGGTATCGTAGTGAG\t1\n-TGCTGCGTTCGGCTGTGG\t1\n-GAATCCCACAAGTCGCTGATGAAA\t1\n-TATTGGCGGAGGCTTTGTTTTCTT\t1\n-AACGCATATCGCAGTCCATGCTGT\t1\n-CAATGACTTCGGCTACCTCGCAG\t1\n-TTCTGTAGTCGTCCTCCGTTTTCGT\t1\n-TATTTTTCCAACTGTTCT\t1\n-TGCTTTTCCGTCGGGATG\t1\n-TGGGGGCGTAGCATTACTAGTGC\t1\n-GTTGTTGGCTTTGAGTTTAAG\t1\n-TGCAAGTAGTCCTGAAGG\t1\n-GATAAGCGTCAGCTTCTGCGGACC\t1\n-CCGTTGTGGTTGTTGTTACTG\t1\n-GGGATGTCGGCTGTATAGATGA\t1\n-CACCGTGGTACGTTCGGAGTGAAAAC\t1\n-GATCCCAGATCCGCTGTGTTT\t1\n-TATCGTCGGCAAATGTGGATA\t1\n-TGCCGAGATATGCTGCGAGTTG\t1\n-CCGTGATTGCGTTGGTAACTGAT\t1\n-TGAGGACGTATTTTGAGAGACC\t1\n-TCGCTTCGCTTTCGACTCCGGT\t1\n-CCGGAAATGATCATCCAGC\t1\n-CAAATGATCAACAGGACTCCACAAC\t1\n-TACCGCTGAGGACGTGCCGCTGG\t1\n-TAGATTGGACAGCCTCTGTAGTT\t1\n-CGGGTATCTTGTTGGTCCTCCTG\t1\n-TCTGAGAACCATCACTGGGGCACC\t1\n-CACCATCTGAAGACCCACCAG\t1\n-CTACTAGCACATTCGCGCTAC\t1\n-GCTCGATGCGTGGCCTGGTACAGTC\t1\n-TCAGAACACATGCCATAAAG\t1\n-GTGTGTGAATATCGAGAACCT\t1\n-TTGCCTTTTGTCGGAGAAATCCGT\t1\n-TTTAAAATCAGGTATGACGCC\t1\n-TTCCTTAAGTTCCGTGATTGCGTT\t1\n-AACATCGCTTCTATCTGACCGGA\t1\n-AAAGTCACTGTGGCGAGCCCA\t1\n-TTCGCTGTGGAAGGCCACGCGCGCAAT\t1\n-CTAGAGGTGGCTCCAGGCTCT\t1\n-TGACCTCGTGTGGCCATACTCTT\t1\n-TGTTGCGGCTGCTGCGGCT\t1\n-CACTCCGTTGAGGGCGTCT\t1\n-TTCAGCTCTTTGTAGATTGGACA\t1\n-TTGTTTCAGAGCGTTGGCCAGTTT\t1\n-AAGGAATTCATCAGGTGGCTGGGC\t1\n-GTGAGTTGCTCTATGTATCGGC\t1\n-CAAGCCGGAAAGGGAGCCCGCCTCCTAC\t1\n-TTGATCAAGGTAGAGTTGTCGCGT\t1\n-GACCTTGTGATCTAGGCTGAGCGGA\t1\n-TTCTCCTACGTCTCACCG\t1\n-TACACATCCTGATTCTGCCAGCGCTC\t1\n-AAAACGTCGCTTACGCAGAGA\t1\n-TTGCTGGTAGATACCGCTGAGGA\t1\n-GAAGTACGCGTTGTTGCGCTG\t1\n-ACAACAAATGTTAAACTGATTT\t1\n-TGTGTCCGCACTTCGTGCCT\t1\n-GTAGGATCACGGTAGAAG\t1\n-GCGGAAAGAATGCAGACCTTTGGTCAGC\t1\n-GGCTAGCTCAGTCGGTAGA\t1\n-TGATTTGTTGGTAGAAGAAG\t1\n-ATCAGACGGAGTGCTAGGGGCT\t1\n-CGATAAGGAATTCATCAGGTGGCT\t1\n-CAAATCGAGCAACTCGTCCACG\t1\n-CCACACGGAAACTGGCCAACGCTC\t1\n-GCAAAAATTGAAGTCGATCCCGG\t1\n-TTCAGTCGGTGGGCGAAGA\t1\n-TCCAGAAAGGACTTCAGCCCTC\t1\n-TCGCCTGTACTAATTCACCT\t1\n-ACCGCCGGCGCAAGTTGCACCTTGG\t1\n-TATCGACTAGAGGCGCCTTCCTCGTG\t1\n-TTGTAAGGATTATGGAAGCCCAG\t1\n-GATGAAGCGACTGTGTGGTTCTTACCA\t1\n-GACTTTTCTGTAGTCGTCCTCCGTT\t1\n-TTTCAGGTCTCTGTGCAGGGTGGTG\t1\n-ACCCTTCGGCTACAGAACCTAGATA\t1\n-TAATAATAACGTTAAGGCA\t1\n-TCTTGAAGAGTGGTTGGGGCTGCC\t1\n-CAAAGATTCTGAGAACCATCACT\t1\n-TTCAGGAGATCGTGCACTAATAGAT\t1\n-CGGTAGAGCATGAGACTC\t1\n+TTTGCCGGATGAAGATATTTATTAA\t1\n+TCGATATGCTTCTCATGTAGGA\t1\n+GGTTTACGGGATAGGACGGTAGCGC\t1\n+CTCGGATCATTGGCAGTGTAGGCTA\t1\n+CCAGCTTAAAAGCAGCAAGGGC\t1\n+GATTTCATCAGCGACTTGTGGGA\t1\n+TTCAGGACTACTTGCAGGCCC\t1\n+TTCAAAGTTCTGGAAGATTTTCTG\t1\n+TGTAGAGGATCGCTTGTCTGG\t1\n+TCTATGACAGAAAGTTTGCAGT\t1\n+TCTGTTCTTATCAGCTTAACATCTGA\t1\n+TTCCATCATGCTCTGTTGTAAG\t1\n+GTACGTTGGTCTTTTTTGAATTAA\t1\n+TGATGTCAATATTGCTGTTGCTGGC\t1\n+TAAAATTAAAACATCCCTACCCGAA\t1\n+TCGTAACTTTTTAGCAACCTGCTCC\t1\n+GTGAGTTGCTCTATGTATCGGCGCT\t1\n+TCTATGTATCGGCGCTGATCGTCGT\t1\n+GTCGACCTGGCAGACTGGAAT\t1\n+AACATTAGCTTAAGGGATACTAT\t1\n+CAGGCAGTAGAGCAGGGGGCCGAGG\t1\n+TGATATTGTTGGTGAGCAGTT\t1\n+CGGAAAAGCACACGGTGGCACCGC\t1\n+CCTTTCGCCGGAGACGGGA\t1\n+CGCACTTTTAGCTGGTCGTTGACAGC\t1\n+TCCGGCTCGAAGGACCAAAAAAAT\t1\n+TGTAGGTGAGCGGCAAATGTGTTG\t1\n+TTCCGATGTACTATCCGTCAATCT\t1\n+ACCGATGTAGATCTAGGCATC\t1\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_sorted.bam |
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| Binary file test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_sorted.bam has changed |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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chrom_5\t1803\t1999\t0\n chrom_6\t0\t440\t0\n-chrom_6\t440\t464\t25.6148\n-chrom_6\t464\t819\t0\n-chrom_6\t819\t845\t25.6148\n-chrom_6\t845\t885\t0\n-chrom_6\t885\t905\t51.2295\n-chrom_6\t905\t906\t25.6148\n-chrom_6\t906\t1038\t0\n-chrom_6\t1038\t1060\t25.6148\n-chrom_6\t1060\t1109\t0\n-chrom_6\t1109\t1110\t25.6148\n-chrom_6\t1110\t1115\t51.2295\n-chrom_6\t1115\t1117\t102.459\n-chrom_6\t1117\t1125\t128.074\n-chrom_6\t1125\t1130\t153.689\n-chrom_6\t1130\t1133\t102.459\n-chrom_6\t1133\t1136\t76.8443\n-chrom_6\t1136\t1142\t51.2295\n-chrom_6\t1142\t1143\t25.6148\n-chrom_6\t1143\t3999\t0\n+chrom_6\t440\t464\t252.016\n+chrom_6\t464\t3999\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/size/duplicates.txt --- a/test-data/res_files/reads-sample-small.fastq/size/duplicates.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/size/duplicates.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,14717 +1,2552 @@\n size\tnumber\n-TGCTTGGACTACATATGGTTGAGG\t1985\n-TGCTTGGACTACATATGGTTGAGGG\t1319\n-TGCTTGGACTACATATGGTTGAG\t943\n-TATAGAATTGTAGAGCAAGACCT\t498\n-TGCTTGGACTACATATGGTTGAGGGT\t300\n-TTGATTAAGATAGCTGCTCCGCCT\t297\n-TATTGGCAAGCCTTTCGTCGAACC\t267\n-ATATCGCAGTCCATGCTG\t240\n-TTTACGGGATAGGACGGTAGCGC\t231\n-TATTGACTGGCGACGCTTTTGAGG\t229\n-TGCTTGGACTACATATGGTTGAGGGTTG\t226\n-TGAAAGACGCAGGATGGTCCGCCT\t226\n-TGAAAGACGCAGGATGGTCCGCCTG\t223\n-TATGTTTAGCGTTGTAGTCGCCT\t193\n-GATTGGACAGCCTCTGTAGTTTGC\t182\n-AACGCATATCGCAGTCCATGCTG\t173\n-TTCGATCTGCCGCGGGCTGCCGAGA\t168\n-TTTCTTCGGTTCGATATCAACGGA\t163\n-GGACTACATATGGTTGAGGGTTGTA\t160\n-TATTGCACTTGAGCCGGCCTGA\t156\n-TATAGAATTGTAGAGCAAGACCTTG\t144\n-CCATATCTAGGTTCTGTAGCCGAAG\t136\n-TATTTGATTGTTGGGCTACAAGCA\t130\n-TCAGAATCTTTGATTGTGCTCGCT\t128\n-ACTACATATGGTTGAGGGTTGTA\t125\n-TTCAGATGGTGCTCGACTATGGCCT\t117\n-CTGCTTGGACTACATATGGTTGAG\t115\n-TAACTGCGAAGTCGATCAGGTCT\t113\n-TCTTTGGTATTCTCGCTGTAGA\t112\n-GCATATCGCAGTCCATGCTG\t107\n-TTTTTGATCAATTGGCACCATGCGAA\t105\n-TTTTTGATCAATTGGCACCATGCGA\t105\n-TCAGATGAGAGACAAATTAGAATTA\t103\n-TGTAGAGGATCGCTTGTCTGGGC\t99\n-AACTCTAAGCGGTGGATCACTCGGC\t94\n-TGAGATCATTTTGCAAGCTGATT\t93\n-TAGATGTGGCCTGAAGATGATTTTC\t91\n-TGCTTGGACTACATATGGTTGA\t90\n-TTAGTGTTGAATGTAGGCCAGGGA\t90\n-CTGCTTGGACTACATATGGTTGAGG\t86\n-GACTACATATGGTTGAGGGTTGTA\t83\n-TCATGAGACGTCTGCTTGTTTGGC\t83\n-TGCGTTTGGGATTGTCGGTGAGAC\t82\n-GCTTGGACTACATATGGTTGAGG\t81\n-TAATACATCGATTTCGTGACGTCGC\t81\n-TATTTGATTGTTGGGCTACAAGCATT\t81\n-AAATGAGAGTCAGTAACTGCC\t80\n-TGCTTGGACTACATATGGTTG\t80\n-TACATATGGTTGAGGGTTGTA\t78\n-TTTCTTCGGTTCGATATCAACGGAT\t76\n-TATTGGCAAGCCTTTCGTCGAAC\t76\n-TCTTGTAAATACTTTGATTGGCCT\t74\n-TTCGATCGCCGACGTGTGAAGACGT\t73\n-TTTTCCGGGCTGAGCTTTCGCTTT\t73\n-TGCGTTTGGGATTGTCGGTGAGA\t71\n-ACATTTCCGTTTCTCGCGACT\t71\n-AACTCTAAGCGGTGGATCACTC\t70\n-TGCGTTTGGGATTGTCGGTGAGACG\t70\n-CCATGTCCCGTTGCTATCGACTAGA\t69\n-TATTGAAGGAATTGATATATGCC\t68\n-ACATATGGTTGAGGGTTGTA\t67\n-TACGAGTAGGATATCGATCTGGT\t65\n-TTGGGTGTTGCAGTAAGAGCTG\t65\n-TGAATGGTTGAAATCGCTCGGCGA\t63\n-TAATGAGATCCCTCGGTTGCCTT\t63\n-TAGAAGACGATTTTCGGGCCGAAAT\t63\n-TCCGAAAACAAGGCCCGTCGCTA\t62\n-TGTGCTAGAAGACGATTTTCGGGC\t61\n-TTCATCAGCGACTTGTGGGATTCC\t61\n-TTTTTGATCAATTGGCACCATGCG\t59\n-GAACGCATATCGCAGTCCATGCTG\t58\n-TTTACGGGATAGGACGGTAGCGCG\t58\n-CTACATATGGTTGAGGGTTGTA\t58\n-TCTGATGTTACGCCCGAAGAGA\t58\n-CCGTAAAGGCTTACATCTGGCT\t56\n-TGTATGAACAGTGGAAGTGG\t56\n-TAATTTGACACTGTTTGGAG\t54\n-TTAGGACGAAACACAATTGGGGTG\t54\n-TGCTAGAAGACGATTTTCGGGC\t54\n-TAAGTTGTTGGCTTTGAGTTTAAG\t53\n-CAAAGTCCTGGATACCATCGGCT\t52\n-TTGTAATGTAGCGGTCCATTCC\t51\n-TAATAGTCAGGGCGCGAATTTTTAA\t51\n-CAGTATGTAGGACTCCCGGGG\t50\n-TATTGGCAAGCCTTTCGTCGAACCA\t50\n-TTTGGTTAAAGCTGAATGTCTGCC\t50\n-TAGTTCTACAGTCCGACGATC\t50\n-TAATGAGATCCCTCGGTTGCCT\t49\n-TTTGACAAAATATGCCCTTCACCT\t49\n-TTTTCCGGGCTGAGCTTTCGC\t49\n-TGATTGCGTTGGTAACTGATGGGA\t48\n-TGAGATCATTTTGCAAGCTGAT\t48\n-TTTTAAACATTAGGCCGTCGAGCCAGA\t47\n-TGGACGGAGAACTGATAAGGGCA\t47\n-TGATTACGCATCATGTCTTGAATG\t46\n-TAGGACGGTAGCGCGAATGTGCTAGT\t46\n-TTTTAAACATTAGGCCGTCGAGCCAG\t45\n-TTTCTGTTTGGGTTTGGACT\t44\n-CAAGCATTCGACAAAGTCTGGC\t44\n-TAGGACTCCCGGGGGAAACATGGTC\t44\n-TATCCAGAAAGGACTTCAGCCCTC\t44\n-TACGAGTAGGATATCGATCTGGTG\t43\n-TATTGACTGGCGACGCTTTTGAG\t43\n-TTAAGTCTCTTTGGATGTTTTCACT\t43\n-TAGGACTCCCGGGGGAAACATGGT\t42\n-TAAAGAGGACAGGCCTTACAGGGTA\t42\n-CCATATCTAGGTTCTGTAGCCGAAGG\t41\n-TTTAAGCTGGTAGGTGTAGAAGCCT\t41\n-TTCAGTATTGAGTTTTGGGCTTAGC\t41\n-CGCTGATGAAATCTCCAGGCTCAG\t41\n-TATGTTTAGCGTTGTAGTCGCCTGC\t41\n-TTTTTGATCAATTGGCACCATGC\t41\n-TTGTAATGTAGCGGTCCATTCCA\t41\n-TATTGCACTTGAGACGGCCTGAA\t41\n-TCTGATGTTACGCCCGAAGAGATAAC\t40\n-TCAGATGAGAGACAAATTAGAAT\t40\n-AACTCTAAGCGGTGGATCACTCG\t40\n-TTTCTGTTTGGGTTTGGAC\t40\n-TCCGGGCTGAGCTTTCGCTTT\t40\n-TATTGCACTTGAGCCGGCCTG\t39\n-TCATACTCTTCGATCTCGAGCCAG\t39\n-TTATTGAATCTTCTTGTATAAGAACT\t39\n-CAAATGTGGATACCGTTAAGCGAC\t38\n-TCAAAGTATTTACAAGACGGCTT\t38\n-TAGAATAACAAGATGCGTAACGGCC\t38\n-TATTGAAGGAATTGATATATGC\t38\n-TTGTAATGTAGCGGTCCATTCCAG\t38\n-TTGCGTTGGTAACTGATGGGAT\t38\n-TAATGAGATCCCTCGGTTGCCTTCT\t37\n-CACAGAGGCCAAGTCATTGAGCGCC\t37\n-TTGATTAAGATAGCTGCTCCGCC\t36\n-TCTCGGTGGGCAGTAGACCGC\t35\n-TAGGACGGTAGCGCGAATGTGCTAG\t35\n-AAGATTCTGAGAACCATCACTGGGG\t35\n-CTAAGGAAATAGTCGCCGTGAT\t35\n-TCATACTCTTCGATCTCGAGCCA\t35\n-TTTGGGTGTTGCAGTAAGAGCTG\t34\n-TTAAAGAGGACAGGCCTTACA'..b'AGTTTAATGAC\t1\n-GAGCGAGAGAGCGGAGAG\t1\n-TTCTGGGAATTCCGAAGATGG\t1\n-TGAATGGTCTAAGTGTACGGA\t1\n-TGGATTGCAATGCACACGTGCAGC\t1\n-TAACGAACAGGACCGTTGTTATTGA\t1\n-TAGGAGTACACCTTGACAG\t1\n-GAAGTTCATTGTTGCAGGCGATT\t1\n-AGAAAAATCAAGAGTGACGAG\t1\n-TCCAGCTGAATGTTGATAGAT\t1\n-TTTATTTTGTAGATCGCAAGC\t1\n-TTTGCTAAGGACTGGCTGAGAA\t1\n-CATTCCTGAGATCGGTTTTACTC\t1\n-TTATAAGGTCGCAGCCGGGGGT\t1\n-TGGGCGAAGAGTTGAGTGGGCT\t1\n-TCTAGGGGTACACTCCAGCGCTCGA\t1\n-AACTGGCCAACGCTCTGAAACA\t1\n-ACCGCCCGTCGCTACTACCGC\t1\n-CAGGTCTCTGTGCAGGGTGGTGT\t1\n-GAGTCGAACAAATGATCCGTCGTT\t1\n-TAAGCTCGAATCTGTTACGGCCC\t1\n-TACCGGTAACTAGCGGCTGCCCGCA\t1\n-TTTTTACGCAATTTAGAGATAATG\t1\n-GTCAACTAGTCCGTCAGGGGT\t1\n-TGAGTAAATTGGACGATGAGGCGT\t1\n-TAAGGGACTATTTTAGGAGAA\t1\n-CGCTGGGTTGGTAGGTCCTTTCG\t1\n-ACTGATCGGCCGGTAGGAGG\t1\n-GTCGATATGCTTCTCATGTAGGAAT\t1\n-TCCGTCGTTTGACTAAGA\t1\n-TAGAGATGGTGAGCTAGACGTT\t1\n-TATTGTTGTGGAAGATCGAGA\t1\n-AGGAGAGAAGGAGAGCGCGAGC\t1\n-AACATCAACATTGGACCTATGCCT\t1\n-GATGTCGGCTGTATAGATGA\t1\n-CCAACGCTGGACGCATTGACCAAAGCT\t1\n-TGAGGCATCTGGGGAGCATTGGA\t1\n-TCAATTGGGTGTAGCTACA\t1\n-TGGACGGAGAACTGATAAGGGTA\t1\n-GCAGCCGATGGTATCCAGGACTT\t1\n-ACAAGCGCGGAACCTTTTGATCGC\t1\n-CATTGCAGCAGTTCCAGGACGGCA\t1\n-TGATGCTATCGAACTGCT\t1\n-TTCGGCGGGTCGTCGCACCCT\t1\n-TGTCAATATTGCTGTTGCTGGCATT\t1\n-ATACACGCGACAACTCTACCT\t1\n-TATTCATAATATTAAAAAA\t1\n-TTTCTGACGAGATTGCGGTCTCCCA\t1\n-GACGAAACACAATTGGGGTGT\t1\n-TGTTTGTCAGCTGTGAGA\t1\n-ACTGGGGATCGCGACTTGTGAAC\t1\n-GGTACTTTGCTGCGTTCGGCT\t1\n-TTAACGAACGAGACCCCCGCC\t1\n-TGCGTTTGGGATTGTCGGTGAGACAT\t1\n-AAGCAGCCAAAGCTCCAGGGC\t1\n-CGCCTTGTTAGCATTAGCGACGG\t1\n-GCATGCACAGAACATAACGTA\t1\n-ACCCATAAAAAGATTGAACGCCT\t1\n-TCGGCTGGCACTCGGTCCGC\t1\n-TTCGAGCCTTTTCAGGTATCTCTCGC\t1\n-TTGGGTTTGGACTGGGGTTGTGG\t1\n-TTATTAAAGTCGTTTTACACC\t1\n-AAGACGTTTTTATCGTGCTCCGCACA\t1\n-ATGACACCGTTGGAAGAA\t1\n-TTACATCATGGATCAGTAACGAGAA\t1\n-TTTTCTTGGGCGTTTGGAG\t1\n-TGTTTGTGCGATCGCGTGGCAGC\t1\n-AGACTCATCACCGGCTGCGAG\t1\n-GAGGACAGCATCCCGAGTGTGAACT\t1\n-ATAGGACCCGGCTCTGCTTAGT\t1\n-TCTCCGCCGCGTAGCCGCTGACGA\t1\n-ATTTCGAGTCGAATAAATGATCCT\t1\n-TGTATTAGCGTCAGCCGCGTAAAGCC\t1\n-ATTGAGAAGTGGCTCTCTGACT\t1\n-TTTATCGAACCGCAGGAACCTCTTG\t1\n-GTTCGGCTTTCTGACGGGAACTCGA\t1\n-CATCACAGTCTGAGTTCTTGCC\t1\n-AGTGGAAGCAGCACGCTTTGTCGT\t1\n-TACCTGTGTGTAACTTCTTTGGCCT\t1\n-TGTTTAATCCAGAGTTGGCCGAACA\t1\n-AAATTGCCAAATGGTTCGACCCTG\t1\n-TTTCTCTGTTGCGATTGAACTTGATT\t1\n-TCTCCGGCGAAAGGACCTACCAA\t1\n-AAAACTAATTGATCTTCGGCT\t1\n-TTTCCGAATAACTTGTGATCTGGCA\t1\n-TACATAAACAGAACTCGGCT\t1\n-TCTATTGCCCCAGCAAGTCTGACTG\t1\n-TAGTCTGTTAGAATCCTACGC\t1\n-GAGTATTCAGAGCAACCATA\t1\n-GGTAGGTCCTTTCGCCGGAGACGG\t1\n-ATATTCTGAATTACCACTTTTAAAAAA\t1\n-TAATAAGGCAATGATTGT\t1\n-TTCTTACCAGGCTTTGGAATC\t1\n-TCTATATTGAAACCAATCTGGACC\t1\n-TTCAATGCCATCGTCGTCAGCGG\t1\n-CACTGTTGCAGCGGCAATTAAGACT\t1\n-AAGGGTCCGCAGAAGCTGACGCT\t1\n-TTATTACTTACTCTGCCAGACCACATC\t1\n-GCCTTCCACAGCGAATGCGTCGC\t1\n-ATCCGTCGAGCGCTGGAGTGTACCC\t1\n-TAACTTAAAGGTAGTGTTAACGGA\t1\n-TTTGTCGAATGCTTGGGATACGTCT\t1\n-AGAGACGAGAACGCGTATATGTG\t1\n-TTTGATACAAATGCTTGTAGCCC\t1\n-CTAGTCGGCTGGACGGATC\t1\n-AACACAAATTCAACTATCGCCGGCC\t1\n-CTTAAGTTCCGTGATTGCGTTGGTA\t1\n-GAGACGGGAACGGCTGCTGAGCT\t1\n-TAACGGATCAAATATTTTTGCTCGC\t1\n-TTGAACCCTGCGAGGTAGCCG\t1\n-TAACGATCAGGGCCTCTGCACC\t1\n-TCGCGACTTGTGAACCCAA\t1\n-AGAGAACCAGAAAAAGATAATCCT\t1\n-TCAAGGACTCAAGGGCTGTTCCT\t1\n-CAAAGGAGCCGCAGCCGGACAAGGGC\t1\n-TCTCGCGGATGTATATTGGCGGA\t1\n-ACAACCTCAACTCATATGGCA\t1\n-ACGGGGTTTGGACTGTCACCC\t1\n-TTTGTAAATTGTCAGCTTGTTGGA\t1\n-GATGAAAATGTAGTGCACGCCA\t1\n+CAACCGTTCGATCAGAGCTGT\t1\n+ATATGGTTGAGGGTTGTAA\t1\n+ACCTCGTGTGGCCATACTCTTGGCAGT\t1\n+AACCTCCTAGTCGCTGTGACT\t1\n+CTACGAGTAGGATATCGATCTGG\t1\n+ATGGTTGAGGGTTGTATT\t1\n+TCATGCTCTGTTGTAAGGCTTG\t1\n+TGCGTTGGTAACTGATGGGAT\t1\n+GCGAAGTCGATCAGGTCTGGC\t1\n+TAATCACAAGTGTCGGATACT\t1\n+TAATACTGAGAAATGTCTAGCATAAA\t1\n+ACTCGACTATAGCATTCTCCGGTT\t1\n+TGCCGTGATCGTCTAGTGGTTAGG\t1\n+ACTCTAAGCGGTGGATCACTCGGCT\t1\n+TATTGCACTTGAGCCGGCCG\t1\n+ACCGCACTGCAAACTTTCTGTCATAG\t1\n+TAAACAGATCTCGCCCACCAAGG\t1\n+TGCTAGAAGACGATTTTCGGG\t1\n+CTAAGATCAACGCCTTTAAAG\t1\n+TCGCGATCCCCAGTGAGTATG\t1\n+TAGCCTGTAGTCACAAAATTAATT\t1\n+CACCGTGGTACGTTCGGAGTGAAAAC\t1\n+ACAGATCTCGCCCACCAAGGAGGCTC\t1\n+TTTCCTTTTGGGTTCACAAGTCGCGA\t1\n+TAACCGCCGGCGCAAGTTGCACCTTG\t1\n+TTTTTGATCTTAGCTTCGAACTCTT\t1\n+CATGACTTTATTGACGGCTTGCTC\t1\n+TAAAAAATCGGCGCAGTTTATG\t1\n+TTGAATCGTACAGTACGCGCTATT\t1\n+GTGTACAATATGACCTCGTGTGGCCA\t1\n' |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/size/histogram.png |
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| Binary file test-data/res_files/reads-sample-small.fastq/size/histogram.png has changed |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/size/reads_size.txt --- a/test-data/res_files/reads-sample-small.fastq/size/reads_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/size/reads_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,13 +1,13 @@ size number percentage -18 859 1.89 -19 895 1.96 -20 1611 3.54 -21 3934 8.63 -22 4498 9.87 -23 7700 16.90 -24 11572 25.39 -25 10297 22.60 -26 3341 7.33 -27 531 1.17 -28 304 0.67 -29 28 0.06 +18 82 1.78 +19 90 1.95 +20 177 3.84 +21 390 8.46 +22 458 9.93 +23 787 17.07 +24 1149 24.92 +25 1034 22.43 +26 355 7.70 +27 56 1.21 +28 28 0.61 +29 4 0.09 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I.html --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I.html Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,295 +0,0 @@\n-\n- <!DOCTYPE html>\n- <html lang="en">\n- <head>\n- <meta charset="utf-8">\n- <title>pipeline</title>\n- <meta name="viewport" content="width=device-width, initial-scale=1.0">\n- <meta name="description" content="">\n- <meta name="author" content="">\n- <!-- Le styles -->\n- <link href="css/bootstrap.css" rel="stylesheet">\n- <link href="css/bootstrap-table.css" rel="stylesheet">\n- <style type="text/css">\n- body {\n- padding-top: 60px;\n- padding-bottom: 40px;\n- }\n- div#page {\n- width: 940px;\n- background-color: #fff;\n- margin: 0 auto;\n- text-align: left;\n- border-color: #fff;\n- border-style: none solid solid;\n- border-width: medium 1px 1px;\n- }\n-\n- div.content {\n- \tdisplay: none;\n-\t float: right;\n-\t width: 550px;\n- }\n- div.content a, div.navigation a {\n- text-decoration: none;\n- \tcolor: #777;\n- }\n- div.content a:focus, div.content a:hover, div.content a:active {\n- text-decoration: underline;\n- }\n- \n- div.controls {\n- margin-top: 5px;\n-\t height: 23px;\n- }\n- \n- div.controls a {\n-\t padding: 5px;\n- }\n- div.ss-controls {\n-\t float: left;\n- }\n- div.nav-controls {\n-\t float: right;\n- }\n- div.slideshow-container {\n-\t position: relative;\n-\t clear: both;\n-\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- }\n- div.loader {\n- \tposition: absolute;\n- \ttop: 0;\n- \tleft: 0;\n- background-image: url(\'loader.gif\');\n- background-repeat: no-repeat;\n- background-position: center;\n- \twidth: 550px;\n- \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- }\n- div.slideshow {\n- \n- }\n- \n- div.slideshow span.image-wrapper {\n-\t display: block;\n-\t position: absolute;\n-\t top: 0;\n-\t left: 0;\n- }\n- div.slideshow a.advance-link {\n-\t display: block;\n- \t width: 550px;\n- height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- text-align: center;\n- }\n- div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n- text-decoration: none;\n- }\n- div.slideshow img {\n- vertical-align: middle;\n-\tborder: 1px solid #ccc;\n- }\n-\n- div.image-title {\n- font-weight: bold;\n- font-size: 1.4em;\n- }\n-\n- div.image-desc {\n- line-height: 1.3em;\n- padding-top: 12px;\n- }\n- div.navigation {\n-\n- }\n- ul.thumbs {\n-\tclear: both;\n-\tmargin: 0;\n-\tpadding: 0;\n- }\n- ul.thumbs li {\n-\tfloat: none;\n-\tpadding: 0;\n-\tmargin: 0;\n- list-style: none;\n- }\n- a.thumb {\n-\tpadding: 0;\n-\tdisplay: inline;\n-\tborder: none;\n- }\n- ul.thumbs li.selected a.thumb {\n-\tcolor: #000;\n- font-weight: bold;\n- }\n- a.thumb:focus {\n-\toutline: none;\n- }\n- ul.thumbs img {\n-\tborder: none;\n-\tdisplay: block;\n- }\n- div.pagination {\n-\tclear: both;\n- }\n- div.navigation div.top {\n- margin-bottom: 12px;\n-\theight: 11px;\n- }\n- div.navigation div.bottom {\n- margin-top: 12px;\n- }\n- div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n-\tdisplay: block;\n-\tfloat: left;\n- margin-right: 2px;\n-\tpadding: 4px 7px 2px 7px;\n-\tborder: 1px solid #ccc;\n- }\n- div.pagination a:hover {\n- background-color: #eee;\n- text-decoration: none;\n- }\n- div.pagination span.current {\n- font-weight: bold;\n- background-color: #000;\n- border-color: #000;\n-\tcolor: #fff;\n- }\n- div.pagination span.ellipsis {\n-\tborder: none;\n-\tpadding: 5px 0 3px 2px;\n- }\n- \n- div.download {\n-\tfloat: right;\n- }\n- \n- div.caption-container {\n-\tposition: relative;\n-\tclear: left;\n-\theight: 75px;\n- }\n- span.image-caption {\n-\tdisplay: block;\n-\tposition: absolute;\n-\twidth: 550px;\n-\ttop: 0;\n-\tleft: 0;\n- }\n- div.caption {\n-\tpadding: 12px;\n- }\n-\n- /* Featurettes\n- ------------------------- */\n-\n- .featurette {\n- padding-top: 20px; /* Vertica'..b'ter images part 2: clear their floats. */\n- text-align: center;\n- }\n-\n- .featurette-p\n- {\n- text-align: left;\n- }\n-\n- .featurette-image {\n- margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n- width: 450px;\n- height: auto;\n- }\n-\n- </style>\n- <link href="css/bootstrap-responsive.css" rel="stylesheet">\n- </head>\n- <body>\n- \n-\t\t\t\t\t<div align="center">\n-\t\t\t\t\t<h2>BATUMI_I</h2>\n-\t\t\t\t\t<p> <img class="featurette-image" src="BATUMI_I/histogram.png"/></p>\n-\t\t\t\t\t<p><a href="BATUMI_I/overlap_size.txt">ping pong signature</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_I/sensPPP.txt">sense reads with PPP</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_I/antisensPPP.txt">reverse reads with PPP</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_I/sens.txt">sense reads without PPP</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_I/antisens.txt">reverse reads without PPP</a></p>\n-\t\t\t\t\t</div>\n- <!-- FOOTER -->\n- <div class="container">\n- <footer>\n- \n- </footer>\n- </div>\n- <!-- Le javascript\n- ================================================== -->\n- <!-- Placed at the end of the document so the pages load faster -->\n- <script type="text/javascript" src="js/filter.js"></script>\n- <script type="text/javascript" src="js/jquery.js"></script>\n- <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n- <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n- <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n- <script type="text/javascript" src="js/bootstrap-table.js"></script>\n- <script type="text/javascript" src="js/bootstrap.min.js"></script>\n- <script type="text/javascript">\n- jQuery(document).ready(function($) {\n- // We only want these styles applied when javascript is enabled\n- $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n- $(\'div.content\').css(\'display\', \'block\');\n- \n- $(".each-gallery").each(function(i){\n- // Initially set opacity on thumbs and add\n- // additional styling for hover effect on thumbs\n- var onMouseOutOpacity = 0.67;\n- $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n- mouseOutOpacity: onMouseOutOpacity,\n- mouseOverOpacity: 1.0,\n- fadeSpeed: \'fast\',\n- exemptionSelector: \'.selected\'\n- });\n- \n- // Initialize Advanced Galleriffic Gallery\n- var gallery = $(\'#thumbs\'+i).galleriffic({\n- delay: 2500,\n- numThumbs: 22,\n- preloadAhead: 10,\n- enableTopPager: true,\n- enableBottomPager: true,\n- maxPagesToShow: 7,\n- imageContainerSel: \'#slideshow\'+ i,\n- controlsContainerSel: \'#controls\' + i,\n- captionContainerSel: \'#caption\' + i,\n- loadingContainerSel: \'#loading\' + i,\n- renderSSControls: true,\n- renderNavControls: true,\n- playLinkText: \'Play\',\n- pauseLinkText: \'Pause\',\n- prevLinkText: \'‹ Previous\',\n- nextLinkText: \'Next ›\',\n- nextPageLinkText: \'Next ›\',\n- prevPageLinkText: \'‹ Prev\',\n- enableHistory: false,\n- autoStart: false,\n- syncTransitions: true,\n- defaultTransitionDuration: 900,\n- onSlideChange: function(prevIndex, nextIndex) {\n- // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n- this.find(\'ul.thumbs\').children()\n- .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n- .eq(nextIndex).fadeTo(\'fast\', 1.0);\n- },\n- onPageTransitionOut: function(callback) {\n- this.fadeTo(\'fast\', 0.0, callback);\n- },\n- onPageTransitionIn: function() {\n- this.fadeTo(\'fast\', 1.0);\n- }\n- });\n- });\n- });\n- </script>\n- </body>\n- </html>\n- \n\\ No newline at end of file\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,116 +0,0 @@ ->5|16|BATUMI_I|3 -CAGGTTATCCGGCTCGAAGGACC ->5|16|BATUMI_I|1 -TCCAGGTTATCCGGCTCGAAGGACC ->13|16|BATUMI_I|1 -TGAAAATCCAGGTTATCCGGCTC ->15|16|BATUMI_I|1 -ACTTGAAAATCCAGGTTATCCGGC ->23|16|BATUMI_I|1 -GGTGGACAAACTTGAAAATCCAGGT ->26|16|BATUMI_I|1 -TGGTGGACAAACTTGAAAATCCA ->54|16|BATUMI_I|1 -TTTCGTACTTATCTTATAATTTG ->94|16|BATUMI_I|1 -TTCGAAACTTTTGCTGCAGACCGGCA ->96|16|BATUMI_I|1 -TTTTCGAAACTTTTGCTGCAGACCGG ->97|16|BATUMI_I|1 -TTTTCGAAACTTTTGCTGCAGACCG ->98|16|BATUMI_I|1 -TTTCGAAACTTTTGCTGCAGACC ->120|16|BATUMI_I|1 -TACAGCAAATTGAACGAAATTGGATT ->124|16|BATUMI_I|1 -TCTTACAGCAAATTGAACGAAATTG ->161|16|BATUMI_I|3 -TTTTGTCGGAGAAATCCGTTAGA ->161|16|BATUMI_I|1 -CCTTTTGTCGGAGAAATCCGTTAGA ->161|16|BATUMI_I|1 -GCCTTTTGTCGGAGAAATCCGTTAGA ->165|16|BATUMI_I|1 -TGCCTTTTGTCGGAGAAATCCGT ->165|16|BATUMI_I|1 -TTGCCTTTTGTCGGAGAAATCCGT ->166|16|BATUMI_I|2 -TTGCCTTTTGTCGGAGAAATCCG ->166|16|BATUMI_I|1 -TAATTGCCTTTTGTCGGAGAAATCCG ->170|16|BATUMI_I|1 -TCTTTAATTGCCTTTTGTCGGAGAAA ->215|16|BATUMI_I|1 -CGGTGGGTAATATGGCGGCGCCCGT ->248|16|BATUMI_I|1 -TTCACGAATGAGGGTGAAAGGAG ->262|16|BATUMI_I|1 -TTGGACTTAGAAATTTTCACGAAT ->296|16|BATUMI_I|1 -TGGACTGGATGAATATTTAAATATA ->296|16|BATUMI_I|2 -TTGGACTGGATGAATATTTAAATATA ->298|16|BATUMI_I|1 -TTGGACTGGATGAATATTTAAATA ->349|16|BATUMI_I|2 -TCACTGAACTTGGCACAAATTATTTT ->350|16|BATUMI_I|4 -TCACTGAACTTGGCACAAATTATTT ->351|16|BATUMI_I|11 -TCACTGAACTTGGCACAAATTATT ->353|16|BATUMI_I|1 -TTTCACTGAACTTGGCACAAATTA ->354|16|BATUMI_I|2 -TTTTCACTGAACTTGGCACAAATT ->355|16|BATUMI_I|1 -ATTTTCACTGAACTTGGCACAAAT ->355|16|BATUMI_I|1 -AATTTTCACTGAACTTGGCACAAAT ->358|16|BATUMI_I|2 -TAGAAATTTTCACTGAACTTGGCACA ->359|16|BATUMI_I|3 -TAGAAATTTTCACTGAACTTGGCAC ->359|16|BATUMI_I|2 -TTAGAAATTTTCACTGAACTTGGCAC ->360|16|BATUMI_I|4 -TAGAAATTTTCACTGAACTTGGCA ->360|16|BATUMI_I|12 -TTAGAAATTTTCACTGAACTTGGCA ->361|16|BATUMI_I|5 -TTAGAAATTTTCACTGAACTTGGC ->370|16|BATUMI_I|1 -GCTTTGGACTTAGAAATTTTCACT ->370|16|BATUMI_I|1 -AGCTTTGGACTTAGAAATTTTCACT ->371|16|BATUMI_I|1 -GCTTTGGACTTAGAAATTTTCAC ->379|16|BATUMI_I|2 -TTTTGGCAGAGCTTTGGACTTAGAA ->380|16|BATUMI_I|1 -TTTGGCAGAGCTTTGGACTTAGA ->380|16|BATUMI_I|1 -TTTTGGCAGAGCTTTGGACTTAGA ->384|16|BATUMI_I|2 -TGCCACTTTTGGCAGAGCTTTGGACT ->385|16|BATUMI_I|1 -CCACTTTTGGCAGAGCTTTGGAC ->385|16|BATUMI_I|5 -TGCCACTTTTGGCAGAGCTTTGGAC ->385|16|BATUMI_I|5 -TTGCCACTTTTGGCAGAGCTTTGGAC ->385|16|BATUMI_I|2 -TTTGCCACTTTTGGCAGAGCTTTGGAC ->386|16|BATUMI_I|2 -TGCCACTTTTGGCAGAGCTTTGGA ->414|16|BATUMI_I|1 -TTGGACACAGTGAAACGAGAACACAA ->419|16|BATUMI_I|3 -TGCGTTGGACACAGTGAAACGAGAA ->420|16|BATUMI_I|4 -TGCGTTGGACACAGTGAAACGAGA ->421|16|BATUMI_I|1 -TTGCGTTGGACACAGTGAAACGAG ->485|16|BATUMI_I|1 -AAGCAAATTGTATTAAGTGGACTG ->7078|16|BATUMI_I|1 -TCCTTGGAGACTCTGTGGTGAAGA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->7005|16|BATUMI_I|3 -TGACAGTCCAAACCCCGTAACTTG ->7006|16|BATUMI_I|2 -TGACAGTCCAAACCCCGTAACTT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -size number percentage of the total overlap number -1 1 1.09 -2 2 2.17 -3 0 0.00 -4 0 0.00 -5 0 0.00 -6 0 0.00 -7 2 2.17 -8 1 1.09 -9 0 0.00 -10 22 23.91 -11 22 23.91 -12 11 11.96 -13 0 0.00 -14 0 0.00 -15 0 0.00 -16 1 1.09 -17 2 2.17 -18 0 0.00 -19 7 7.61 -20 6 6.52 -21 7 7.61 -22 3 3.26 -23 5 5.43 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,52 +0,0 @@ ->1|0|BATUMI_I|1 -TTTTTTGGTCCTTCGAGCCGGATA ->2|0|BATUMI_I|1 -TTTGGTCCTTCGAGCCGGATAACCT ->7|0|BATUMI_I|1 -TCCTTCGAGCCGGATAACCTGGATTT ->120|0|BATUMI_I|2 -AATCCAATTTCGTTCAATTTGCTGT ->151|0|BATUMI_I|1 -TATTGTCAAATCTAACGGATTTCTCC ->161|0|BATUMI_I|1 -TCTAACGGATTTCTCCGACAAAAGG ->387|0|BATUMI_I|1 -CCAAAGCTCTGCCAAAAGTGGCAAA ->418|0|BATUMI_I|1 -GTTCTCGTTTCACTGTGTCCAACGC ->419|0|BATUMI_I|1 -TTCTCGTTTCACTGTGTCCAACGC ->419|0|BATUMI_I|2 -TTCTCGTTTCACTGTGTCCAACGCA ->419|0|BATUMI_I|1 -TTCTCGTTTCACTGTGTCCAACGCAA ->420|0|BATUMI_I|1 -TCTCGTTTCACTGTGTCCAACGCA ->7007|0|BATUMI_I|1 -AGTTACGGGGTTTGGACTGTCACCC ->7008|0|BATUMI_I|1 -GTTACGGGGTTTGGACTGTCACCC ->7009|0|BATUMI_I|3 -TTACGGGGTTTGGACTGTCACCC ->7010|0|BATUMI_I|1 -TACGGGGTTTGGACTGTCACCCGC ->7010|0|BATUMI_I|5 -TACGGGGTTTGGACTGTCACCCGCT ->7017|0|BATUMI_I|1 -TTTGGACTGTCACCCGCTCTCCGC ->7017|0|BATUMI_I|11 -TTTGGACTGTCACCCGCTCTCCGCT ->7017|0|BATUMI_I|1 -TTTGGACTGTCACCCGCTCTCCGCTC ->7017|0|BATUMI_I|1 -TTTGGACTGTCACCCGCTCTCCGCTCC ->7018|0|BATUMI_I|7 -TTGGACTGTCACCCGCTCTCCGC ->7018|0|BATUMI_I|13 -TTGGACTGTCACCCGCTCTCCGCT ->7018|0|BATUMI_I|3 -TTGGACTGTCACCCGCTCTCCGCTC ->7018|0|BATUMI_I|16 -TTGGACTGTCACCCGCTCTCCGCTCC ->7018|0|BATUMI_I|1 -TTGGACTGTCACCCGCTCTCCGCTCCC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ ->7019|0|BATUMI_I|15 -TGGACTGTCACCCGCTCTCCGCT ->7019|0|BATUMI_I|4 -TGGACTGTCACCCGCTCTCCGCTC ->7019|0|BATUMI_I|31 -TGGACTGTCACCCGCTCTCCGCTCC ->7019|0|BATUMI_I|9 -TGGACTGTCACCCGCTCTCCGCTCCC ->7019|0|BATUMI_I|1 -TGGACTGTCACCCGCTCTCCGCTCCCT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR.html --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR.html Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,295 +0,0 @@\n-\n- <!DOCTYPE html>\n- <html lang="en">\n- <head>\n- <meta charset="utf-8">\n- <title>pipeline</title>\n- <meta name="viewport" content="width=device-width, initial-scale=1.0">\n- <meta name="description" content="">\n- <meta name="author" content="">\n- <!-- Le styles -->\n- <link href="css/bootstrap.css" rel="stylesheet">\n- <link href="css/bootstrap-table.css" rel="stylesheet">\n- <style type="text/css">\n- body {\n- padding-top: 60px;\n- padding-bottom: 40px;\n- }\n- div#page {\n- width: 940px;\n- background-color: #fff;\n- margin: 0 auto;\n- text-align: left;\n- border-color: #fff;\n- border-style: none solid solid;\n- border-width: medium 1px 1px;\n- }\n-\n- div.content {\n- \tdisplay: none;\n-\t float: right;\n-\t width: 550px;\n- }\n- div.content a, div.navigation a {\n- text-decoration: none;\n- \tcolor: #777;\n- }\n- div.content a:focus, div.content a:hover, div.content a:active {\n- text-decoration: underline;\n- }\n- \n- div.controls {\n- margin-top: 5px;\n-\t height: 23px;\n- }\n- \n- div.controls a {\n-\t padding: 5px;\n- }\n- div.ss-controls {\n-\t float: left;\n- }\n- div.nav-controls {\n-\t float: right;\n- }\n- div.slideshow-container {\n-\t position: relative;\n-\t clear: both;\n-\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- }\n- div.loader {\n- \tposition: absolute;\n- \ttop: 0;\n- \tleft: 0;\n- background-image: url(\'loader.gif\');\n- background-repeat: no-repeat;\n- background-position: center;\n- \twidth: 550px;\n- \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- }\n- div.slideshow {\n- \n- }\n- \n- div.slideshow span.image-wrapper {\n-\t display: block;\n-\t position: absolute;\n-\t top: 0;\n-\t left: 0;\n- }\n- div.slideshow a.advance-link {\n-\t display: block;\n- \t width: 550px;\n- height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- text-align: center;\n- }\n- div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n- text-decoration: none;\n- }\n- div.slideshow img {\n- vertical-align: middle;\n-\tborder: 1px solid #ccc;\n- }\n-\n- div.image-title {\n- font-weight: bold;\n- font-size: 1.4em;\n- }\n-\n- div.image-desc {\n- line-height: 1.3em;\n- padding-top: 12px;\n- }\n- div.navigation {\n-\n- }\n- ul.thumbs {\n-\tclear: both;\n-\tmargin: 0;\n-\tpadding: 0;\n- }\n- ul.thumbs li {\n-\tfloat: none;\n-\tpadding: 0;\n-\tmargin: 0;\n- list-style: none;\n- }\n- a.thumb {\n-\tpadding: 0;\n-\tdisplay: inline;\n-\tborder: none;\n- }\n- ul.thumbs li.selected a.thumb {\n-\tcolor: #000;\n- font-weight: bold;\n- }\n- a.thumb:focus {\n-\toutline: none;\n- }\n- ul.thumbs img {\n-\tborder: none;\n-\tdisplay: block;\n- }\n- div.pagination {\n-\tclear: both;\n- }\n- div.navigation div.top {\n- margin-bottom: 12px;\n-\theight: 11px;\n- }\n- div.navigation div.bottom {\n- margin-top: 12px;\n- }\n- div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n-\tdisplay: block;\n-\tfloat: left;\n- margin-right: 2px;\n-\tpadding: 4px 7px 2px 7px;\n-\tborder: 1px solid #ccc;\n- }\n- div.pagination a:hover {\n- background-color: #eee;\n- text-decoration: none;\n- }\n- div.pagination span.current {\n- font-weight: bold;\n- background-color: #000;\n- border-color: #000;\n-\tcolor: #fff;\n- }\n- div.pagination span.ellipsis {\n-\tborder: none;\n-\tpadding: 5px 0 3px 2px;\n- }\n- \n- div.download {\n-\tfloat: right;\n- }\n- \n- div.caption-container {\n-\tposition: relative;\n-\tclear: left;\n-\theight: 75px;\n- }\n- span.image-caption {\n-\tdisplay: block;\n-\tposition: absolute;\n-\twidth: 550px;\n-\ttop: 0;\n-\tleft: 0;\n- }\n- div.caption {\n-\tpadding: 12px;\n- }\n-\n- /* Featurettes\n- ------------------------- */\n-\n- .featurette {\n- padding-top: 20px; /* Vertica'..b't 2: clear their floats. */\n- text-align: center;\n- }\n-\n- .featurette-p\n- {\n- text-align: left;\n- }\n-\n- .featurette-image {\n- margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n- width: 450px;\n- height: auto;\n- }\n-\n- </style>\n- <link href="css/bootstrap-responsive.css" rel="stylesheet">\n- </head>\n- <body>\n- \n-\t\t\t\t\t<div align="center">\n-\t\t\t\t\t<h2>BATUMI_LTR</h2>\n-\t\t\t\t\t<p> <img class="featurette-image" src="BATUMI_LTR/histogram.png"/></p>\n-\t\t\t\t\t<p><a href="BATUMI_LTR/overlap_size.txt">ping pong signature</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_LTR/sensPPP.txt">sense reads with PPP</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_LTR/antisensPPP.txt">reverse reads with PPP</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_LTR/sens.txt">sense reads without PPP</a></p>\n-\t\t\t\t\t<p><a href="BATUMI_LTR/antisens.txt">reverse reads without PPP</a></p>\n-\t\t\t\t\t</div>\n- <!-- FOOTER -->\n- <div class="container">\n- <footer>\n- \n- </footer>\n- </div>\n- <!-- Le javascript\n- ================================================== -->\n- <!-- Placed at the end of the document so the pages load faster -->\n- <script type="text/javascript" src="js/filter.js"></script>\n- <script type="text/javascript" src="js/jquery.js"></script>\n- <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n- <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n- <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n- <script type="text/javascript" src="js/bootstrap-table.js"></script>\n- <script type="text/javascript" src="js/bootstrap.min.js"></script>\n- <script type="text/javascript">\n- jQuery(document).ready(function($) {\n- // We only want these styles applied when javascript is enabled\n- $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n- $(\'div.content\').css(\'display\', \'block\');\n- \n- $(".each-gallery").each(function(i){\n- // Initially set opacity on thumbs and add\n- // additional styling for hover effect on thumbs\n- var onMouseOutOpacity = 0.67;\n- $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n- mouseOutOpacity: onMouseOutOpacity,\n- mouseOverOpacity: 1.0,\n- fadeSpeed: \'fast\',\n- exemptionSelector: \'.selected\'\n- });\n- \n- // Initialize Advanced Galleriffic Gallery\n- var gallery = $(\'#thumbs\'+i).galleriffic({\n- delay: 2500,\n- numThumbs: 22,\n- preloadAhead: 10,\n- enableTopPager: true,\n- enableBottomPager: true,\n- maxPagesToShow: 7,\n- imageContainerSel: \'#slideshow\'+ i,\n- controlsContainerSel: \'#controls\' + i,\n- captionContainerSel: \'#caption\' + i,\n- loadingContainerSel: \'#loading\' + i,\n- renderSSControls: true,\n- renderNavControls: true,\n- playLinkText: \'Play\',\n- pauseLinkText: \'Pause\',\n- prevLinkText: \'‹ Previous\',\n- nextLinkText: \'Next ›\',\n- nextPageLinkText: \'Next ›\',\n- prevPageLinkText: \'‹ Prev\',\n- enableHistory: false,\n- autoStart: false,\n- syncTransitions: true,\n- defaultTransitionDuration: 900,\n- onSlideChange: function(prevIndex, nextIndex) {\n- // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n- this.find(\'ul.thumbs\').children()\n- .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n- .eq(nextIndex).fadeTo(\'fast\', 1.0);\n- },\n- onPageTransitionOut: function(callback) {\n- this.fadeTo(\'fast\', 0.0, callback);\n- },\n- onPageTransitionIn: function() {\n- this.fadeTo(\'fast\', 1.0);\n- }\n- });\n- });\n- });\n- </script>\n- </body>\n- </html>\n- \n\\ No newline at end of file\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,38 +0,0 @@ ->70|16|BATUMI_LTR|1 -TCCTTGGAGACTCTGTGGTGAAGA ->100|16|BATUMI_LTR|1 -TAATTAGTTAGGCTCTCCCAAGCGC ->103|16|BATUMI_LTR|1 -TTCTAATTAGTTAGGCTCTCCCAAG ->106|16|BATUMI_LTR|34 -TTATTCTAATTAGTTAGGCTCTCCC ->107|16|BATUMI_LTR|30 -TTATTCTAATTAGTTAGGCTCTCC ->108|16|BATUMI_LTR|1 -TTATTCTAATTAGTTAGGCTCTC ->112|16|BATUMI_LTR|1 -CTGGTGCTTATTCTAATTAGTTAGGC ->178|16|BATUMI_LTR|2 -CACTAGACTTTTCATAATTGCGCGG ->180|16|BATUMI_LTR|1 -CACTAGACTTTTCATAATTGCGC ->192|16|BATUMI_LTR|1 -GAAGAAAAGCGAACACTAGACTTT ->193|16|BATUMI_LTR|1 -CGAAGAAAAGCGAACACTAGACTT ->193|16|BATUMI_LTR|1 -TCGAAGAAAAGCGAACACTAGACTT ->193|16|BATUMI_LTR|1 -CTCGAAGAAAAGCGAACACTAGACTT ->194|16|BATUMI_LTR|4 -TCGAAGAAAAGCGAACACTAGACT ->194|16|BATUMI_LTR|1 -CTCGAAGAAAAGCGAACACTAGACT ->194|16|BATUMI_LTR|1 -ACTCGAAGAAAAGCGAACACTAGACT ->205|16|BATUMI_LTR|1 -AAAAGAAACACTCGAAGAAAAGCG ->208|16|BATUMI_LTR|1 -TGAAAAGAAACACTCGAAGAAAA ->218|16|BATUMI_LTR|1 -TTCCAAATATGCTGAAAAGAAACAC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ ->103|16|BATUMI_LTR|1 -ATTCTAATTAGTTAGGCTCTCCCAAG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -size number percentage of the total overlap number -1 0 0.00 -2 0 0.00 -3 0 0.00 -4 0 0.00 -5 0 0.00 -6 1 7.69 -7 2 15.38 -8 0 0.00 -9 1 7.69 -10 1 7.69 -11 0 0.00 -12 3 23.08 -13 0 0.00 -14 0 0.00 -15 0 0.00 -16 0 0.00 -17 0 0.00 -18 0 0.00 -19 1 7.69 -20 1 7.69 -21 1 7.69 -22 2 15.38 -23 0 0.00 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->33|0|BATUMI_LTR|1 -TGTCACCCGCTCTCCGCTCCCTCTT ->196|0|BATUMI_LTR|1 -TCTAGTGTTCGCTTTTCTTCGAG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ ->119|0|BATUMI_LTR|1 -TAATTAGAATAAGCACCAGTGTCA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,1770 +1,436 @@\n->13|16|BS2|2\n-TGCGTATTGTTAGACACGAACCT\n->14|16|BS2|1\n-AGGTGCGTATTGTTAGACACGAACC\n->120|16|BS2|1\n-TTCACTGTTAGTGACTTGGGGGGTCAC\n->122|16|BS2|4\n+>122|16|BS2|1\n TTCACTGTTAGTGACTTGGGGGGTC\n->122|16|BS2|1\n-CACTGTTAGTGACTTGGGGGGTC\n->135|16|BS2|2\n+>135|16|BS2|1\n TTTCACTATTATTTCACTGTTAGT\n >139|16|BS2|1\n TTCGTTTCACTATTATTTCACTGT\n->140|16|BS2|3\n-TTTCGTTTCACTATTATTTCACTG\n->206|16|BS2|1\n-CGCGTGGCAGCTGGGCAGCGGAGCC\n >215|16|BS2|1\n-TTTGTGCGATCGCGTGGCAGCTGGGC\n->215|16|BS2|5\n TTGTGCGATCGCGTGGCAGCTGGGC\n->215|16|BS2|1\n-TGTGCGATCGCGTGGCAGCTGGGC\n->216|16|BS2|1\n-TTTGTGCGATCGCGTGGCAGCTGGG\n->216|16|BS2|1\n-TTGTGCGATCGCGTGGCAGCTGGG\n >216|16|BS2|1\n TGTGCGATCGCGTGGCAGCTGGG\n->217|16|BS2|2\n-TTTGTGCGATCGCGTGGCAGCTGG\n->217|16|BS2|1\n-TTGTGCGATCGCGTGGCAGCTGG\n->218|16|BS2|2\n-TGTTTGTGCGATCGCGTGGCAGCTG\n->218|16|BS2|16\n+>218|16|BS2|5\n TTTGTGCGATCGCGTGGCAGCTG\n->219|16|BS2|1\n-TGTTTGTGCGATCGCGTGGCAGCT\n->219|16|BS2|1\n-GTTTGTGCGATCGCGTGGCAGCT\n->220|16|BS2|1\n-TGTTTGTGCGATCGCGTGGCAGC\n->221|16|BS2|1\n-GCTGTTTGTGCGATCGCGTGGCAG\n->222|16|BS2|1\n-ACAGCTGTTTGTGCGATCGCGTGGCA\n->226|16|BS2|1\n-AACAGCTGTTTGTGCGATCGCGT\n->237|16|BS2|1\n-TTTAAGCTCGCAAACAGCTGTTTG\n->252|16|BS2|1\n-CCCTGGGATAGAAAGCTTTAAGCTC\n >262|16|BS2|1\n AACTTGAACCCTGGGATAGAAAG\n >264|16|BS2|1\n CAAAACTTGAACCCTGGGATAGAA\n->264|16|BS2|1\n-AAAACTTGAACCCTGGGATAGAA\n->268|16|BS2|1\n-TCTAGCCAAAACTTGAACCCTGGGAT\n->268|16|BS2|1\n-TAGCCAAAACTTGAACCCTGGGAT\n->269|16|BS2|11\n+>269|16|BS2|1\n TCTAGCCAAAACTTGAACCCTGGGA\n->270|16|BS2|3\n-TCTAGCCAAAACTTGAACCCTGGG\n->271|16|BS2|1\n-TCTAGCCAAAACTTGAACCCTGG\n->357|16|BS2|1\n-AGAGAAACGCAGTATCCAACGAT\n->368|16|BS2|1\n-TTGGGGGCTCGAGAGAAACGCAG\n->381|16|BS2|2\n+>381|16|BS2|1\n TGCGGGGCAGCACATTGGGGGCTC\n->381|16|BS2|3\n-GCGGGGCAGCACATTGGGGGCTC\n->382|16|BS2|1\n-TGCGGGGCAGCACATTGGGGGCT\n->395|16|BS2|1\n-TATTTTTTGAAAGCGCTGCGGGGCAG\n->395|16|BS2|1\n-TTTTTTGAAAGCGCTGCGGGGCAG\n >422|16|BS2|1\n TCCGGAGAAGCACGAGACTTTCGCT\n->425|16|BS2|1\n-TCTCCGGAGAAGCACGAGACTTTC\n->439|16|BS2|1\n-TTTTTTCCTTTCAGTCTCCGGAGA\n->444|16|BS2|3\n-TTTGGGTTTTTTCCTTTCAGTCTCC\n->467|16|BS2|2\n-TCCCCTTGTTTGCCGATGGTTGATT\n->468|16|BS2|1\n-TTTCCCCTTGTTTGCCGATGGTTGAT\n->469|16|BS2|1\n-TTTCCCCTTGTTTGCCGATGGTTGA\n->470|16|BS2|2\n-TTTCCCCTTGTTTGCCGATGGTTG\n->484|16|BS2|1\n-TTCTGTAGCCGAAGGGTTTTCCCCTTG\n->485|16|BS2|5\n-TTCTGTAGCCGAAGGGTTTTCCCCTT\n->486|16|BS2|1\n-TTCTGTAGCCGAAGGGTTTTCCCCT\n->487|16|BS2|1\n-TTCTGTAGCCGAAGGGTTTTCCCC\n->492|16|BS2|1\n-TAGGTTCTGTAGCCGAAGGGTTT\n->493|16|BS2|2\n-TATCTAGGTTCTGTAGCCGAAGGGTT\n->496|16|BS2|5\n-TATCTAGGTTCTGTAGCCGAAGG\n->497|16|BS2|2\n-GCCATATCTAGGTTCTGTAGCCGAAG\n->499|16|BS2|1\n-CGCCATATCTAGGTTCTGTAGCCGA\n->499|16|BS2|1\n-GCCATATCTAGGTTCTGTAGCCGA\n->501|16|BS2|1\n-CGCCATATCTAGGTTCTGTAGCC\n->504|16|BS2|1\n-TTGCCGCCATATCTAGGTTCTGTA\n->520|16|BS2|1\n-TAAACCAAATCGGTTTGAATTGCCGCC\n->523|16|BS2|1\n-AGTAAACCAAATCGGTTTGAATTGCC\n->550|16|BS2|1\n-TTGTTTGTCAGCTGTGAGATGCGC\n->551|16|BS2|1\n-TTGTTTGTCAGCTGTGAGATGCG\n->552|16|BS2|4\n+>552|16|BS2|5\n+TACTTGTTTGTCAGCTGTGAGATGC\n+>552|16|BS2|2\n ACTTGTTTGTCAGCTGTGAGATGC\n->561|16|BS2|1\n-TTCATTGCCTACTTGTTTGTCAGCT\n->562|16|BS2|1\n-TTCATTGCCTACTTGTTTGTCAGC\n >574|16|BS2|1\n TACAGATCGCCAATTTCATTGCCTAC\n->576|16|BS2|1\n-TACAGATCGCCAATTTCATTGCCT\n->577|16|BS2|1\n-TACAGATCGCCAATTTCATTGCC\n->588|16|BS2|1\n-CTGGGCTGGTCATACAGATCGCCA\n->589|16|BS2|31\n+>589|16|BS2|6\n TACTGGGCTGGTCATACAGATCGCC\n->589|16|BS2|1\n-ACTGGGCTGGTCATACAGATCGCC\n->590|16|BS2|8\n+>590|16|BS2|1\n TACTGGGCTGGTCATACAGATCGC\n->592|16|BS2|5\n-TGGTACTGGGCTGGTCATACAGATC\n->593|16|BS2|1\n-TGGTACTGGGCTGGTCATACAGAT\n->600|16|BS2|1\n-TTGATGACTGGTACTGGGCTGGTCA\n->601|16|BS2|1\n-TTGATGACTGGTACTGGGCTGGTC\n->602|16|BS2|3\n-TTGATGACTGGTACTGGGCTGGT\n->603|16|BS2|1\n-CTTGATGACTGGTACTGGGCTGG\n->606|16|BS2|12\n-TGCAGCTTGATGACTGGTACTGGGC\n >606|16|BS2|2\n-GCAGCTTGATGACTGGTACTGGGC\n->610|16|BS2|2\n-AATTGCAGCTTGATGACTGGTACT\n->613|16|BS2|1\n-GCAATTGCAGCTTGATGACTGGT\n->617|16|BS2|1\n-GCGGCAGCAATTGCAGCTTGATGAC\n->635|16|BS2|1\n-GGCTGCATCCCGCTTAGCGGCAG\n->649|16|BS2|1\n-TAGTGGTACCAGCGGAGGCTGCATC\n->649|16|BS2|1\n-AGTGGTACCAGCGGAGGCTGCATC\n->651|16|BS2|1\n-TAGTGGTACCAGCGGAGGCTGCA\n->653|16|BS2|2\n-TGAGCTAGTGGTACCAGCGGAGGCTG\n->655|16|BS2|1\n'..b'TCC\n->4311|16|BS2|1\n-ACTCGCAGCCGGTGATGAGTCTTGC\n->4311|16|BS2|1\n-CTCGCAGCCGGTGATGAGTCTTGC\n->4317|16|BS2|1\n-CAAACCACTCGCAGCCGGTGATGAG\n->4323|16|BS2|2\n-TTCGAACAAACCACTCGCAGCCGGT\n->4323|16|BS2|1\n-TCGAACAAACCACTCGCAGCCGGT\n->4325|16|BS2|1\n-TTCGAACAAACCACTCGCAGCCG\n->4347|16|BS2|2\n-TCAGGTCTCTGTGCAGGGTGGTGTT\n->4348|16|BS2|8\n-TCAGGTCTCTGTGCAGGGTGGTGT\n->4348|16|BS2|1\n-CAGGTCTCTGTGCAGGGTGGTGT\n->4349|16|BS2|8\n+>4349|16|BS2|1\n+TTCAGGTCTCTGTGCAGGGTGGTG\n+>4349|16|BS2|1\n TCAGGTCTCTGTGCAGGGTGGTG\n->4352|16|BS2|1\n-GTTTCAGGTCTCTGTGCAGGGTG\n->4353|16|BS2|1\n-TGCGAGTTTCAGGTCTCTGTGCAGGGT\n->4357|16|BS2|1\n-TTGCGAGTTTCAGGTCTCTGTGCA\n->4408|16|BS2|1\n-TCCAGCCTGTCATGGTATCTGCTCG\n->4412|16|BS2|1\n-TGGCGCTCCAGCCTGTCATGGTATCTG\n->4412|16|BS2|1\n-GGCGCTCCAGCCTGTCATGGTATCTG\n->4418|16|BS2|2\n-TTCTGTGGCGCTCCAGCCTGTCATGG\n+>4350|16|BS2|1\n+TTCAGGTCTCTGTGCAGGGTGGT\n+>4374|16|BS2|1\n+TTATTTCGTCAAATACCGTTGCGAG\n >4419|16|BS2|1\n TTTCTGTGGCGCTCCAGCCTGTCATG\n->4419|16|BS2|4\n+>4419|16|BS2|1\n TTCTGTGGCGCTCCAGCCTGTCATG\n >4421|16|BS2|1\n-TTTCTGTGGCGCTCCAGCCTGTCA\n->4421|16|BS2|2\n TTCTGTGGCGCTCCAGCCTGTCA\n->4422|16|BS2|1\n-TTTCTGTGGCGCTCCAGCCTGTC\n->4424|16|BS2|3\n-AGCCGATTTCTGTGGCGCTCCAGCCTG\n->4424|16|BS2|1\n-GCCGATTTCTGTGGCGCTCCAGCCTG\n->4424|16|BS2|2\n-CCGATTTCTGTGGCGCTCCAGCCTG\n->4424|16|BS2|1\n-CGATTTCTGTGGCGCTCCAGCCTG\n->4425|16|BS2|1\n-CAGCCGATTTCTGTGGCGCTCCAGCCT\n->4425|16|BS2|1\n-AGCCGATTTCTGTGGCGCTCCAGCCT\n->4426|16|BS2|1\n-CAGCCGATTTCTGTGGCGCTCCAGCC\n->4433|16|BS2|1\n-CGCTGGCCAGCCGATTTCTGTGGCGC\n >4433|16|BS2|1\n TGGCCAGCCGATTTCTGTGGCGC\n->4436|16|BS2|1\n-AGCGCTGGCCAGCCGATTTCTGTGG\n->4445|16|BS2|2\n-TGTTTAAAGCGCTGGCCAGCCGA\n->4450|16|BS2|1\n-AGATCTGTTTAAAGCGCTGGCCA\n->4456|16|BS2|1\n-TTGGTGGGCGAGATCTGTTTAAAGCGC\n->4456|16|BS2|1\n-GTGGGCGAGATCTGTTTAAAGCGC\n->4456|16|BS2|4\n+>4445|16|BS2|5\n+TCTGTTTAAAGCGCTGGCCAGCCGA\n+>4447|16|BS2|1\n+TCTGTTTAAAGCGCTGGCCAGCC\n+>4456|16|BS2|2\n TGGGCGAGATCTGTTTAAAGCGC\n->4458|16|BS2|1\n-TTGGTGGGCGAGATCTGTTTAAAGC\n >4459|16|BS2|1\n TTGGTGGGCGAGATCTGTTTAAAG\n->4462|16|BS2|1\n-TCCTTGGTGGGCGAGATCTGTTTA\n->4470|16|BS2|8\n-TATTGAGCCTCCTTGGTGGGCGAGA\n->4477|16|BS2|1\n-TGCCTTCTATTGAGCCTCCTTGGTG\n->4484|16|BS2|2\n-CCTCGGTTGCCTTCTATTGAGCCTC\n->4485|16|BS2|1\n-TCCCTCGGTTGCCTTCTATTGAGCCT\n->4485|16|BS2|1\n-CCCTCGGTTGCCTTCTATTGAGCCT\n->4485|16|BS2|1\n-CCTCGGTTGCCTTCTATTGAGCCT\n->4485|16|BS2|1\n-CTCGGTTGCCTTCTATTGAGCCT\n->4486|16|BS2|3\n-TCCCTCGGTTGCCTTCTATTGAGCC\n->4487|16|BS2|2\n-TCCCTCGGTTGCCTTCTATTGAGC\n->4493|16|BS2|2\n-TAATGAGATCCCTCGGTTGCCTTCTA\n->4494|16|BS2|37\n+>4494|16|BS2|3\n TAATGAGATCCCTCGGTTGCCTTCT\n->4495|16|BS2|23\n+>4495|16|BS2|4\n TAATGAGATCCCTCGGTTGCCTTC\n->4496|16|BS2|63\n+>4496|16|BS2|4\n TAATGAGATCCCTCGGTTGCCTT\n->4497|16|BS2|1\n-CGGGTAATGAGATCCCTCGGTTGCCT\n->4497|16|BS2|1\n-GTAATGAGATCCCTCGGTTGCCT\n->4498|16|BS2|4\n-TCGGGTAATGAGATCCCTCGGTTGCC\n->4498|16|BS2|2\n-CGGGTAATGAGATCCCTCGGTTGCC\n->4507|16|BS2|1\n-TCAAAGGAGATCGGGTAATGAGATCCC\n->4507|16|BS2|1\n-AAAGGAGATCGGGTAATGAGATCCC\n->4509|16|BS2|1\n-AAAGGAGATCGGGTAATGAGATC\n->4511|16|BS2|1\n-TGTCAAAGGAGATCGGGTAATGAGA\n >4517|16|BS2|1\n CCCTTGTCAAAGGAGATCGGGTA\n->4518|16|BS2|1\n-GACCCTTGTCAAAGGAGATCGGGT\n->4522|16|BS2|3\n-TGCGGACCCTTGTCAAAGGAGATC\n->4525|16|BS2|1\n-TTCTGCGGACCCTTGTCAAAGGAG\n->4534|16|BS2|1\n-TAAGCGTCAGCTTCTGCGGACCCTTG\n >4536|16|BS2|1\n GATAAGCGTCAGCTTCTGCGGACCCT\n->4536|16|BS2|1\n-TAAGCGTCAGCTTCTGCGGACCCT\n >4537|16|BS2|1\n GATAAGCGTCAGCTTCTGCGGACCC\n->4537|16|BS2|1\n-TAAGCGTCAGCTTCTGCGGACCC\n >4538|16|BS2|1\n GATAAGCGTCAGCTTCTGCGGACC\n->4539|16|BS2|3\n-TAAGATAAGCGTCAGCTTCTGCGGAC\n->4540|16|BS2|1\n-TTTAAGATAAGCGTCAGCTTCTGCGGA\n->4540|16|BS2|1\n-TTAAGATAAGCGTCAGCTTCTGCGGA\n->4540|16|BS2|12\n-TAAGATAAGCGTCAGCTTCTGCGGA\n->4540|16|BS2|1\n-AAGATAAGCGTCAGCTTCTGCGGA\n->4541|16|BS2|1\n-TAAGATAAGCGTCAGCTTCTGCGG\n->4546|16|BS2|10\n-TAGGATTTAAGATAAGCGTCAGCTTC\n->4567|16|BS2|1\n-TAACAATCACATATAACAAATAGGA\n->4629|16|BS2|1\n-TTGGGCTCGCCGGCTAACTATAGTTA\n->4629|16|BS2|1\n-TGGGCTCGCCGGCTAACTATAGTTA\n->4630|16|BS2|6\n+>4630|16|BS2|1\n TTTGGGCTCGCCGGCTAACTATAGTT\n->4630|16|BS2|5\n+>4630|16|BS2|1\n TTGGGCTCGCCGGCTAACTATAGTT\n->4631|16|BS2|19\n+>4631|16|BS2|1\n TTTGGGCTCGCCGGCTAACTATAGT\n->4631|16|BS2|4\n-TTGGGCTCGCCGGCTAACTATAGT\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,324 +1,56 @@ ->53|16|BS2|2 -TTATTACCGCGAAAACTAATTTCACT ->56|16|BS2|1 -TTATTACCGCGAAAACTAATTTC ->269|16|BS2|2 -TTCTAGCCAAAACTTGAACCCTGGGA ->271|16|BS2|1 -TTCTAGCCAAAACTTGAACCCTGG ->324|16|BS2|1 -CGCAGCGGTTTCATTTAAAGTGTTC >443|16|BS2|1 TGGGTTTTTTCCTTTCAGTCTCCG ->462|16|BS2|1 -TGTTTGCCGATGGTTGATTTGGGT ->493|16|BS2|4 -TCTAGGTTCTGTAGCCGAAGGGTT ->495|16|BS2|3 +>495|16|BS2|1 CCATATCTAGGTTCTGTAGCCGAAGGG ->496|16|BS2|41 +>496|16|BS2|8 CCATATCTAGGTTCTGTAGCCGAAGG ->497|16|BS2|136 +>497|16|BS2|7 CCATATCTAGGTTCTGTAGCCGAAG ->498|16|BS2|5 +>498|16|BS2|1 CCATATCTAGGTTCTGTAGCCGAA ->499|16|BS2|2 -CCATATCTAGGTTCTGTAGCCGA ->548|16|BS2|2 +>548|16|BS2|1 TGTTTGTCAGCTGTGAGATGCGCAA ->549|16|BS2|6 -TGTTTGTCAGCTGTGAGATGCGCA ->550|16|BS2|7 -TGTTTGTCAGCTGTGAGATGCGC ->552|16|BS2|18 -TACTTGTTTGTCAGCTGTGAGATGC ->553|16|BS2|1 -TACTTGTTTGTCAGCTGTGAGATG ->562|16|BS2|1 -TTTCATTGCCTACTTGTTTGTCAGC ->577|16|BS2|1 -TCATACAGATCGCCAATTTCATTGCC ->578|16|BS2|1 -TCATACAGATCGCCAATTTCATTGC ->580|16|BS2|1 -TCATACAGATCGCCAATTTCATT ->635|16|BS2|2 -GGAGGCTGCATCCCGCTTAGCGGCAG ->856|16|BS2|1 -TCATACTCTTCGATCTCGAGCCAGCT ->857|16|BS2|8 -TCATACTCTTCGATCTCGAGCCAGC ->858|16|BS2|39 -TCATACTCTTCGATCTCGAGCCAG ->859|16|BS2|35 -TCATACTCTTCGATCTCGAGCCA ->1023|16|BS2|1 -TTTTGAGGTACCCGGTTCGTTTCGC ->1047|16|BS2|2 -GAAGAACATATTGACTGGCGACGCT ->1048|16|BS2|6 -GAAGAACATATTGACTGGCGACGC ->1123|16|BS2|1 -TCAATAACTACTCTCATATGGCATAG ->1124|16|BS2|8 -TCAATAACTACTCTCATATGGCATA ->1158|16|BS2|1 -GCACTGGACAATAGCGTTACGCTTG ->1237|16|BS2|1 -TGTTCGCCGGCACATTTCACACA ->1390|16|BS2|14 -TTACTTCTGTTCTTCCAGCCACTCC ->1391|16|BS2|2 -TTACTTCTGTTCTTCCAGCCACTC ->1392|16|BS2|1 -TTACTTCTGTTCTTCCAGCCACT ->1463|16|BS2|1 -TGCATAAGATATTCCGCCTCGAGAAG ->1464|16|BS2|1 -TGCATAAGATATTCCGCCTCGAGAA ->1500|16|BS2|1 -TGGTTGCTTGTGGTGAATGGACCCT ->1591|16|BS2|1 -GACGCCCTTGTCCGGCTGCGGCTCCT ->1593|16|BS2|2 -GACGCCCTTGTCCGGCTGCGGCTC ->1599|16|BS2|1 -TACCCCTAGACGCCCTTGTCCGGCTG ->1615|16|BS2|1 -CGAGCGCTGGAGTGTACCCCTAGA ->1615|16|BS2|1 -GAGCGCTGGAGTGTACCCCTAGA ->1872|16|BS2|6 -GCACTCTACTTCAGGCAACTTCGT ->1899|16|BS2|1 -TAATACATCGATTTCGTGACGTCGCAC ->1900|16|BS2|5 -TAATACATCGATTTCGTGACGTCGCA ->1901|16|BS2|81 +>1901|16|BS2|9 TAATACATCGATTTCGTGACGTCGC ->1901|16|BS2|1 -ATACATCGATTTCGTGACGTCGC ->1902|16|BS2|4 +>1902|16|BS2|1 TAATACATCGATTTCGTGACGTCG >1903|16|BS2|1 TAATACATCGATTTCGTGACGTC ->1948|16|BS2|1 -TAGCTTAGGCGTCTCTGCCCCCT ->1966|16|BS2|2 -TGTAGGCTACAAATCCGAATAGCT ->1967|16|BS2|1 -TGTAGGCTACAAATCCGAATAGC ->2020|16|BS2|20 -TTGATTAAGATAGCTGCTCCGCCTT ->2021|16|BS2|297 -TTGATTAAGATAGCTGCTCCGCCT ->2022|16|BS2|36 -TTGATTAAGATAGCTGCTCCGCC ->2087|16|BS2|12 +>2087|16|BS2|1 TAACCGCCGGCGCAAGTTGCACCTTG ->2089|16|BS2|2 -TAACCGCCGGCGCAAGTTGCACCT ->2090|16|BS2|7 -TAACCGCCGGCGCAAGTTGCACC ->2108|16|BS2|1 -TAGGACCAAGTGCCGTTTCAATAACC ->2113|16|BS2|5 -TTATAGGACCAAGTGCCGTTTCAA ->2142|16|BS2|8 -AATCTCGGTGGGCAGTAGACCGCTCC ->2143|16|BS2|3 -AATCTCGGTGGGCAGTAGACCGCTC ->2144|16|BS2|6 -AATCTCGGTGGGCAGTAGACCGCT ->2145|16|BS2|14 -AATCTCGGTGGGCAGTAGACCGC ->2169|16|BS2|1 -TCCTTAAACTCTTCCGTAGTCCATGC ->2170|16|BS2|4 +>2170|16|BS2|1 TCCTTAAACTCTTCCGTAGTCCATG ->2288|16|BS2|1 -TTAGGACGAGATTCGCTAATGCAATG ->2289|16|BS2|30 +>2289|16|BS2|1 TTAGGACGAGATTCGCTAATGCAAT ->2290|16|BS2|19 +>2290|16|BS2|6 TTAGGACGAGATTCGCTAATGCAA ->2291|16|BS2|6 -TTAGGACGAGATTCGCTAATGCA ->2331|16|BS2|1 -TCTTGTTGGTCCTCCTGTTGCTAG ->2333|16|BS2|2 -TATCTTGTTGGTCCTCCTGTTGCT ->2338|16|BS2|1 -CGGGTATCTTGTTGGTCCTCCTG >2339|16|BS2|1 TACGGGTATCTTGTTGGTCCTCCT ->2367|16|BS2|5 -TCGATGTACCCTGGTGAGCCTCTACA ->2368|16|BS2|25 -TCGATGTACCCTGGTGAGCCTCTAC ->2369|16|BS2|2 -TCGATGTACCCTGGTGAGCCTCTA ->2435|16|BS2|1 -TCGGAGCTAAGCTCAACAACCGCACTT ->2436|16|BS2|14 -TCGGAGCTAAGCTCAACAACCGCACT ->2437|16|BS2|1 -TCGGAGCTAAGCTCAACAACCGCAC ->2438|16|BS2|1 -TCGGAGCTAAGCTCAACAACCGCA ->2457|16|BS2|1 -TAATTACCAGAGGCAGGTGGTCGGA ->2600|16|BS2|1 -TAGCATCATCAACGTCCTGTCCAGAG ->2601|16|BS2|12 -TAGCATCATCAACGTCCTGTCCAGA ->2602|16|BS2|1 -TAGCATCATCAACGTCCTGTCCAG ->2681|16|BS2|1 -TCGATCTGCCGCGGGCTGCCGAGAT ->2682|16|BS2|3 -TCGATCTGCCGCGGGCTGCCGAGA ->2809|16|BS2|1 -GCGCATCGGAGCCTACTCAGAGCTC ->2813|16|BS2|1 -CCAACGCGCATCGGAGCCTACTCAGA ->2856|16|BS2|50 +>2856|16|BS2|10 TATTGGCAAGCCTTTCGTCGAACCA ->2857|16|BS2|267 +>2857|16|BS2|33 TATTGGCAAGCCTTTCGTCGAACC ->2858|16|BS2|76 +>2858|16|BS2|10 TATTGGCAAGCCTTTCGTCGAAC ->2917|16|BS2|1 -CGCCTTTTGATTGCGCGCGTGGCCT ->2957|16|BS2|1 -CCATGTCCCGTTGCTATCGACTAGAGGC ->2959|16|BS2|7 +>2959|16|BS2|1 CCATGTCCCGTTGCTATCGACTAGAG ->2960|16|BS2|69 +>2960|16|BS2|8 CCATGTCCCGTTGCTATCGACTAGA ->2961|16|BS2|7 -CCATGTCCCGTTGCTATCGACTAG ->2962|16|BS2|4 +>2962|16|BS2|1 CCATGTCCCGTTGCTATCGACTA ->2983|16|BS2|1 -CTTGTCCCAAGTCGGTCCGACACC ->3026|16|BS2|4 -TGAATGGTTGAAATCGCTCGGCGAGG ->3027|16|BS2|13 +>3027|16|BS2|2 TGAATGGTTGAAATCGCTCGGCGAG ->3028|16|BS2|63 +>3028|16|BS2|7 TGAATGGTTGAAATCGCTCGGCGA ->3028|16|BS2|1 -GAATGGTTGAAATCGCTCGGCGA ->3029|16|BS2|1 -TGAATGGTTGAAATCGCTCGGCG ->3082|16|BS2|1 -AGCGCTTGGTTCAGCTGGTCCTGAG ->3114|16|BS2|1 -TTCAAACGGCGTGATTGGCATATC ->3161|16|BS2|8 -TGCTTTGTTGTTACTCTGGCGCACA ->3162|16|BS2|14 -TGCTTTGTTGTTACTCTGGCGCAC ->3163|16|BS2|4 -TGCTTTGTTGTTACTCTGGCGCA ->3275|16|BS2|2 -TGATAAGGGAAGTATTGCAACCTC ->3348|16|BS2|6 -TCGGCCGGTAGGAGGCGGGCTCCCT ->3349|16|BS2|2 +>3349|16|BS2|1 TCGGCCGGTAGGAGGCGGGCTCCC ->3350|16|BS2|3 +>3350|16|BS2|1 TCGGCCGGTAGGAGGCGGGCTCC ->3374|16|BS2|1 -TTCGAAATTGAAGGGAGGAGACTG ->3830|16|BS2|1 -ATCGGCAAATGTGGCCAACATAGAT ->3879|16|BS2|1 -TCGGCTGCGTCGTGCTCGCATCG ->3880|16|BS2|1 -CCATCGGCTGCGTCGTGCTCGCATC ->3880|16|BS2|3 -CATCGGCTGCGTCGTGCTCGCATC ->3880|16|BS2|1 -ATCGGCTGCGTCGTGCTCGCATC ->3881|16|BS2|1 -TACCATCGGCTGCGTCGTGCTCGCAT ->3882|16|BS2|2 -TACCATCGGCTGCGTCGTGCTCGCA ->3883|16|BS2|9 -TACCATCGGCTGCGTCGTGCTCGC ->3884|16|BS2|3 -TACCATCGGCTGCGTCGTGCTCG ->3894|16|BS2|1 -CAAAGTCCTGGATACCATCGGCTGC ->3896|16|BS2|3 -TGCAAAGTCCTGGATACCATCGGCT ->3896|16|BS2|52 +>3896|16|BS2|9 CAAAGTCCTGGATACCATCGGCT ->3897|16|BS2|8 -TATGCAAAGTCCTGGATACCATCGGC ->3897|16|BS2|4 -TGCAAAGTCCTGGATACCATCGGC ->3958|16|BS2|1 -TTGTTGGATTTACTGCTATTGATGC ->4048|16|BS2|2 -TCCAAGGTACTTTGCTGCGTTCGGCT ->4049|16|BS2|1 -TCCAAGGTACTTTGCTGCGTTCGGC ->4073|16|BS2|1 -TGTGAGTCTGCGATCCAGAAGCACT ->4101|16|BS2|10 -TTCTGATGTCGGTCACATGCTTGGA ->4102|16|BS2|13 -TTCTGATGTCGGTCACATGCTTGG ->4262|16|BS2|1 -TTTTGATGTGGCTGTCGCAGGCT ->4348|16|BS2|1 -TTTCAGGTCTCTGTGCAGGGTGGTGT ->4348|16|BS2|3 -TTCAGGTCTCTGTGCAGGGTGGTGT ->4349|16|BS2|1 -TTTCAGGTCTCTGTGCAGGGTGGTG ->4349|16|BS2|4 -TTCAGGTCTCTGTGCAGGGTGGTG ->4350|16|BS2|6 -TTTCAGGTCTCTGTGCAGGGTGGT ->4350|16|BS2|6 -TTCAGGTCTCTGTGCAGGGTGGT ->4351|16|BS2|3 -TTTCAGGTCTCTGTGCAGGGTGG ->4374|16|BS2|5 -TTATTTCGTCAAATACCGTTGCGAG ->4375|16|BS2|4 -TTATTTCGTCAAATACCGTTGCGA ->4403|16|BS2|1 -TGTCATGGTATCTGCTCGAGTGC ->4424|16|BS2|2 -GATTTCTGTGGCGCTCCAGCCTG ->4429|16|BS2|1 -CCAGCCGATTTCTGTGGCGCTCCA ->4430|16|BS2|1 -CCAGCCGATTTCTGTGGCGCTCC ->4431|16|BS2|1 -GGCCAGCCGATTTCTGTGGCGCTC ->4445|16|BS2|20 -TCTGTTTAAAGCGCTGGCCAGCCGA ->4446|16|BS2|1 -TCTGTTTAAAGCGCTGGCCAGCCG ->4447|16|BS2|2 +>4447|16|BS2|1 GATCTGTTTAAAGCGCTGGCCAGCC ->4447|16|BS2|2 -TCTGTTTAAAGCGCTGGCCAGCC ->4449|16|BS2|6 -GAGATCTGTTTAAAGCGCTGGCCAG ->4450|16|BS2|4 -CGAGATCTGTTTAAAGCGCTGGCCA ->4450|16|BS2|1 -GAGATCTGTTTAAAGCGCTGGCCA ->4451|16|BS2|14 +>4451|16|BS2|2 CGAGATCTGTTTAAAGCGCTGGCC ->4451|16|BS2|12 -GAGATCTGTTTAAAGCGCTGGCC ->4452|16|BS2|4 +>4452|16|BS2|1 CGAGATCTGTTTAAAGCGCTGGC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number -1 109 2.47 -2 179 4.05 -3 117 2.65 -4 134 3.03 -5 162 3.67 -6 214 4.84 -7 194 4.39 -8 192 4.35 -9 171 3.87 -10 610 13.81 -11 199 4.50 -12 201 4.55 -13 149 3.37 -14 176 3.98 -15 194 4.39 -16 154 3.49 -17 195 4.41 -18 208 4.71 -19 217 4.91 -20 143 3.24 -21 207 4.69 -22 179 4.05 -23 114 2.58 +1 4 2.16 +2 7 3.78 +3 2 1.08 +4 3 1.62 +5 7 3.78 +6 11 5.95 +7 4 2.16 +8 10 5.41 +9 6 3.24 +10 51 27.57 +11 9 4.86 +12 10 5.41 +13 5 2.70 +14 9 4.86 +15 5 2.70 +16 6 3.24 +17 7 3.78 +18 6 3.24 +19 9 4.86 +20 0 0.00 +21 9 4.86 +22 2 1.08 +23 3 1.62 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,822 +1,152 @@\n->22|0|BS2|2\n-TCTAACAATACGCACCTGACAAAG\n->43|0|BS2|1\n-AAGTGGATTAAGTGAAATTAGTTTTC\n->70|0|BS2|1\n-CGGTAATAAACTTATGGACAAGACC\n->70|0|BS2|1\n-CGGTAATAAACTTATGGACAAGAC\n->73|0|BS2|1\n-TAATAAACTTATGGACAAGACCAGAA\n->73|0|BS2|1\n-TAATAAACTTATGGACAAGACCAGA\n->78|0|BS2|1\n-AACTTATGGACAAGACCAGAATACT\n->80|0|BS2|1\n-CTTATGGACAAGACCAGAATACTGGCA\n->81|0|BS2|1\n-TTATGGACAAGACCAGAATACTGGCA\n->82|0|BS2|2\n-TATGGACAAGACCAGAATACTGGCACA\n->82|0|BS2|1\n-TATGGACAAGACCAGAATACTGGCAC\n->82|0|BS2|3\n-TATGGACAAGACCAGAATACTGGCA\n->83|0|BS2|1\n-ATGGACAAGACCAGAATACTGGCAC\n+>69|0|BS2|2\n+GCGGTAATAAACTTATGGACAAGAC\n >187|0|BS2|1\n GTTAAGTTTCTCGAACTGGGGCTCC\n->188|0|BS2|1\n-TTAAGTTTCTCGAACTGGGGCTCC\n->189|0|BS2|1\n-TAAGTTTCTCGAACTGGGGCTCCGCT\n->189|0|BS2|1\n-TAAGTTTCTCGAACTGGGGCTCCGC\n->193|0|BS2|1\n-TTTCTCGAACTGGGGCTCCGCTG\n->194|0|BS2|1\n-TTCTCGAACTGGGGCTCCGCTGCCCAGC\n->195|0|BS2|2\n+>195|0|BS2|1\n TCTCGAACTGGGGCTCCGCTGCCCAGC\n->195|0|BS2|2\n-TCTCGAACTGGGGCTCCGCTGCCCA\n->197|0|BS2|1\n-TCGAACTGGGGCTCCGCTGCCCAG\n >212|0|BS2|1\n GCTGCCCAGCTGCCACGCGATCGC\n->215|0|BS2|1\n-GCCCAGCTGCCACGCGATCGCACAAAC\n->215|0|BS2|1\n-GCCCAGCTGCCACGCGATCGCACA\n->215|0|BS2|2\n-GCCCAGCTGCCACGCGATCGCAC\n->222|0|BS2|2\n-TGCCACGCGATCGCACAAACAGCTG\n->223|0|BS2|1\n-GCCACGCGATCGCACAAACAGCTGTT\n->223|0|BS2|1\n-GCCACGCGATCGCACAAACAGCTG\n->224|0|BS2|1\n-CCACGCGATCGCACAAACAGCTGTT\n->225|0|BS2|11\n-CACGCGATCGCACAAACAGCTGTT\n->286|0|BS2|2\n+>285|0|BS2|1\n+TTGGCTAGAACCCTGGTGATTTGG\n+>286|0|BS2|1\n TGGCTAGAACCCTGGTGATTTGG\n->304|0|BS2|1\n-TTTGGTGCACACTTCAATATGAACAC\n->305|0|BS2|1\n-TTGGTGCACACTTCAATATGAACACT\n->331|0|BS2|1\n-TTAAATGAAACCGCTGCGGCTGA\n >336|0|BS2|1\n TGAAACCGCTGCGGCTGATGAATCG\n->340|0|BS2|2\n-ACCGCTGCGGCTGATGAATCGTTGG\n->340|0|BS2|3\n-ACCGCTGCGGCTGATGAATCGTTG\n->342|0|BS2|1\n-CGCTGCGGCTGATGAATCGTTGG\n->345|0|BS2|2\n-TGCGGCTGATGAATCGTTGGATAC\n->345|0|BS2|1\n-TGCGGCTGATGAATCGTTGGATA\n->351|0|BS2|1\n-TGATGAATCGTTGGATACTGCGTT\n->361|0|BS2|1\n-TTGGATACTGCGTTTCTCTCGAGCCC\n->366|0|BS2|1\n-TACTGCGTTTCTCTCGAGCCCCCAA\n->431|0|BS2|1\n-CTCGTGCTTCTCCGGAGACTGAAA\n->441|0|BS2|1\n-TCCGGAGACTGAAAGGAAAAAACCC\n+>339|0|BS2|2\n+AACCGCTGCGGCTGATGAATCGTT\n >441|0|BS2|1\n TCCGGAGACTGAAAGGAAAAAAC\n->456|0|BS2|1\n-GAAAAAACCCAAATCAACCATCGGC\n->458|0|BS2|1\n-AAAAACCCAAATCAACCATCGGCAAA\n->472|0|BS2|1\n-ACCATCGGCAAACAAGGGGAAAACCC\n->485|0|BS2|1\n-AAGGGGAAAACCCTTCGGCTACAGAAC\n->493|0|BS2|1\n-AACCCTTCGGCTACAGAACCTAGA\n >494|0|BS2|1\n ACCCTTCGGCTACAGAACCTAGATA\n->496|0|BS2|1\n-CCTTCGGCTACAGAACCTAGATAT\n->498|0|BS2|1\n-TTCGGCTACAGAACCTAGATATGGC\n->500|0|BS2|2\n-CGGCTACAGAACCTAGATATGGC\n->504|0|BS2|2\n+>504|0|BS2|1\n TACAGAACCTAGATATGGCGGCAAT\n->510|0|BS2|1\n-ACCTAGATATGGCGGCAATTCAAAC\n->583|0|BS2|1\n-GAAATTGGCGATCTGTATGACCAGCC\n->588|0|BS2|2\n-TGGCGATCTGTATGACCAGCCCAGT\n >592|0|BS2|1\n GATCTGTATGACCAGCCCAGTACCAG\n->594|0|BS2|1\n-TCTGTATGACCAGCCCAGTACCAGT\n+>593|0|BS2|1\n+ATCTGTATGACCAGCCCAGTACC\n >627|0|BS2|1\n TGCAATTGCTGCCGCTAAGCGGGATG\n->639|0|BS2|1\n-CGCTAAGCGGGATGCAGCCTCCGCT\n->747|0|BS2|1\n-GCAGAGCATCGAAAATATAGTGGA\n->764|0|BS2|1\n-TAGTGGACCTAGAAAAGATTGAGGC\n->771|0|BS2|1\n-CCTAGAAAAGATTGAGGCTAGGGC\n->772|0|BS2|5\n-CTAGAAAAGATTGAGGCTAGGGC\n->773|0|BS2|1\n-TAGAAAAGATTGAGGCTAGGGCGTC\n->796|0|BS2|2\n-TCAATGAGCGGTGTCCTAAGGCTT\n->796|0|BS2|1\n-TCAATGAGCGGTGTCCTAAGGCT\n->797|0|BS2|1\n-CAATGAGCGGTGTCCTAAGGCTTT\n->860|0|BS2|1\n-GGCTCGAGATCGAAGAGTATGAGTT\n->863|0|BS2|1\n-TCGAGATCGAAGAGTATGAGTTC\n->899|0|BS2|34\n+>899|0|BS2|3\n TTAAAGAGGACAGGCCTTACAGGGTA\n->899|0|BS2|2\n-TTAAAGAGGACAGGCCTTACAGGGT\n->899|0|BS2|4\n-TTAAAGAGGACAGGCCTTACAGGG\n->899|0|BS2|1\n-TTAAAGAGGACAGGCCTTACAGG\n >900|0|BS2|1\n TAAAGAGGACAGGCCTTACAGGGTATG\n->900|0|BS2|42\n+>900|0|BS2|5\n TAAAGAGGACAGGCCTTACAGGGTA\n >900|0|BS2|1\n TAAAGAGGACAGGCCTTACAGGGT\n->900|0|BS2|2\n-TAAAGAGGACAGGCCTTACAGGG\n->902|0|BS2|3\n-AAGAGGACAGGCCTTACAGGGTATG\n->903|0|BS2|1\n-AGAGGACAGGCCTTACAGGGTATG\n->925|0|BS2|1\n-TGCGTGAAAGGCCTGCACCACAGTA\n->1011|0|BS2|1\n-CACACCGCTTAGGCGAAACGAACC\n >1020|0|BS2|1\n TAGGCGAAACGAACCGGGTACCT\n->1032|0|BS2|2\n-ACCGGGTACCTCAAAAGCGTCGCCAG\n->1067|0|BS2|1\n-TCTTCCTAAATATTGCTGCTGCGGC\n->1071|0|BS2|1\n-CCTAAATATTGCTGCTGCGGCAAA\n >1090|0|BS2|1\n-GCAAACAATAAGGAGATCCTGGCG\n->1090|0|BS2|4\n GCAAACAATAAGGAGATCCTGGC\n >10'..b'CCGGCCGA\n->3347|0|BS2|5\n-AAGGGAGCCCGCCTCCTACCGGCCG\n->3347|0|BS2|5\n-AAGGGAGCCCGCCTCCTACCGGCC\n->3353|0|BS2|1\n-GCCCGCCTCCTACCGGCCGATCAGTC\n->3356|0|BS2|1\n-CGCCTCCTACCGGCCGATCAGTC\n->3360|0|BS2|1\n-TCCTACCGGCCGATCAGTCTCCTCCCT\n->3360|0|BS2|1\n-TCCTACCGGCCGATCAGTCTCCT\n->3427|0|BS2|1\n-TTGTAAGGATTATGGAAGCCCAGGG\n->3427|0|BS2|1\n-TTGTAAGGATTATGGAAGCCCAG\n->3430|0|BS2|17\n+>3430|0|BS2|1\n TAAGGATTATGGAAGCCCAGGGGAT\n->3430|0|BS2|4\n+>3430|0|BS2|2\n TAAGGATTATGGAAGCCCAGGGGA\n->3861|0|BS2|1\n-TGCGTCACCTACAGGTCCCGATG\n->3882|0|BS2|1\n-TGCGAGCACGACGCAGCCGATGGTA\n->3890|0|BS2|1\n-CGACGCAGCCGATGGTATCCAGGAC\n->3891|0|BS2|1\n-GACGCAGCCGATGGTATCCAGGAC\n->3900|0|BS2|1\n-GATGGTATCCAGGACTTTGCATAC\n->3906|0|BS2|1\n-ATCCAGGACTTTGCATACCGGTTC\n->3915|0|BS2|1\n-TTTGCATACCGGTTCTCGGAATGGGC\n->3921|0|BS2|3\n-TACCGGTTCTCGGAATGGGCAAGAC\n->3934|0|BS2|1\n-AATGGGCAAGACGATGGAATATTG\n->3936|0|BS2|1\n-TGGGCAAGACGATGGAATATTGGCA\n->3969|0|BS2|3\n-AGTAAATCCAACAACGTCTGCTTC\n->3969|0|BS2|1\n-AGTAAATCCAACAACGTCTGCTT\n >3992|0|BS2|1\n CACTTTAAAGCGGAGAACGCCACC\n >3995|0|BS2|1\n TTTAAAGCGGAGAACGCCACCGCCCG\n->3995|0|BS2|1\n-TTTAAAGCGGAGAACGCCACCGCCC\n->3996|0|BS2|1\n-TTAAAGCGGAGAACGCCACCGCCCG\n->3997|0|BS2|1\n-TAAAGCGGAGAACGCCACCGCCCGTCT\n->3997|0|BS2|2\n-TAAAGCGGAGAACGCCACCGCCCGTC\n->3997|0|BS2|1\n-TAAAGCGGAGAACGCCACCGCCCG\n->4057|0|BS2|1\n-CAGCAAAGTACCTTGGAGTGCTTC\n->4065|0|BS2|1\n-TACCTTGGAGTGCTTCTGGATCGCAGA\n->4065|0|BS2|3\n-TACCTTGGAGTGCTTCTGGATCGCA\n->4065|0|BS2|2\n-TACCTTGGAGTGCTTCTGGATCGC\n->4068|0|BS2|1\n-CTTGGAGTGCTTCTGGATCGCAGAC\n->4069|0|BS2|1\n-TTGGAGTGCTTCTGGATCGCAGACTC\n->4069|0|BS2|6\n-TTGGAGTGCTTCTGGATCGCAGACT\n->4069|0|BS2|2\n-TTGGAGTGCTTCTGGATCGCAGA\n->4107|0|BS2|3\n-CATGTGACCGACATCAGAACGCGCC\n->4108|0|BS2|2\n-ATGTGACCGACATCAGAACGCGCC\n->4111|0|BS2|1\n-TGACCGACATCAGAACGCGCCTACG\n->4112|0|BS2|1\n-GACCGACATCAGAACGCGCCTACG\n->4113|0|BS2|1\n-ACCGACATCAGAACGCGCCTACGTGCT\n->4113|0|BS2|1\n-ACCGACATCAGAACGCGCCTACGTGC\n->4139|0|BS2|2\n+>4139|0|BS2|1\n TAAGGTGGCGAAGCACTACTGGCT\n->4139|0|BS2|1\n-TAAGGTGGCGAAGCACTACTGGC\n->4245|0|BS2|1\n-TGCCAAATCTGGGGCTTAGCCTGCGA\n->4245|0|BS2|1\n-TGCCAAATCTGGGGCTTAGCCTGC\n->4246|0|BS2|1\n-GCCAAATCTGGGGCTTAGCCTGCGA\n->4251|0|BS2|1\n-ATCTGGGGCTTAGCCTGCGACAGCC\n->4252|0|BS2|2\n-TCTGGGGCTTAGCCTGCGACAGCCA\n->4252|0|BS2|2\n-TCTGGGGCTTAGCCTGCGACAGCC\n->4279|0|BS2|2\n+>4279|0|BS2|1\n TCAAAAGGATCCAGGCTATTCAAAA\n->4314|0|BS2|2\n-AGACTCATCACCGGCTGCGAGTGG\n->4347|0|BS2|1\n-AACACCACCCTGCACAGAGACCTGAA\n >4349|0|BS2|1\n CACCACCCTGCACAGAGACCTGAAAC\n->4351|0|BS2|2\n-CCACCCTGCACAGAGACCTGAAACT\n->4357|0|BS2|1\n-TGCACAGAGACCTGAAACTCGCAACGG\n->4357|0|BS2|1\n-TGCACAGAGACCTGAAACTCGCA\n->4360|0|BS2|1\n-ACAGAGACCTGAAACTCGCAACGG\n->4368|0|BS2|1\n-CTGAAACTCGCAACGGTATTTGACGA\n->4386|0|BS2|1\n-TTTGACGAAATAAACAAGCACTCGA\n->4419|0|BS2|1\n-CATGACAGGCTGGAGCGCCACAGAAA\n->4425|0|BS2|1\n-AGGCTGGAGCGCCACAGAAATCGGC\n->4444|0|BS2|1\n-ATCGGCTGGCCAGCGCTTTAAACAGA\n->4444|0|BS2|5\n-ATCGGCTGGCCAGCGCTTTAAACAG\n->4478|0|BS2|1\n-ACCAAGGAGGCTCAATAGAAGGC\n+>4416|0|BS2|2\n+TACCATGACAGGCTGGAGCGCCACA\n+>4416|0|BS2|2\n+TACCATGACAGGCTGGAGCGCCA\n+>4443|0|BS2|1\n+AATCGGCTGGCCAGCGCTTTAAAC\n+>4445|0|BS2|2\n+TCGGCTGGCCAGCGCTTTAAACAGA\n+>4464|0|BS2|1\n+AACAGATCTCGCCCACCAAGGAGGC\n+>4464|0|BS2|1\n+AACAGATCTCGCCCACCAAGGAGG\n >4484|0|BS2|1\n GAGGCTCAATAGAAGGCAACCGAGG\n->4527|0|BS2|1\n-CCTTTGACAAGGGTCCGCAGAAGCTG\n->4529|0|BS2|4\n+>4529|0|BS2|1\n TTTGACAAGGGTCCGCAGAAGCTGA\n->4529|0|BS2|1\n-TTTGACAAGGGTCCGCAGAAGCTG\n->4531|0|BS2|1\n-TGACAAGGGTCCGCAGAAGCTGA\n >4534|0|BS2|1\n-CAAGGGTCCGCAGAAGCTGACGCTT\n->4534|0|BS2|2\n CAAGGGTCCGCAGAAGCTGACGCT\n->4535|0|BS2|1\n-AAGGGTCCGCAGAAGCTGACGCT\n->4565|0|BS2|1\n-AATCCTATTTGTTATATGTGATTGT\n->4597|0|BS2|1\n-TTGTAGTTAAATTACTGTAAATTT\n->4607|0|BS2|1\n-ATTACTGTAAATTTGAAAAAGCTAAC\n->4609|0|BS2|1\n-TACTGTAAATTTGAAAAAGCTAAC\n->4637|0|BS2|3\n-GTTAGCCGGCGAGCCCAAATGGGCTGA\n->4638|0|BS2|2\n-TTAGCCGGCGAGCCCAAATGGGCTGA\n->4638|0|BS2|1\n-TTAGCCGGCGAGCCCAAATGGGCTG\n->4639|0|BS2|6\n+>4639|0|BS2|1\n TAGCCGGCGAGCCCAAATGGGCTGA\n->4639|0|BS2|1\n-TAGCCGGCGAGCCCAAATGGGCTG\n->4666|0|BS2|1\n-TAATAGATAAGAAGGACACAAAGGGGC\n >4669|0|BS2|1\n TAGATAAGAAGGACACAAAGGGGCT\n->4669|0|BS2|2\n+>4669|0|BS2|1\n TAGATAAGAAGGACACAAAGGGGC\n->4678|0|BS2|1\n-AGGACACAAAGGGGCTTCAAGACT\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,274 +1,34 @@ ->69|0|BS2|2 -GCGGTAATAAACTTATGGACAAGACC ->69|0|BS2|12 -GCGGTAATAAACTTATGGACAAGAC ->69|0|BS2|1 -GCGGTAATAAACTTATGGACAAG ->285|0|BS2|1 -TTGGCTAGAACCCTGGTGATTTGG ->339|0|BS2|4 -AACCGCTGCGGCTGATGAATCGTTG ->339|0|BS2|5 -AACCGCTGCGGCTGATGAATCGTT ->457|0|BS2|6 +>457|0|BS2|3 AAAAAACCCAAATCAACCATCGGC ->476|0|BS2|1 -TCGGCAAACAAGGGGAAAACCCTTCG ->507|0|BS2|1 -AGAACCTAGATATGGCGGCAATTC >512|0|BS2|1 -CTAGATATGGCGGCAATTCAAACCGA ->512|0|BS2|2 CTAGATATGGCGGCAATTCAAACC ->512|0|BS2|5 -CTAGATATGGCGGCAATTCAAAC ->563|0|BS2|1 -CTGACAAACAAGTAGGCAATGAAATT ->563|0|BS2|2 -CTGACAAACAAGTAGGCAATGAAAT >563|0|BS2|1 CTGACAAACAAGTAGGCAATGAAA ->567|0|BS2|2 -CAAACAAGTAGGCAATGAAATTGGC ->577|0|BS2|1 -GGCAATGAAATTGGCGATCTGTATG ->593|0|BS2|2 -ATCTGTATGACCAGCCCAGTACC ->651|0|BS2|1 -TGCAGCCTCCGCTGGTACCACTAGCTC ->872|0|BS2|2 -AAGAGTATGAGTTCCACTGCTACC ->1038|0|BS2|1 -TACCTCAAAAGCGTCGCCAGTCAA ->1038|0|BS2|1 -TACCTCAAAAGCGTCGCCAGTCA ->1062|0|BS2|1 -TATGTTCTTCCTAAATATTGCTGC ->1139|0|BS2|1 -TAGTTATTGAGCCTCTCCGCAAGC ->1173|0|BS2|2 -TGTCCAGTGCCATCGTTGTCAGCAG ->1173|0|BS2|1 -TGTCCAGTGCCATCGTTGTCAGCA ->1250|0|BS2|1 -CCGGCGAACACCCAGCCAAGGACT ->1405|0|BS2|3 -ACAGAAGTAAGCGAGCGACCAACTC ->1479|0|BS2|1 -ATCTTATGCAGATGTGGCTAGAG ->1515|0|BS2|1 -CAAGCAACCAATGAGCCTGACGCACC ->1515|0|BS2|1 -CAAGCAACCAATGAGCCTGACGCAC ->1607|0|BS2|1 -CAAGGGCGTCTAGGGGTACACTC ->1615|0|BS2|1 -TCTAGGGGTACACTCCAGCGCTCGA ->1628|0|BS2|1 -TCCAGCGCTCGACGGATGCTAGCAG ->1628|0|BS2|2 -TCCAGCGCTCGACGGATGCTAGC ->1629|0|BS2|1 -CCAGCGCTCGACGGATGCTAGCAGC ->1886|0|BS2|1 -AGTAGAGTGCTTCGTGCGACGTCAC ->1914|0|BS2|1 -ATCGATGTATTACTGCTCAGCGA ->1916|0|BS2|7 +>1916|0|BS2|1 CGATGTATTACTGCTCAGCGAGACA ->1916|0|BS2|5 -CGATGTATTACTGCTCAGCGAGAC ->1916|0|BS2|11 +>1916|0|BS2|2 CGATGTATTACTGCTCAGCGAGA ->1961|0|BS2|2 -GCCTAAGCTATTCGGATTTGTAGCC ->1980|0|BS2|1 -GTAGCCTACACTGCCAATGATCCGA ->2035|0|BS2|1 -TCTTAATCAAAAATAGCCTTGCCC >2103|0|BS2|1 CCGGCGGTTATTGAAACGGCACT ->2124|0|BS2|1 -CTTGGTCCTATAAGCTTTGGAGC ->2127|0|BS2|1 -GGTCCTATAAGCTTTGGAGCGGTCT ->2127|0|BS2|1 -GGTCCTATAAGCTTTGGAGCGGTC ->2158|0|BS2|1 -CACCGAGATTTGCATGGACTACGGA ->2158|0|BS2|1 -CACCGAGATTTGCATGGACTACG ->2185|0|BS2|1 -AGTTTAAGGACATTTTGGAAGAGTTC ->2185|0|BS2|16 +>2185|0|BS2|3 AGTTTAAGGACATTTTGGAAGAGT ->2185|0|BS2|8 -AGTTTAAGGACATTTTGGAAGAG ->2304|0|BS2|4 +>2304|0|BS2|1 CTCGTCCTAAATTCGGAGGTGGACT ->2304|0|BS2|2 -CTCGTCCTAAATTCGGAGGTGGAC ->2304|0|BS2|1 -CTCGTCCTAAATTCGGAGGTGGA ->2345|0|BS2|4 -ACCAACAAGATACCCGTACGGCTGTA ->2345|0|BS2|3 -ACCAACAAGATACCCGTACGGCTGT ->2345|0|BS2|2 -ACCAACAAGATACCCGTACGGCT ->2347|0|BS2|4 -CAACAAGATACCCGTACGGCTGTA ->2347|0|BS2|1 -CAACAAGATACCCGTACGGCTGT ->2351|0|BS2|1 -AAGATACCCGTACGGCTGTAGAGGC >2353|0|BS2|1 -GATACCCGTACGGCTGTAGAGGCTC ->2353|0|BS2|2 GATACCCGTACGGCTGTAGAGGCT ->2353|0|BS2|3 -GATACCCGTACGGCTGTAGAGGC ->2383|0|BS2|1 -GGTACATCGATTTTGCACTGACAAAG ->2452|0|BS2|1 -TTAGCTCCGACCACCTGCCTCTGGTAAT ->2452|0|BS2|2 -TTAGCTCCGACCACCTGCCTCTGGTA ->2472|0|BS2|1 -CTGGTAATTACGCTGGATGCGGG ->2616|0|BS2|2 -GATGATGCTATCGAACTGCTCACC ->2696|0|BS2|1 -GGCAGATCGAATCCCAATACCCAGGG ->2824|0|BS2|1 -TCCGATGCGCGTTGGTGCTGCACAAA ->2824|0|BS2|1 -TCCGATGCGCGTTGGTGCTGCAC ->2829|0|BS2|1 -TGCGCGTTGGTGCTGCACAAAGCCGC ->2829|0|BS2|1 -TGCGCGTTGGTGCTGCACAAAGCCG ->2871|0|BS2|28 +>2871|0|BS2|5 CTTGCCAATACCGGAGTCGAAAGC ->2871|0|BS2|15 +>2871|0|BS2|1 CTTGCCAATACCGGAGTCGAAAG ->2932|0|BS2|2 -TCAAAAGGCGTTGCACGAGGAAGGC ->2975|0|BS2|12 +>2975|0|BS2|2 CGGGACATGGTGTCGGACCGACT ->2997|0|BS2|1 -TTGGGACAAGCGGAGGTATTCGCTG ->2997|0|BS2|1 -TTGGGACAAGCGGAGGTATTCGCT ->3041|0|BS2|2 -TCAACCATTCAAGCTTGCCAGCCTG ->3042|0|BS2|17 +>3042|0|BS2|3 CAACCATTCAAGCTTGCCAGCCTG ->3097|0|BS2|1 -ACCAAGCGCTTCAAATGGATATGC ->3128|0|BS2|1 -GCCGTTTGAACCCTGCGAGGTAGC ->3176|0|BS2|1 -CAACAAAGCACCTGGACATGACGTCA ->3176|0|BS2|2 -CAACAAAGCACCTGGACATGACGT ->3176|0|BS2|1 -CAACAAAGCACCTGGACATGACG ->3289|0|BS2|1 -TCCCTTATCAGTGGAAGCTCGGGAT ->3363|0|BS2|6 -TACCGGCCGATCAGTCTCCTCCCT ->3363|0|BS2|3 +>3363|0|BS2|1 TACCGGCCGATCAGTCTCCTCCC ->3388|0|BS2|1 -CAATTTCGAAGGTGTTTGAGAGACT ->3845|0|BS2|1 -ATTTGCCGATGACGTGTGCGTCACC ->3892|0|BS2|1 -ACGCAGCCGATGGTATCCAGGACTT ->3893|0|BS2|1 -CGCAGCCGATGGTATCCAGGACTTT ->3893|0|BS2|10 -CGCAGCCGATGGTATCCAGGACTT ->3894|0|BS2|1 -GCAGCCGATGGTATCCAGGACTTTG ->3894|0|BS2|1 -GCAGCCGATGGTATCCAGGACTT ->3895|0|BS2|1 -CAGCCGATGGTATCCAGGACTTTGC ->3897|0|BS2|1 -GCCGATGGTATCCAGGACTTTGCAT ->3897|0|BS2|4 -GCCGATGGTATCCAGGACTTTGCA ->3909|0|BS2|1 -CAGGACTTTGCATACCGGTTCTCGGA ->3909|0|BS2|4 -CAGGACTTTGCATACCGGTTCTCGG >3909|0|BS2|1 CAGGACTTTGCATACCGGTTCTC ->3911|0|BS2|1 -GGACTTTGCATACCGGTTCTCGGA ->3913|0|BS2|1 -ACTTTGCATACCGGTTCTCGGAAT ->3973|0|BS2|1 -AATCCAACAACGTCTGCTTCACT ->4064|0|BS2|1 -GTACCTTGGAGTGCTTCTGGATCGC ->4064|0|BS2|2 -GTACCTTGGAGTGCTTCTGGATC ->4088|0|BS2|1 -CAGACTCACATTTTCCAAGCATG ->4116|0|BS2|1 -GACATCAGAACGCGCCTACGTGCT ->4275|0|BS2|1 -CACATCAAAAGGATCCAGGCTATT ->4363|0|BS2|1 -GAGACCTGAAACTCGCAACGGTATT ->4364|0|BS2|1 -AGACCTGAAACTCGCAACGGTATT ->4389|0|BS2|2 -GACGAAATAAACAAGCACTCGAGCA ->4389|0|BS2|1 -GACGAAATAAACAAGCACTCGAGC ->4416|0|BS2|9 -TACCATGACAGGCTGGAGCGCCACA ->4416|0|BS2|1 -TACCATGACAGGCTGGAGCGCCAC ->4416|0|BS2|6 -TACCATGACAGGCTGGAGCGCCA ->4437|0|BS2|2 -CACAGAAATCGGCTGGCCAGCGCT ->4437|0|BS2|3 -CACAGAAATCGGCTGGCCAGCGC ->4443|0|BS2|1 -AATCGGCTGGCCAGCGCTTTAAACAG ->4443|0|BS2|1 -AATCGGCTGGCCAGCGCTTTAAAC ->4445|0|BS2|18 -TCGGCTGGCCAGCGCTTTAAACAGA ->4445|0|BS2|6 -TCGGCTGGCCAGCGCTTTAAACAG ->4460|0|BS2|1 -TTTAAACAGATCTCGCCCACCAAGGA ->4460|0|BS2|2 -TTTAAACAGATCTCGCCCACCAAGG ->4462|0|BS2|9 -TAAACAGATCTCGCCCACCAAGGAGGC ->4462|0|BS2|1 -TAAACAGATCTCGCCCACCAAGGAG ->4462|0|BS2|1 -TAAACAGATCTCGCCCACCAAGGA >4462|0|BS2|1 TAAACAGATCTCGCCCACCAAGG ->4464|0|BS2|3 -AACAGATCTCGCCCACCAAGGAGGC ->4464|0|BS2|4 -AACAGATCTCGCCCACCAAGGAGG ->4464|0|BS2|2 -AACAGATCTCGCCCACCAAGGAG ->4465|0|BS2|4 +>4465|0|BS2|1 ACAGATCTCGCCCACCAAGGAGGCTC ->4465|0|BS2|3 -ACAGATCTCGCCCACCAAGGAGGC ->4465|0|BS2|1 -ACAGATCTCGCCCACCAAGGAGG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,230 +1,62 @@ >6|16|DMCR1A|1 AAAAACACGACCGTTCGCTTTGAAA ->65|16|DMCR1A|1 -AAGATTATTAAAAACCACTGCTG ->341|16|DMCR1A|1 -ACCGCACGAGAGCAGTCTGCACGCT ->341|16|DMCR1A|1 -AACCGCACGAGAGCAGTCTGCACGCT ->541|16|DMCR1A|1 -TTCGGCCATTAAAACCAGCGCACT ->546|16|DMCR1A|1 -TCACTCGTTCGGCCATTAAAACCAGC ->550|16|DMCR1A|1 -TCATCACTCGTTCGGCCATTAAAAC ->558|16|DMCR1A|2 -TGCTAGGTCATCACTCGTTCGGCC ->662|16|DMCR1A|1 -GTTGATCAGTTCTTTCAAGCCACCT ->703|16|DMCR1A|2 -TCATCGGCTCGACGGAAACAATCTC ->705|16|DMCR1A|2 -TATCATCGGCTCGACGGAAACAATC ->733|16|DMCR1A|2 -TAAACTGTGAATTAAGCGCGCACA ->734|16|DMCR1A|2 -TTAAACTGTGAATTAAGCGCGCAC ->774|16|DMCR1A|1 -TTTTTTGATCTTTGGAGATTTATC ->861|16|DMCR1A|1 -TTGCTGCGATTGACAGCTGATCAGT ->867|16|DMCR1A|1 -TGCGGATTTGCTGCGATTGACAGCTG ->868|16|DMCR1A|1 -TGCGGATTTGCTGCGATTGACAGCT ->869|16|DMCR1A|1 -TGCGGATTTGCTGCGATTGACAGC ->869|16|DMCR1A|4 -TATGCGGATTTGCTGCGATTGACAGC ->870|16|DMCR1A|2 -TGCGGATTTGCTGCGATTGACAG ->870|16|DMCR1A|1 -TATGCGGATTTGCTGCGATTGACAG ->928|16|DMCR1A|1 -TCACAGCGAATTGATCGGATTGCT ->1024|16|DMCR1A|2 -CCTTGTGGTTGTAAACTATTCGGGA >1025|16|DMCR1A|1 CCTTGTGGTTGTAAACTATTCGGG ->1026|16|DMCR1A|1 -TCCCTTGTGGTTGTAAACTATTCGG ->1056|16|DMCR1A|1 -TGCCCACTTGTGCCGGTAGACCGGACTC ->1057|16|DMCR1A|1 -CACTTGTGCCGGTAGACCGGACT ->1058|16|DMCR1A|1 -TGCCCACTTGTGCCGGTAGACCGGAC ->1058|16|DMCR1A|1 -AGTGCCCACTTGTGCCGGTAGACCGGAC ->1150|16|DMCR1A|2 +>1150|16|DMCR1A|1 TTTGATCAGGGGAAAGCCGAGAAA ->1151|16|DMCR1A|1 -TGTTTGATCAGGGGAAAGCCGAGAA ->1152|16|DMCR1A|1 -TGTTTGATCAGGGGAAAGCCGAGA ->1175|16|DMCR1A|2 -TATATAATACAATACATCAGACGAT ->1200|16|DMCR1A|1 -TATTATCGGCTTTTGTTTTGTCTTG ->1202|16|DMCR1A|10 +>1202|16|DMCR1A|1 TATTATCGGCTTTTGTTTTGTCT ->1210|16|DMCR1A|2 +>1210|16|DMCR1A|1 TTCCACTTTTATATTATCGGCTTTTG ->1214|16|DMCR1A|3 -TTTTCCACTTTTATATTATCGGCT >1214|16|DMCR1A|1 -TTTTTCCACTTTTATATTATCGGCT ->1343|16|DMCR1A|1 -TCTTAGCTTCGAACTCTTTTACC ->1347|16|DMCR1A|1 -TTTGATCTTAGCTTCGAACTCTTT ->1348|16|DMCR1A|1 -TTTGATCTTAGCTTCGAACTCTT +TTTTCCACTTTTATATTATCGGCT >1348|16|DMCR1A|1 TTTTTGATCTTAGCTTCGAACTCTT ->1351|16|DMCR1A|2 -TATTTTTGATCTTAGCTTCGAACT ->1411|16|DMCR1A|2 -CGGATGGTGCAGTGGTCTGGCCAC >1413|16|DMCR1A|1 GCGGATGGTGCAGTGGTCTGGCC ->1414|16|DMCR1A|3 +>1414|16|DMCR1A|1 GGCGGATGGTGCAGTGGTCTGGC >1416|16|DMCR1A|1 GAGGCGGATGGTGCAGTGGTCTG ->1425|16|DMCR1A|2 +>1425|16|DMCR1A|1 GAAGATGAAGAGGCGGATGGTGC ->1538|16|DMCR1A|5 -TTATATGGGATGCAAATGAAAGACT ->1539|16|DMCR1A|1 -TTATATGGGATGCAAATGAAAGAC ->1555|16|DMCR1A|1 -TCGCTGTGAACACTATTATATGG ->1576|16|DMCR1A|3 -TAAGTATCTCCGGCTTTAACCAAGTC ->1578|16|DMCR1A|7 +>1578|16|DMCR1A|1 TAAGTATCTCCGGCTTTAACCAAG ->1592|16|DMCR1A|1 -GAAGACTTCGGAGTTAAGTATCTC +>1602|16|DMCR1A|1 +TACATACCTGGGAAGACTTCGGAGT +>1603|16|DMCR1A|2 +TACATACCTGGGAAGACTTCGGAG >1681|16|DMCR1A|1 TCCTCCGGCGCGAGGGTAGATCTAACC ->1753|16|DMCR1A|1 -TAAACTGAACTGTCGGAAAAAGACAGC ->1755|16|DMCR1A|1 -TAAACTGAACTGTCGGAAAAAGACA ->1756|16|DMCR1A|2 -TATAAACTGAACTGTCGGAAAAAGAC ->1757|16|DMCR1A|3 +>1757|16|DMCR1A|1 TATAAACTGAACTGTCGGAAAAAGA ->1770|16|DMCR1A|1 -TACGAGAACGTAATATAAACTGAAC >1773|16|DMCR1A|1 TATACGAGAACGTAATATAAACTG ->1783|16|DMCR1A|1 -GATGGCGGAATATACGAGAACGTA ->1800|16|DMCR1A|2 -TATTCTGGGAATTCCGAAGATGGCG ->1802|16|DMCR1A|1 -TATTCTGGGAATTCCGAAGATGG ->1805|16|DMCR1A|1 -TCTGATATTCTGGGAATTCCGAAGA ->1807|16|DMCR1A|1 -TTCTGATATTCTGGGAATTCCGAA ->1813|16|DMCR1A|5 +>1813|16|DMCR1A|1 GATGATTCTGATATTCTGGGAAT ->1820|16|DMCR1A|2 -TAGAGGACAGATGATTCTGATATTC ->1838|16|DMCR1A|1 -TATTCAAGGTGGACTGGATAGAGGA ->1863|16|DMCR1A|3 +>1863|16|DMCR1A|2 TACCAATTGGTCCCTGTCAGACAGTT ->1864|16|DMCR1A|1 -TACCAATTGGTCCCTGTCAGACAGT ->1864|16|DMCR1A|1 -CTACCAATTGGTCCCTGTCAGACAGT ->1865|16|DMCR1A|2 -TACCAATTGGTCCCTGTCAGACAG ->1865|16|DMCR1A|1 -CTACCAATTGGTCCCTGTCAGACAG ->1865|16|DMCR1A|2 -ACTACCAATTGGTCCCTGTCAGACAG ->1872|16|DMCR1A|6 +>1872|16|DMCR1A|1 CCTAGAACTACCAATTGGTCCCTGT >1873|16|DMCR1A|1 TCACCTAGAACTACCAATTGGTCCCTG >1874|16|DMCR1A|1 -CCTAGAACTACCAATTGGTCCCT ->1874|16|DMCR1A|6 TCACCTAGAACTACCAATTGGTCCCT ->1875|16|DMCR1A|1 -CACCTAGAACTACCAATTGGTCCC ->1875|16|DMCR1A|16 +>1875|16|DMCR1A|2 TCACCTAGAACTACCAATTGGTCCC ->1876|16|DMCR1A|1 -TCACCTAGAACTACCAATTGGTCC ->1879|16|DMCR1A|3 +>1879|16|DMCR1A|2 TAAAATCACCTAGAACTACCAATTGG ->1882|16|DMCR1A|1 -TAAAATCACCTAGAACTACCAAT ->1883|16|DMCR1A|1 -TTAAAATCACCTAGAACTACCAA ->1884|16|DMCR1A|1 -TATATTAAAATCACCTAGAACTACCA ->1895|16|DMCR1A|2 -TTGTGCCAGGTATATTAAAATCACC ->1925|16|DMCR1A|1 -TATATTCGATTGTTTTTCTGGGGA ->1971|16|DMCR1A|1 -TAAGTCGAGCAAGCCGTCAATAAAGT ->1981|16|DMCR1A|1 -ACAACGATAAGTCGAGCAAGCCG ->1988|16|DMCR1A|1 -TTAACTTGCGACAACGATAAGTCGAG ->2100|16|DMCR1A|1 -TGATATGGATATTCAGGTTGAGTTC ->2126|16|DMCR1A|1 -TATGTCGATTGCCACCTCGAAAGTAGG ->2130|16|DMCR1A|1 -CCTATGTCGATTGCCACCTCGAAAG ->2131|16|DMCR1A|1 -TACCTATGTCGATTGCCACCTCGAAA ->2132|16|DMCR1A|1 -TACCTATGTCGATTGCCACCTCGAA ->2133|16|DMCR1A|1 -TACCTATGTCGATTGCCACCTCGA ->2153|16|DMCR1A|2 +>2153|16|DMCR1A|1 TCTGAATTTACTTTTAATACCGTACC ->2160|16|DMCR1A|1 -ACTTCTCTGAATTTACTTTTAATA ->2161|16|DMCR1A|1 -TGACTTCTCTGAATTTACTTTTAAT ->2211|16|DMCR1A|2 -TGTTTAGCCTCCGAAAATTTGCCT ->2211|16|DMCR1A|3 +>2211|16|DMCR1A|1 TTGTTTAGCCTCCGAAAATTTGCCT ->2335|16|DMCR1A|1 -TTGACGGATAGTACATCGGAACACAA ->2343|16|DMCR1A|1 -TTTCGAGATTGACGGATAGTACATCG ->2346|16|DMCR1A|1 -TTTCGAGATTGACGGATAGTACA ->2350|16|DMCR1A|1 -GAGGTTTCGAGATTGACGGATAG ->2350|16|DMCR1A|1 -GGAGGTTTCGAGATTGACGGATAG >2386|16|DMCR1A|1 TACATTTCTTAGGTGTGTCAACTCT ->2413|16|DMCR1A|1 -TTTTTAAATTTTATATAGAGTCTGGAC ->2436|16|DMCR1A|1 -GGATGGACTGAGAACCGGTATTTT ->2437|16|DMCR1A|1 -GGATGGACTGAGAACCGGTATTT ->2442|16|DMCR1A|5 +>2430|16|DMCR1A|1 +TGGACTGAGAACCGGTATTTTTAAATT +>2432|16|DMCR1A|3 +TGGACTGAGAACCGGTATTTTTAAA +>2433|16|DMCR1A|2 +TGGACTGAGAACCGGTATTTTTAA +>2442|16|DMCR1A|1 TTACAAAGGATGGACTGAGAACCGG ->2444|16|DMCR1A|5 -TTACAAAGGATGGACTGAGAACC ->2446|16|DMCR1A|6 -TATTTACAAAGGATGGACTGAGAA ->2447|16|DMCR1A|2 -TATTTACAAAGGATGGACTGAGA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,32 +1,2 @@ ->830|16|DMCR1A|1 -TCCTGTTGATCATTTGGCCGTGGT ->831|16|DMCR1A|2 -TCCTGTTGATCATTTGGCCGTGG ->1026|16|DMCR1A|1 -CCCTTGTGGTTGTAAACTATTCGG ->1321|16|DMCR1A|2 -TACCAACATACTATCCGGCAAAAAAC ->1602|16|DMCR1A|8 -TACATACCTGGGAAGACTTCGGAGT ->1603|16|DMCR1A|9 -TACATACCTGGGAAGACTTCGGAG ->1604|16|DMCR1A|1 -TACATACCTGGGAAGACTTCGGA ->1953|16|DMCR1A|1 -TAAAGTCATGTTGTGCTAAAGGGA >2323|16|DMCR1A|1 CATCGGAACACAAGAGTCAAAAAAT ->2324|16|DMCR1A|2 -TACATCGGAACACAAGAGTCAAAAAA ->2327|16|DMCR1A|1 -TACATCGGAACACAAGAGTCAAA ->2430|16|DMCR1A|1 -TGGACTGAGAACCGGTATTTTTAAATT ->2431|16|DMCR1A|3 -TGGACTGAGAACCGGTATTTTTAAAT ->2432|16|DMCR1A|9 -TGGACTGAGAACCGGTATTTTTAAA ->2433|16|DMCR1A|8 -TGGACTGAGAACCGGTATTTTTAA ->2434|16|DMCR1A|1 -TGGACTGAGAACCGGTATTTTTA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number 1 0 0.00 -2 1 0.92 -3 1 0.92 -4 1 0.92 -5 2 1.83 +2 0 0.00 +3 0 0.00 +4 0 0.00 +5 0 0.00 6 0 0.00 -7 1 0.92 -8 5 4.59 -9 2 1.83 -10 30 27.52 -11 1 0.92 -12 8 7.34 -13 4 3.67 -14 10 9.17 -15 3 2.75 -16 3 2.75 +7 0 0.00 +8 1 12.50 +9 0 0.00 +10 1 12.50 +11 0 0.00 +12 1 12.50 +13 0 0.00 +14 0 0.00 +15 1 12.50 +16 1 12.50 17 0 0.00 -18 1 0.92 -19 12 11.01 -20 5 4.59 -21 11 10.09 -22 3 2.75 -23 5 4.59 +18 1 12.50 +19 2 25.00 +20 0 0.00 +21 0 0.00 +22 0 0.00 +23 0 0.00 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,66 +1,16 @@ ->7|0|DMCR1A|1 -TTCAAAGCGAACGGTCGTGTTTTT ->116|0|DMCR1A|1 -TTATTAAAGATCCGTTCGCTTCGCGAG ->117|0|DMCR1A|2 -TATTAAAGATCCGTTCGCTTCGCGAG ->119|0|DMCR1A|3 -TTAAAGATCCGTTCGCTTCGCGAG ->119|0|DMCR1A|1 -TTAAAGATCCGTTCGCTTCGCGAGTG ->153|0|DMCR1A|1 -TGATTTGTGCAGTAGTTTAAACAA ->552|0|DMCR1A|1 -TTTAATGGCCGAACGAGTGATGACC ->635|0|DMCR1A|1 -GATGAAATCGTTTATGCGCCAAACT ->662|0|DMCR1A|1 -AGGTGGCTTGAAAGAACTGATCAACA ->665|0|DMCR1A|4 -TGGCTTGAAAGAACTGATCAACAGT ->838|0|DMCR1A|1 -CAAATGATCAACAGGACTCCACAAC ->840|0|DMCR1A|2 -AATGATCAACAGGACTCCACAACT ->849|0|DMCR1A|1 -CAGGACTCCACAACTGATCAGCTG ->975|0|DMCR1A|1 -AAAGATTCCGAATTGTCTGCACTGG ->979|0|DMCR1A|2 -ATTCCGAATTGTCTGCACTGGTTT ->980|0|DMCR1A|1 -TTCCGAATTGTCTGCACTGGTTTT ->987|0|DMCR1A|1 -TTGTCTGCACTGGTTTTTCAACCAGT ->1145|0|DMCR1A|1 -TTTCGTTTCTCGGCTTTCCCCTGATC ->1161|0|DMCR1A|1 -TCCCCTGATCAAACATCGTCTGATG ->1162|0|DMCR1A|7 +>1162|0|DMCR1A|1 CCCCTGATCAAACATCGTCTGAT ->1162|0|DMCR1A|6 -CCCCTGATCAAACATCGTCTGATG ->1162|0|DMCR1A|1 -CCCCTGATCAAACATCGTCTGATGTA +>1337|0|DMCR1A|1 +TATGTTGGTAAAAGAGTTCGAAG >1421|0|DMCR1A|1 CACTGCACCATCCGCCTCTTCAT ->1583|0|DMCR1A|3 +>1583|0|DMCR1A|1 TTAAAGCCGGAGATACTTAACTC ->1863|0|DMCR1A|1 -AACTGTCTGACAGGGACCAATTGG ->1868|0|DMCR1A|1 -TCTGACAGGGACCAATTGGTAGTTC ->1870|0|DMCR1A|2 +>1870|0|DMCR1A|1 TGACAGGGACCAATTGGTAGTTC ->1969|0|DMCR1A|1 -TGACTTTATTGACGGCTTGCTCGAC ->1970|0|DMCR1A|1 -GACTTTATTGACGGCTTGCTCGACT ->1973|0|DMCR1A|1 -TTTATTGACGGCTTGCTCGACTT ->2205|0|DMCR1A|1 -TTCGCAAGGCAAATTTTCGGAGGCT ->2329|0|DMCR1A|1 -TGACTCTTGTGTTCCGATGTACTA ->2371|0|DMCR1A|1 -TCCTTGGTTTAATAAAGAGTTGAC +>1967|0|DMCR1A|2 +CATGACTTTATTGACGGCTTGCT +>1967|0|DMCR1A|1 +CATGACTTTATTGACGGCTTGCTC +>2340|0|DMCR1A|1 +TTCCGATGTACTATCCGTCAATCT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,26 +1,2 @@ ->844|0|DMCR1A|1 -ATCAACAGGACTCCACAACTGATCAG ->1040|0|DMCR1A|1 -ACCACAAGGGAACATTGAGTCCGG ->1337|0|DMCR1A|1 -TATGTTGGTAAAAGAGTTCGAAG ->1617|0|DMCR1A|2 -CAGGTATGTACACTATATATAGG ->1617|0|DMCR1A|1 -CAGGTATGTACACTATATATAGGT ->1967|0|DMCR1A|8 -CATGACTTTATTGACGGCTTGCT ->1967|0|DMCR1A|2 -CATGACTTTATTGACGGCTTGCTC ->2338|0|DMCR1A|2 +>2338|0|DMCR1A|1 TGTTCCGATGTACTATCCGTCAATC ->2340|0|DMCR1A|1 -TTCCGATGTACTATCCGTCAATC ->2340|0|DMCR1A|3 -TTCCGATGTACTATCCGTCAATCT ->2340|0|DMCR1A|2 -TTCCGATGTACTATCCGTCAATCTC ->2340|0|DMCR1A|1 -TTCCGATGTACTATCCGTCAATCTCG ->2447|0|DMCR1A|1 -TCTCAGTCCATCCTTTGTAAATAT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,74 +1,20 @@ ->58|16|DMRT1B|1 -TCTGATCGAACGGTTGATCTGGCAAC ->416|16|DMRT1B|1 -TCGTTGCGATCAGGGGGACTGCCCC ->417|16|DMRT1B|2 -TCGTTGCGATCAGGGGGACTGCCC ->429|16|DMRT1B|1 -TCCTGAACGGGTCGTTGCGATCA ->430|16|DMRT1B|5 +>430|16|DMRT1B|2 TCCTCCTGAACGGGTCGTTGCGATC ->430|16|DMRT1B|1 -CTCCTGAACGGGTCGTTGCGATC ->439|16|DMRT1B|1 -TCTGGAGCTCCTCCTGAACGGGTC ->491|16|DMRT1B|1 -TTCCGTCACCCTGAGTCGGGTTAC ->534|16|DMRT1B|1 -GCTGGGGGCCTGCTTGCTTACCCCTT ->547|16|DMRT1B|1 -TAGTCAACAGTGGCTGGGGGCCTGC ->593|16|DMRT1B|1 -TGCTGTAGGAGCCAAGTTCTCCACCT >635|16|DMRT1B|1 AATGTGGTCCATCGTTTTCTGAC >1076|16|DMRT1B|2 GATGCGTAGCTGCCTGGCTTGGACT ->1076|16|DMRT1B|3 +>1076|16|DMRT1B|1 TGCGTAGCTGCCTGGCTTGGACT ->1077|16|DMRT1B|9 +>1077|16|DMRT1B|1 GATGCGTAGCTGCCTGGCTTGGAC >1089|16|DMRT1B|1 TTCTTGGCAACAGATGCGTAGCTG ->1105|16|DMRT1B|1 -TCTGCACCCGTGCTAGCATTCTTGGC ->1106|16|DMRT1B|5 +>1106|16|DMRT1B|1 TCTGCACCCGTGCTAGCATTCTTGG ->1191|16|DMRT1B|1 -TCTGCGTACGAAGCCTCACCCGTC ->1234|16|DMRT1B|1 -CCAGTTCGCTAAGGCTCGTGTCCGA ->1241|16|DMRT1B|4 -TGGCTGCCCAGTTCGCTAAGGCTCG ->1242|16|DMRT1B|3 -CGTGGCTGCCCAGTTCGCTAAGGCTC ->1242|16|DMRT1B|4 -TGGCTGCCCAGTTCGCTAAGGCTC ->1243|16|DMRT1B|2 -CGTGGCTGCCCAGTTCGCTAAGGCT ->1254|16|DMRT1B|3 -TTTTGCGTACGTGGCTGCCCAGT ->1332|16|DMRT1B|2 -TCGCTCTTAAACTTGGGAACGCTT ->1333|16|DMRT1B|2 -TCGCTCTTAAACTTGGGAACGCT ->1336|16|DMRT1B|2 +>1336|16|DMRT1B|1 TCCAGGTCGCTCTTAAACTTGGGAAC >1336|16|DMRT1B|2 CAGGTCGCTCTTAAACTTGGGAAC ->1341|16|DMRT1B|1 -CGCTTCCAGGTCGCTCTTAAACTTG ->1364|16|DMRT1B|1 -CACAGAGGCCAAGTCATTGAGCGCCG ->1365|16|DMRT1B|37 +>1365|16|DMRT1B|2 CACAGAGGCCAAGTCATTGAGCGCC ->1369|16|DMRT1B|1 -TGCGCACAGAGGCCAAGTCATTGAG ->1381|16|DMRT1B|1 -TTGCGCTCCCGTGCGCACAGAGGC ->1410|16|DMRT1B|1 -TCCAGTCCGCTGCAGGATAGCGCT ->1413|16|DMRT1B|1 -TCGTCCAGTCCGCTGCAGGATAGC ->1422|16|DMRT1B|3 -TCGTAGCCTCGTCCAGTCCGCTG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,12 +1,2 @@ ->619|16|DMRT1B|5 +>619|16|DMRT1B|1 TTCTGACTTGTCGCGGTGGTAGC ->1220|16|DMRT1B|1 -TCGTGTCCGATCTTAGCTTCCTAA ->1328|16|DMRT1B|1 -TCTTAAACTTGGGAACGCTTTCCG ->1353|16|DMRT1B|1 -TCATTGAGCGCCGCTTCCAGGTCG ->1365|16|DMRT1B|9 -CAGAGGCCAAGTCATTGAGCGCC ->1366|16|DMRT1B|1 -ACAGAGGCCAAGTCATTGAGCGC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number -1 7 2.34 -2 3 1.00 -3 8 2.68 -4 4 1.34 -5 6 2.01 -6 5 1.67 -7 8 2.68 -8 3 1.00 -9 6 2.01 -10 13 4.35 -11 5 1.67 -12 6 2.01 -13 2 0.67 -14 23 7.69 -15 12 4.01 -16 30 10.03 -17 16 5.35 -18 30 10.03 -19 26 8.70 -20 43 14.38 -21 9 3.01 -22 25 8.36 -23 9 3.01 +1 0 0.00 +2 0 0.00 +3 0 0.00 +4 0 0.00 +5 1 7.69 +6 0 0.00 +7 1 7.69 +8 0 0.00 +9 0 0.00 +10 1 7.69 +11 0 0.00 +12 0 0.00 +13 0 0.00 +14 0 0.00 +15 0 0.00 +16 2 15.38 +17 1 7.69 +18 0 0.00 +19 2 15.38 +20 2 15.38 +21 1 7.69 +22 1 7.69 +23 1 7.69 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,96 +1,26 @@ ->414|0|DMRT1B|1 -GGGGGGCAGTCCCCCTGATCGCAACGA ->419|0|DMRT1B|1 -GCAGTCCCCCTGATCGCAACGACCC ->422|0|DMRT1B|1 -GTCCCCCTGATCGCAACGACCCGTT ->422|0|DMRT1B|1 -GTCCCCCTGATCGCAACGACCCGT ->423|0|DMRT1B|1 -TCCCCCTGATCGCAACGACCCGT ->433|0|DMRT1B|1 -CGCAACGACCCGTTCAGGAGGAG >438|0|DMRT1B|1 CGACCCGTTCAGGAGGAGCTCCAGAC >553|0|DMRT1B|1 CCCCAGCCACTGTTGACTAGCGAC ->796|0|DMRT1B|1 -TCCACATTCGAGACTCAACGGCGC ->796|0|DMRT1B|1 -TCCACATTCGAGACTCAACGGCG ->799|0|DMRT1B|1 -ACATTCGAGACTCAACGGCGCGT ->824|0|DMRT1B|1 -CAAGAGAGACACAGGGCGTAGCT ->1224|0|DMRT1B|22 +>1224|0|DMRT1B|1 GAAGCTAAGATCGGACACGAGCCT >1229|0|DMRT1B|1 -TAAGATCGGACACGAGCCTTAGCG ->1229|0|DMRT1B|20 TAAGATCGGACACGAGCCTTAGC ->1232|0|DMRT1B|3 -GATCGGACACGAGCCTTAGCGAAC ->1232|0|DMRT1B|1 -GATCGGACACGAGCCTTAGCGAA ->1323|0|DMRT1B|1 -AGTTTCGGAAAGCGTTCCCAAGTT ->1337|0|DMRT1B|1 -TTCCCAAGTTTAAGAGCGACCTG ->1353|0|DMRT1B|1 -CGACCTGGAAGCGGCGCTCAATGAC >1355|0|DMRT1B|1 ACCTGGAAGCGGCGCTCAATGACTT ->1355|0|DMRT1B|1 -ACCTGGAAGCGGCGCTCAATGAC ->1357|0|DMRT1B|1 -CTGGAAGCGGCGCTCAATGACTTG ->1360|0|DMRT1B|4 -GAAGCGGCGCTCAATGACTTGGCC ->1360|0|DMRT1B|1 -GAAGCGGCGCTCAATGACTTGGC ->1361|0|DMRT1B|4 -AAGCGGCGCTCAATGACTTGGCCT ->1362|0|DMRT1B|1 -AGCGGCGCTCAATGACTTGGCCTCT ->1362|0|DMRT1B|2 -AGCGGCGCTCAATGACTTGGCCTC ->1362|0|DMRT1B|2 -AGCGGCGCTCAATGACTTGGCCT ->1368|0|DMRT1B|8 +>1367|0|DMRT1B|1 +CGCTCAATGACTTGGCCTCTGTGC +>1368|0|DMRT1B|1 GCTCAATGACTTGGCCTCTGTGCGCA ->1368|0|DMRT1B|4 -GCTCAATGACTTGGCCTCTGTGCGC >1369|0|DMRT1B|1 CTCAATGACTTGGCCTCTGTGCGCA ->1370|0|DMRT1B|7 -TCAATGACTTGGCCTCTGTGCGCACG ->1370|0|DMRT1B|4 +>1370|0|DMRT1B|2 TCAATGACTTGGCCTCTGTGCGCAC ->1370|0|DMRT1B|3 -TCAATGACTTGGCCTCTGTGCGCA ->1370|0|DMRT1B|4 -TCAATGACTTGGCCTCTGTGCGC ->1371|0|DMRT1B|5 +>1371|0|DMRT1B|1 CAATGACTTGGCCTCTGTGCGCACG ->1371|0|DMRT1B|3 -CAATGACTTGGCCTCTGTGCGCAC >1371|0|DMRT1B|1 -CAATGACTTGGCCTCTGTGCGCA ->1372|0|DMRT1B|2 -AATGACTTGGCCTCTGTGCGCACGG ->1372|0|DMRT1B|1 -AATGACTTGGCCTCTGTGCGCACG ->1373|0|DMRT1B|1 -ATGACTTGGCCTCTGTGCGCACGG ->1374|0|DMRT1B|12 -TGACTTGGCCTCTGTGCGCACGGGA ->1374|0|DMRT1B|4 +CAATGACTTGGCCTCTGTGCGCAC +>1374|0|DMRT1B|1 TGACTTGGCCTCTGTGCGCACGGG ->1374|0|DMRT1B|5 +>1374|0|DMRT1B|1 TGACTTGGCCTCTGTGCGCACGG ->1376|0|DMRT1B|1 -ACTTGGCCTCTGTGCGCACGGGA ->1415|0|DMRT1B|1 -TATCCTGCAGCGGACTGGACGAGGC ->1425|0|DMRT1B|1 -CGGACTGGACGAGGCTACGACAG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,2 @@ ->632|0|DMRT1B|7 +>632|0|DMRT1B|2 CAAGTCAGAAAACGATGGACCACAT ->632|0|DMRT1B|1 -CAAGTCAGAAAACGATGGACCACA ->1234|0|DMRT1B|1 -TCGGACACGAGCCTTAGCGAACTGG ->1342|0|DMRT1B|1 -AAGTTTAAGAGCGACCTGGAAGC ->1367|0|DMRT1B|1 -CGCTCAATGACTTGGCCTCTGTGCGCA ->1367|0|DMRT1B|2 -CGCTCAATGACTTGGCCTCTGTGCG ->1367|0|DMRT1B|1 -CGCTCAATGACTTGGCCTCTGTGC ->1378|0|DMRT1B|1 -TTGGCCTCTGTGCGCACGGGAGCGCA ->1379|0|DMRT1B|1 -TGGCCTCTGTGCGCACGGGAGCGC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,2732 +1,764 @@\n >218|16|FW|1\n TGAATTGAGAGTCGGCGTTCGTCAT\n->219|16|FW|34\n+>219|16|FW|3\n TGAATTGAGAGTCGGCGTTCGTCA\n->220|16|FW|17\n+>220|16|FW|1\n TGAATTGAGAGTCGGCGTTCGTC\n->223|16|FW|1\n-CGCTGAATTGAGAGTCGGCGTTC\n->224|16|FW|1\n-GTTGCGCTGAATTGAGAGTCGGCGTT\n->224|16|FW|1\n-TGCGCTGAATTGAGAGTCGGCGTT\n->226|16|FW|2\n-TGTTGCGCTGAATTGAGAGTCGGCG\n->226|16|FW|5\n-GTTGCGCTGAATTGAGAGTCGGCG\n->227|16|FW|1\n-TGTTGCGCTGAATTGAGAGTCGGC\n >228|16|FW|1\n-GTTGTTGCGCTGAATTGAGAGTCGG\n->228|16|FW|2\n-TTGTTGCGCTGAATTGAGAGTCGG\n->228|16|FW|4\n TGTTGCGCTGAATTGAGAGTCGG\n->230|16|FW|1\n-CGTTGTTGCGCTGAATTGAGAGTC\n->233|16|FW|1\n-TACGCGTTGTTGCGCTGAATTGAGA\n->237|16|FW|14\n-GAAGTACGCGTTGTTGCGCTGAATT\n >238|16|FW|2\n AGAAGTACGCGTTGTTGCGCTGAAT\n->238|16|FW|2\n-GAAGTACGCGTTGTTGCGCTGAAT\n->239|16|FW|1\n-GAAGTACGCGTTGTTGCGCTGAA\n->240|16|FW|3\n-GGAGAAGTACGCGTTGTTGCGCTGA\n->241|16|FW|8\n+>241|16|FW|1\n TAGGAGAAGTACGCGTTGTTGCGCTG\n->241|16|FW|3\n-GGAGAAGTACGCGTTGTTGCGCTG\n->242|16|FW|6\n+>241|16|FW|1\n+GAGAAGTACGCGTTGTTGCGCTG\n+>242|16|FW|1\n TAGGAGAAGTACGCGTTGTTGCGCT\n->243|16|FW|3\n-CGTAGGAGAAGTACGCGTTGTTGCGC\n->243|16|FW|1\n-TAGGAGAAGTACGCGTTGTTGCGC\n->245|16|FW|9\n+>245|16|FW|1\n CGTAGGAGAAGTACGCGTTGTTGC\n->246|16|FW|2\n+>246|16|FW|1\n CGTAGGAGAAGTACGCGTTGTTG\n->250|16|FW|1\n-TGAGACGTAGGAGAAGTACGCGTT\n->256|16|FW|1\n-TTGTCGGTGAGACGTAGGAGAAGTA\n->257|16|FW|1\n-TTGTCGGTGAGACGTAGGAGAAGT\n->258|16|FW|2\n-TTGTCGGTGAGACGTAGGAGAAG\n->259|16|FW|1\n-GATTGTCGGTGAGACGTAGGAGAA\n->259|16|FW|1\n-ATTGTCGGTGAGACGTAGGAGAA\n->268|16|FW|1\n-TCTGCGTTTGGGATTGTCGGTGAGAC\n->269|16|FW|6\n+>269|16|FW|2\n TCTGCGTTTGGGATTGTCGGTGAGA\n->272|16|FW|1\n-TGTCTGCGTTTGGGATTGTCGGTG\n->273|16|FW|1\n-TGTCTGCGTTTGGGATTGTCGGT\n->276|16|FW|1\n-CGATGTCTGCGTTTGGGATTGTC\n->286|16|FW|1\n-TTATTGACCGCTCGATGTCTGCGTT\n->286|16|FW|7\n+>286|16|FW|2\n TATTGACCGCTCGATGTCTGCGTT\n->287|16|FW|1\n-TATTGACCGCTCGATGTCTGCGT\n->291|16|FW|3\n-TATGGGTTATTGACCGCTCGATGTCT\n->292|16|FW|1\n-TATGGGTTATTGACCGCTCGATGTC\n->292|16|FW|1\n-ATGGGTTATTGACCGCTCGATGTC\n->293|16|FW|1\n-TATGGGTTATTGACCGCTCGATGT\n->294|16|FW|1\n-GCTATGGGTTATTGACCGCTCGATG\n->294|16|FW|1\n-TATGGGTTATTGACCGCTCGATG\n->298|16|FW|5\n-CCTGGGCTATGGGTTATTGACCGCTC\n->298|16|FW|2\n-CTGGGCTATGGGTTATTGACCGCTC\n->298|16|FW|2\n-TGGGCTATGGGTTATTGACCGCTC\n->299|16|FW|27\n+>299|16|FW|3\n TCCTGGGCTATGGGTTATTGACCGCT\n->299|16|FW|24\n+>299|16|FW|1\n CCTGGGCTATGGGTTATTGACCGCT\n->299|16|FW|3\n-CTGGGCTATGGGTTATTGACCGCT\n->300|16|FW|2\n-TTCCTGGGCTATGGGTTATTGACCGC\n->300|16|FW|5\n-TCCTGGGCTATGGGTTATTGACCGC\n >300|16|FW|1\n CCTGGGCTATGGGTTATTGACCGC\n->300|16|FW|2\n-CTGGGCTATGGGTTATTGACCGC\n->301|16|FW|6\n-TCCTGGGCTATGGGTTATTGACCG\n->301|16|FW|2\n+>301|16|FW|1\n CCTGGGCTATGGGTTATTGACCG\n->302|16|FW|2\n-TTTCCTGGGCTATGGGTTATTGACC\n->302|16|FW|4\n+>302|16|FW|1\n TTCCTGGGCTATGGGTTATTGACC\n->302|16|FW|9\n+>302|16|FW|1\n TCCTGGGCTATGGGTTATTGACC\n->303|16|FW|2\n-TTTCCTGGGCTATGGGTTATTGAC\n >303|16|FW|1\n-TTCCTGGGCTATGGGTTATTGAC\n->315|16|FW|1\n-GTAGAAGAAGGTTTCCTGGGCTA\n->319|16|FW|1\n-TGTTGGTAGAAGAAGGTTTCCTGG\n->323|16|FW|6\n-TGATTTGTTGGTAGAAGAAGGTTTC\n->324|16|FW|7\n-TGATTTGTTGGTAGAAGAAGGTTT\n->325|16|FW|1\n-TTGATTTGTTGGTAGAAGAAGGTT\n->325|16|FW|22\n-TGATTTGTTGGTAGAAGAAGGTT\n->327|16|FW|1\n-TTCTTGATTTGTTGGTAGAAGAAGG\n->330|16|FW|1\n-TTTCTTGATTTGTTGGTAGAAGA\n->365|16|FW|1\n-CGGAGCCAATAGAGCGGGAGAGC\n->367|16|FW|1\n-CTGTCGGAGCCAATAGAGCGGGAGA\n->369|16|FW|24\n+TTTCCTGGGCTATGGGTTATTGAC\n+>369|16|FW|2\n TTCTGTCGGAGCCAATAGAGCGGGA\n->371|16|FW|1\n-TTCTGTCGGAGCCAATAGAGCGG\n->376|16|FW|1\n-TAGCGGGGCTTCTGTCGGAGCCAATAG\n->378|16|FW|1\n-AGCGGGGCTTCTGTCGGAGCCAAT\n >379|16|FW|1\n TAGCGGGGCTTCTGTCGGAGCCAA\n->381|16|FW|2\n-GGTAGCGGGGCTTCTGTCGGAGCC\n->382|16|FW|1\n-GGTAGCGGGGCTTCTGTCGGAGC\n->390|16|FW|1\n-TTGTTGGAGGTAGCGGGGCTTCT\n->391|16|FW|6\n+>391|16|FW|3\n TGTTGTTGGAGGTAGCGGGGCTTC\n->392|16|FW|1\n-TTGTTGTTGGAGGTAGCGGGGCTT\n->392|16|FW|4\n-TGTTGTTGGAGGTAGCGGGGCTT\n->398|16|FW|1\n-TCCAGCTGTTGTTGTTGGAGGTAGCG\n->407|16|FW|2\n-TCCCTCTCCAGCTGTTGTTGTTG\n->410|16|FW|1\n-CGGTCCCTCTCCAGCTGTTGTTG\n->416|16|FW|3\n-GCGGGCTGCCGGTCCCTCTCCAGCTG\n->416|16|FW|1\n-CGGGCTGCCGGTCCCTCTCCAGCTG\n->417|16|FW|1\n-GCGGGCTGCCGGTCCCTCTCCAGCT\n->418|16|FW|3\n+>418|16|FW|1\n GCGGGCTGCCGGTCCCTCTCCAGC\n->419|16|FW|1\n-GCGGGC'..b'FW|1\n-AATGATGTCAATATTGCTGTTGC\n->4286|16|FW|7\n-TGAATGATGTCAATATTGCTGTTG\n->4286|16|FW|2\n-GAATGATGTCAATATTGCTGTTG\n->4288|16|FW|2\n+>4288|16|FW|1\n TCGCTGAATGATGTCAATATTGCTGT\n >4289|16|FW|1\n TCGCTGAATGATGTCAATATTGCTG\n@@ -2734,169 +766,45 @@\n TGCTCGCTGAATGATGTCAATATTGC\n >4291|16|FW|1\n CTCGCTGAATGATGTCAATATTGC\n->4291|16|FW|1\n-TCGCTGAATGATGTCAATATTGC\n->4292|16|FW|1\n-GCTCGCTGAATGATGTCAATATTG\n->4299|16|FW|2\n+>4299|16|FW|1\n TGATTGTGCTCGCTGAATGATGTC\n->4300|16|FW|1\n-TTTGATTGTGCTCGCTGAATGATGT\n->4301|16|FW|1\n-TTTGATTGTGCTCGCTGAATGATG\n->4318|16|FW|2\n-TGATGGTTCTCAGAATCTTTGATT\n >4345|16|FW|1\n-TTCACTCCGAACGTACCACGGTGCCC\n->4345|16|FW|3\n TCACTCCGAACGTACCACGGTGCCC\n->4354|16|FW|1\n-TTTGGATGTTTTCACTCCGAACGTACC\n->4354|16|FW|1\n-TGGATGTTTTCACTCCGAACGTACC\n->4360|16|FW|1\n-GTCTCTTTGGATGTTTTCACTCCGAA\n->4360|16|FW|1\n-TCTCTTTGGATGTTTTCACTCCGAA\n->4365|16|FW|2\n-TAAGTCTCTTTGGATGTTTTCACT\n->4381|16|FW|3\n-TAACTGATGGGATATTTAAGTCTC\n->4384|16|FW|3\n+>4365|16|FW|8\n+TTAAGTCTCTTTGGATGTTTTCACT\n+>4384|16|FW|1\n TTGGTAACTGATGGGATATTTAAGT\n->4386|16|FW|1\n-GTTGGTAACTGATGGGATATTTAA\n->4389|16|FW|8\n+>4389|16|FW|1\n TTGCGTTGGTAACTGATGGGATATT\n->4389|16|FW|8\n-TGCGTTGGTAACTGATGGGATATT\n->4390|16|FW|1\n-ATTGCGTTGGTAACTGATGGGATAT\n->4390|16|FW|12\n-TTGCGTTGGTAACTGATGGGATAT\n->4390|16|FW|3\n-TGCGTTGGTAACTGATGGGATAT\n >4391|16|FW|2\n-GATTGCGTTGGTAACTGATGGGATA\n->4391|16|FW|1\n-ATTGCGTTGGTAACTGATGGGATA\n->4391|16|FW|13\n TTGCGTTGGTAACTGATGGGATA\n->4392|16|FW|3\n-TGATTGCGTTGGTAACTGATGGGAT\n->4392|16|FW|12\n+>4392|16|FW|1\n GATTGCGTTGGTAACTGATGGGAT\n->4392|16|FW|3\n+>4392|16|FW|1\n ATTGCGTTGGTAACTGATGGGAT\n->4393|16|FW|48\n+>4393|16|FW|5\n TGATTGCGTTGGTAACTGATGGGA\n->4393|16|FW|32\n+>4393|16|FW|3\n GATTGCGTTGGTAACTGATGGGA\n->4396|16|FW|1\n-TCCGTGATTGCGTTGGTAACTGATG\n->4397|16|FW|2\n-TCCGTGATTGCGTTGGTAACTGAT\n->4397|16|FW|1\n-CCGTGATTGCGTTGGTAACTGAT\n->4398|16|FW|7\n+>4398|16|FW|1\n TTCCGTGATTGCGTTGGTAACTGA\n->4398|16|FW|3\n-TCCGTGATTGCGTTGGTAACTGA\n >4402|16|FW|1\n TTCCTTAAGTTCCGTGATTGCGTTGGTAA\n->4403|16|FW|1\n-CTTAAGTTCCGTGATTGCGTTGGTA\n->4407|16|FW|1\n-TTCCTTAAGTTCCGTGATTGCGTT\n->4408|16|FW|1\n-TTTCCTTAAGTTCCGTGATTGCGT\n->4416|16|FW|8\n-TATGGTATTTTTCCTTAAGTTCCGT\n->4417|16|FW|6\n+>4417|16|FW|1\n TATGGTATTTTTCCTTAAGTTCCG\n->4457|16|FW|1\n-TAGACCTCGCGCTAGGTGGTTGGGG\n->4463|16|FW|1\n-GCTGGATTAGACCTCGCGCTAGGTGG\n->4465|16|FW|2\n-GCTGGATTAGACCTCGCGCTAGGT\n->4466|16|FW|4\n-AGCTGGATTAGACCTCGCGCTAGG\n->4466|16|FW|2\n+>4466|16|FW|1\n GCTGGATTAGACCTCGCGCTAGG\n >4468|16|FW|1\n CTGAGCTGGATTAGACCTCGCGCTA\n->4468|16|FW|5\n-TGAGCTGGATTAGACCTCGCGCTA\n->4469|16|FW|1\n-CTGAGCTGGATTAGACCTCGCGCT\n->4472|16|FW|4\n-GCTGCTGAGCTGGATTAGACCTCGC\n->4475|16|FW|6\n+>4475|16|FW|2\n AACGGCTGCTGAGCTGGATTAGACCT\n->4475|16|FW|5\n+>4475|16|FW|1\n ACGGCTGCTGAGCTGGATTAGACCT\n->4476|16|FW|2\n-GAACGGCTGCTGAGCTGGATTAGACC\n->4476|16|FW|6\n-AACGGCTGCTGAGCTGGATTAGACC\n->4476|16|FW|4\n+>4476|16|FW|1\n ACGGCTGCTGAGCTGGATTAGACC\n->4486|16|FW|3\n-CGGAGACGGGAACGGCTGCTGAGCT\n->4489|16|FW|1\n-CGCCGGAGACGGGAACGGCTGCTGA\n->4494|16|FW|1\n-TCCTTTCGCCGGAGACGGGAACGGCT\n >4494|16|FW|1\n CCTTTCGCCGGAGACGGGAACGGCT\n->4498|16|FW|3\n-TAGGTCCTTTCGCCGGAGACGGGAAC\n->4498|16|FW|1\n-GGTCCTTTCGCCGGAGACGGGAAC\n->4500|16|FW|1\n-GTAGGTCCTTTCGCCGGAGACGGGA\n->4500|16|FW|1\n-TAGGTCCTTTCGCCGGAGACGGGA\n->4502|16|FW|4\n-TTGGTAGGTCCTTTCGCCGGAGACGG\n->4503|16|FW|1\n-TTGGTAGGTCCTTTCGCCGGAGACG\n->4504|16|FW|4\n-TTGGTAGGTCCTTTCGCCGGAGAC\n->4505|16|FW|3\n-GTTGGTAGGTCCTTTCGCCGGAGA\n->4505|16|FW|1\n-TTGGTAGGTCCTTTCGCCGGAGA\n->4506|16|FW|1\n-GTTGGTAGGTCCTTTCGCCGGAG\n->4509|16|FW|1\n-GCTGGGTTGGTAGGTCCTTTCGCCG\n->4510|16|FW|4\n-GCTGGGTTGGTAGGTCCTTTCGCC\n->4510|16|FW|1\n-CTGGGTTGGTAGGTCCTTTCGCC\n->4511|16|FW|6\n-CGCTGGGTTGGTAGGTCCTTTCGC\n->4511|16|FW|2\n-GCTGGGTTGGTAGGTCCTTTCGC\n->4512|16|FW|1\n-TCGCTGGGTTGGTAGGTCCTTTCG\n->4512|16|FW|1\n-CGCTGGGTTGGTAGGTCCTTTCG\n->4513|16|FW|4\n-TTCGCTGGGTTGGTAGGTCCTTTC\n->4515|16|FW|5\n-TATTCGCTGGGTTGGTAGGTCCTT\n >4515|16|FW|1\n ATTCGCTGGGTTGGTAGGTCCTT\n->4516|16|FW|4\n+>4516|16|FW|1\n TATTCGCTGGGTTGGTAGGTCCT\n->4517|16|FW|2\n-TTTATTCGCTGGGTTGGTAGGTCC\n->4522|16|FW|1\n-TAATAATTTATTCGCTGGGTTGGTA\n->4547|16|FW|1\n-CAACTGTTCTATGTTTAAACGGCCC\n->4558|16|FW|1\n-TATTATTTTTCCAACTGTTCTATGT\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,720 +1,60 @@\n->237|16|FW|1\n-GAGAAGTACGCGTTGTTGCGCTGAATT\n->240|16|FW|2\n-GAGAAGTACGCGTTGTTGCGCTGA\n->241|16|FW|7\n-GAGAAGTACGCGTTGTTGCGCTG\n->265|16|FW|3\n-TGCGTTTGGGATTGTCGGTGAGACGTA\n->267|16|FW|70\n+>267|16|FW|4\n TGCGTTTGGGATTGTCGGTGAGACG\n->267|16|FW|1\n-GCGTTTGGGATTGTCGGTGAGACG\n->268|16|FW|82\n+>268|16|FW|6\n TGCGTTTGGGATTGTCGGTGAGAC\n->269|16|FW|71\n+>269|16|FW|6\n TGCGTTTGGGATTGTCGGTGAGA\n->276|16|FW|6\n-TCGATGTCTGCGTTTGGGATTGTC\n->277|16|FW|1\n-TCGATGTCTGCGTTTGGGATTGT\n >367|16|FW|1\n TCTGTCGGAGCCAATAGAGCGGGAGA\n->369|16|FW|22\n+>369|16|FW|2\n TCTGTCGGAGCCAATAGAGCGGGA\n >370|16|FW|1\n TCTGTCGGAGCCAATAGAGCGGG\n->422|16|FW|1\n-CAGAGCGGGCTGCCGGTCCCTCTC\n->434|16|FW|1\n-CGATGACGAGGCAGAGCGGGCTG\n->436|16|FW|3\n-TGCAGCCGATGACGAGGCAGAGCGGGC\n->447|16|FW|1\n-TGAGCGGGTGCAGCCGATGACGAG\n->448|16|FW|1\n-TGAGCGGGTGCAGCCGATGACGA\n->487|16|FW|1\n-TATTGCTAGCGGTTTTGCTTTCGC\n->531|16|FW|1\n-TGTTTACGTTTTCGTTTTGTTTTGCT\n->532|16|FW|3\n-TGTTTACGTTTTCGTTTTGTTTTGC\n->613|16|FW|6\n-ATCTGAATTTTCCGGGCTGAGCTT\n->614|16|FW|6\n-ATCTGAATTTTCCGGGCTGAGCT\n->660|16|FW|1\n-TTGATCAAGGTAGAGTTGTCGCGT\n->660|16|FW|1\n-TGATCAAGGTAGAGTTGTCGCGT\n->663|16|FW|4\n-TTTTTGATCAAGGTAGAGTTGTCG\n->664|16|FW|11\n-TTTTTGATCAAGGTAGAGTTGTC\n->687|16|FW|4\n-TCTGTTGGTATTTGCAGGGGCTACA\n->688|16|FW|9\n-TCTGTTGGTATTTGCAGGGGCTAC\n->689|16|FW|1\n-TCTGTTGGTATTTGCAGGGGCTA\n->698|16|FW|1\n-GCAAGGCAAATCTGTTGGTATTTG\n->706|16|FW|1\n-TATCTACCAGCAAGGCAAATCTGTT\n->707|16|FW|1\n-TATCTACCAGCAAGGCAAATCTGT\n->740|16|FW|8\n-TATCAACGGATCCCAGCGGCACGT\n->814|16|FW|4\n-TCAAAGTATTTACAAGACGGCTTGT\n->815|16|FW|14\n-TCAAAGTATTTACAAGACGGCTTG\n->816|16|FW|38\n+>816|16|FW|3\n TCAAAGTATTTACAAGACGGCTT\n->886|16|FW|25\n+>886|16|FW|2\n TGAAGTTTGATTTCGTTGATAGTACC\n->888|16|FW|1\n-TGAAGTTTGATTTCGTTGATAGTA\n->893|16|FW|3\n-TTCGTCTGAAGTTTGATTTCGTTGA\n->900|16|FW|1\n-CTCCGTTTTCGTCTGAAGTTTGATT\n->943|16|FW|1\n-TTTTTGTGCGGTAAAATAGTTTGT\n->966|16|FW|2\n-TAAGCTGGTAGGTGTAGAAGCCTATT\n->967|16|FW|3\n-TAAGCTGGTAGGTGTAGAAGCCTAT\n->968|16|FW|1\n-TTTTAAGCTGGTAGGTGTAGAAGCCTA\n->968|16|FW|3\n-TTTAAGCTGGTAGGTGTAGAAGCCTA\n->968|16|FW|4\n-TAAGCTGGTAGGTGTAGAAGCCTA\n->969|16|FW|14\n-TTTTAAGCTGGTAGGTGTAGAAGCCT\n->969|16|FW|41\n-TTTAAGCTGGTAGGTGTAGAAGCCT\n->969|16|FW|7\n-TAAGCTGGTAGGTGTAGAAGCCT\n->970|16|FW|21\n-TTTTAAGCTGGTAGGTGTAGAAGCC\n->970|16|FW|16\n-TTTAAGCTGGTAGGTGTAGAAGCC\n->971|16|FW|7\n-TTTTAAGCTGGTAGGTGTAGAAGC\n->971|16|FW|3\n-TTTAAGCTGGTAGGTGTAGAAGC\n->1014|16|FW|5\n-TCAGACTCAATGCCCTTCAGGACT\n->1015|16|FW|1\n-TCAGACTCAATGCCCTTCAGGAC\n->1017|16|FW|5\n-TAACATCAGACTCAATGCCCTTCAGG\n->1018|16|FW|2\n-TAACATCAGACTCAATGCCCTTCAG\n->1019|16|FW|2\n-TAACATCAGACTCAATGCCCTTCA\n->1020|16|FW|1\n-TAACATCAGACTCAATGCCCTTC\n->1137|16|FW|11\n-TTCTGGTTCAAGCTCAATCTTGAAG\n->1138|16|FW|9\n+>1138|16|FW|2\n TTCTGGTTCAAGCTCAATCTTGAA\n->1139|16|FW|8\n+>1139|16|FW|2\n TTCTGGTTCAAGCTCAATCTTGA\n->1179|16|FW|1\n-TTGTAAATTGGGTGAACCTCGTTT\n->1179|16|FW|1\n-TGTAAATTGGGTGAACCTCGTTT\n->1180|16|FW|1\n-TTGTAAATTGGGTGAACCTCGTT\n->1183|16|FW|5\n-GAGTTTGTAAATTGGGTGAACCTC\n->1184|16|FW|4\n-GAGTTTGTAAATTGGGTGAACCT\n->1202|16|FW|1\n-TACGGTGCAAAAGGAGCTGGAGTT\n->1203|16|FW|3\n-TACGGTGCAAAAGGAGCTGGAGT\n->1204|16|FW|1\n-TCCTACGGTGCAAAAGGAGCTGGAG\n->1229|16|FW|4\n-CGTTTGTGCGGCTCTTCTACCGTGA\n->1230|16|FW|2\n-CGTTTGTGCGGCTCTTCTACCGTG\n->1231|16|FW|1\n-CGTTTGTGCGGCTCTTCTACCGT\n->1278|16|FW|1\n-TGACCTCGTGTGGCCATACTCTTGGCAG\n->1278|16|FW|1\n-CCTCGTGTGGCCATACTCTTGGCAG\n->1279|16|FW|5\n+>1279|16|FW|1\n TGACCTCGTGTGGCCATACTCTTGGCA\n->1280|16|FW|2\n-TGACCTCGTGTGGCCATACTCTTGGC\n->1281|16|FW|3\n-TGACCTCGTGTGGCCATACTCTTGG\n->1282|16|FW|5\n+>1282|16|FW|1\n TGACCTCGTGTGGCCATACTCTTG\n >1283|16|FW|1\n TGACCTCGTGTGGCCATACTCTT\n->1411|16|FW|4\n-TGTAGTTTGCTGTGTGATTGCCCCC\n->1412|16|FW|12\n-TGTAGTTTGCTGTGTGATTGCCCC\n->1413|16|FW|11\n-TGTAGTTTGCTGTGTGATTGCCC\n->1537|16|FW|7\n-TTTCGAGAAAATTACTTCAGGATT\n->1599|16|FW|6\n-TAAAACGTTAGCAAATGTTGTCTTG\n->1673|16|FW|1\n-TTGTTGTGTGTCTAATTTTGTGTGCA\n->1676|16|FW|2\n-TTGTTGTGTGTCTAATTTTGTGT\n->1836|16|FW|81\n-TATTTGATTGTTGGGCTACAAGCATT\n->1837|16|FW|13\n-TATTTGATTGTTGGGCTACAAGCAT\n->1838|16|FW|130\n-TATTTGATTGTTGGGCTACAAGCA\n->1839|16|FW|34\n-TATTTGATTGTTGGGCTACAAGC\n->1890|16|FW|1\n-TGCGCTGTGAAACGCCATTGGCGTTCCA\n->1893|16|FW|5\n-TGCG'..b'TGAGAGTAGACTTATTGGTCTGT\n->3455|16|FW|1\n-GTATATCAGATGTTGATTAAGTCGG\n->3456|16|FW|3\n-GTATATCAGATGTTGATTAAGTCG\n->3521|16|FW|1\n-TTCACCTGTTCAATGGTTCCGTGG\n->3524|16|FW|1\n-TACGATTCACCTGTTCAATGGTTCCG\n->3525|16|FW|1\n-TACGATTCACCTGTTCAATGGTTCC\n->3526|16|FW|1\n-TACGATTCACCTGTTCAATGGTTC\n->3554|16|FW|2\n-TTCAAATGCAGTTCTTATTTCCGTT\n->3555|16|FW|4\n+>3555|16|FW|1\n TTCAAATGCAGTTCTTATTTCCGT\n->3556|16|FW|1\n-TTCAAATGCAGTTCTTATTTCCG\n->3599|16|FW|1\n-TGCTTGGGATACGTCTAAAAATACT\n->3600|16|FW|1\n-TGCTTGGGATACGTCTAAAAATAC\n->3603|16|FW|9\n-CGAATGCTTGGGATACGTCTAAAAA\n->3604|16|FW|1\n-CGAATGCTTGGGATACGTCTAAAA\n->3605|16|FW|2\n+>3605|16|FW|1\n CGAATGCTTGGGATACGTCTAAA\n->3608|16|FW|1\n-TTTGTCGAATGCTTGGGATACGTCT\n->3609|16|FW|8\n+>3609|16|FW|1\n TTTGTCGAATGCTTGGGATACGTC\n->3688|16|FW|1\n-TAGAGGTAAGACTTTAGAAGTTTGT\n->3689|16|FW|2\n-TAGAGGTAAGACTTTAGAAGTTTG\n->3690|16|FW|23\n-TAGAGGTAAGACTTTAGAAGTTT\n->3744|16|FW|5\n-AATTGTATGAACAGTGGAAGTGGC\n->3745|16|FW|7\n-AATTGTATGAACAGTGGAAGTGG\n->3799|16|FW|5\n-TGTATAGATGAGGTATAAGGTTGGCC\n->3800|16|FW|5\n-TGTATAGATGAGGTATAAGGTTGGC\n->3801|16|FW|2\n-TGTATAGATGAGGTATAAGGTTGG\n->3802|16|FW|6\n-TGTATAGATGAGGTATAAGGTTG\n->3843|16|FW|1\n-AAATGTGGATACCGTTAAGCGACT\n->3844|16|FW|1\n-AAATGTGGATACCGTTAAGCGAC\n->3900|16|FW|2\n-CTGTGCTGTAGCTTGGATAGGGGA\n->3900|16|FW|26\n+>3900|16|FW|3\n TGTGCTGTAGCTTGGATAGGGGA\n->3949|16|FW|4\n-TATTCGCCAGTCAGAGAGCCACTTCT\n->3950|16|FW|15\n-TATTCGCCAGTCAGAGAGCCACTTC\n->3952|16|FW|24\n-TATTCGCCAGTCAGAGAGCCACT\n->3967|16|FW|1\n-TTTTTGCTCGTTTACTTTTATTCGCC\n->3996|16|FW|5\n-TGTTTAGCGTAAACGTCACGTGCTT\n->3997|16|FW|14\n+>3997|16|FW|2\n TGTTTAGCGTAAACGTCACGTGCT\n->4023|16|FW|1\n-TTCAACAAGAGCGGAGGACAGTCTTG\n->4023|16|FW|2\n-TCAACAAGAGCGGAGGACAGTCTTG\n->4023|16|FW|1\n-AACAAGAGCGGAGGACAGTCTTG\n->4024|16|FW|1\n-TTCAACAAGAGCGGAGGACAGTCTT\n->4025|16|FW|30\n-TTCAACAAGAGCGGAGGACAGTCT\n->4025|16|FW|11\n-TCAACAAGAGCGGAGGACAGTCT\n->4027|16|FW|1\n-CTGTTCAACAAGAGCGGAGGACAGT\n->4030|16|FW|1\n-TGCTGTTCAACAAGAGCGGAGGAC\n->4083|16|FW|1\n-TTCTGTCAAGGTGTACTCCTAGGTA\n->4085|16|FW|5\n-TCTTCTGTCAAGGTGTACTCCTAGG\n->4085|16|FW|4\n-TTCTGTCAAGGTGTACTCCTAGG\n->4086|16|FW|1\n-TCTTCTGTCAAGGTGTACTCCTAG\n->4090|16|FW|3\n-TGAGTCTTCTGTCAAGGTGTACTC\n->4091|16|FW|1\n-TGTGAGTCTTCTGTCAAGGTGTACT\n->4134|16|FW|3\n-GAGTTTAAGTTGGGTTTTTTTGGC\n->4148|16|FW|27\n-TAAGTTGTTGGCTTTGAGTTTAAGT\n->4149|16|FW|53\n-TAAGTTGTTGGCTTTGAGTTTAAG\n->4150|16|FW|3\n-TAAGTTGTTGGCTTTGAGTTTAA\n->4183|16|FW|2\n-TAGGCTGAGCGGAGAACCAGAGTTGA\n->4185|16|FW|4\n-TAGGCTGAGCGGAGAACCAGAGTT\n->4186|16|FW|4\n-TAGGCTGAGCGGAGAACCAGAGT\n->4216|16|FW|1\n-CAATATAGAATTGTAGAGCAAGACCT\n->4218|16|FW|1\n-CAATATAGAATTGTAGAGCAAGAC\n->4227|16|FW|1\n-GATTGGTTTCAATATAGAATTGTA\n->4308|16|FW|4\n+>4308|16|FW|1\n TCAGAATCTTTGATTGTGCTCGCTG\n->4309|16|FW|3\n-TCTCAGAATCTTTGATTGTGCTCGCT\n->4309|16|FW|7\n+>4309|16|FW|1\n CTCAGAATCTTTGATTGTGCTCGCT\n->4309|16|FW|128\n+>4309|16|FW|15\n TCAGAATCTTTGATTGTGCTCGCT\n >4310|16|FW|1\n-TCTCAGAATCTTTGATTGTGCTCGC\n->4310|16|FW|1\n-CTCAGAATCTTTGATTGTGCTCGC\n->4310|16|FW|6\n TCAGAATCTTTGATTGTGCTCGC\n->4311|16|FW|1\n-CTCAGAATCTTTGATTGTGCTCG\n->4312|16|FW|1\n-GTTCTCAGAATCTTTGATTGTGCTC\n->4312|16|FW|4\n-TTCTCAGAATCTTTGATTGTGCTC\n->4313|16|FW|1\n-GGTTCTCAGAATCTTTGATTGTGCT\n->4313|16|FW|1\n-GTTCTCAGAATCTTTGATTGTGCT\n->4315|16|FW|4\n-TGGTTCTCAGAATCTTTGATTGTG\n->4339|16|FW|1\n-TCCGAACGTACCACGGTGCCCCAGTGA\n->4341|16|FW|2\n-TCCGAACGTACCACGGTGCCCCAGT\n->4342|16|FW|1\n-TCCGAACGTACCACGGTGCCCCAG\n->4365|16|FW|43\n-TTAAGTCTCTTTGGATGTTTTCACT\n->4366|16|FW|5\n-TTAAGTCTCTTTGGATGTTTTCAC\n->4457|16|FW|1\n-TTAGACCTCGCGCTAGGTGGTTGGGG\n->4470|16|FW|1\n-TGCTGAGCTGGATTAGACCTCGCGC\n->4471|16|FW|1\n-TGCTGAGCTGGATTAGACCTCGCG\n->4476|16|FW|1\n-CGGCTGCTGAGCTGGATTAGACC\n->4484|16|FW|1\n-GAGACGGGAACGGCTGCTGAGCTGG\n->4484|16|FW|2\n-GACGGGAACGGCTGCTGAGCTGG\n->4486|16|FW|1\n-GAGACGGGAACGGCTGCTGAGCT\n->4487|16|FW|1\n-GGAGACGGGAACGGCTGCTGAGC\n->4491|16|FW|1\n-TTTCGCCGGAGACGGGAACGGCTGCT\n->4491|16|FW|1\n-TCGCCGGAGACGGGAACGGCTGCT\n >4492|16|FW|1\n TTCGCCGGAGACGGGAACGGCTGC\n->4493|16|FW|2\n-TTCGCCGGAGACGGGAACGGCTG\n >4494|16|FW|1\n CTTTCGCCGGAGACGGGAACGGCT\n->4502|16|FW|1\n-GGTAGGTCCTTTCGCCGGAGACGG\n->4515|16|FW|1\n-TTATTCGCTGGGTTGGTAGGTCCTT\n >4517|16|FW|1\n TTATTCGCTGGGTTGGTAGGTCC\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number -1 324 3.24 -2 377 3.77 -3 320 3.20 -4 399 3.99 -5 421 4.21 -6 442 4.42 -7 449 4.49 -8 323 3.23 -9 367 3.67 -10 1042 10.43 -11 442 4.42 -12 465 4.65 -13 442 4.42 -14 351 3.51 -15 399 3.99 -16 364 3.64 -17 539 5.39 -18 374 3.74 -19 432 4.32 -20 415 4.15 -21 445 4.45 -22 516 5.16 -23 347 3.47 +1 15 4.07 +2 14 3.79 +3 11 2.98 +4 10 2.71 +5 21 5.69 +6 10 2.71 +7 12 3.25 +8 8 2.17 +9 16 4.34 +10 54 14.63 +11 18 4.88 +12 14 3.79 +13 19 5.15 +14 5 1.36 +15 18 4.88 +16 18 4.88 +17 15 4.07 +18 9 2.44 +19 12 3.25 +20 11 2.98 +21 12 3.25 +22 33 8.94 +23 14 3.79 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,720 +1,208 @@\n->220|0|FW|1\n-GACGAACGCCGACTCTCAATTCAG\n->283|0|FW|1\n-CCAAACGCAGACATCGAGCGGTCAA\n->288|0|FW|1\n-CGCAGACATCGAGCGGTCAATAACC\n->291|0|FW|1\n-AGACATCGAGCGGTCAATAACCC\n->294|0|FW|1\n-CATCGAGCGGTCAATAACCCATAGC\n->296|0|FW|1\n-TCGAGCGGTCAATAACCCATAGCCC\n->361|0|FW|2\n-TCCTGCTCTCCCGCTCTATTGGCTCC\n->362|0|FW|9\n-CCTGCTCTCCCGCTCTATTGGCTCC\n->362|0|FW|1\n-CCTGCTCTCCCGCTCTATTGGCTC\n->367|0|FW|1\n-TCTCCCGCTCTATTGGCTCCGACAGA\n->370|0|FW|1\n-CCCGCTCTATTGGCTCCGACAGAA\n->409|0|FW|1\n-ACAACAACAGCTGGAGAGGGACC\n->424|0|FW|1\n-GAGGGACCGGCAGCCCGCTCTGCCT\n+>281|0|FW|1\n+TCCCAAACGCAGACATCGAGCGG\n+>290|0|FW|1\n+CAGACATCGAGCGGTCAATAACC\n >429|0|FW|1\n ACCGGCAGCCCGCTCTGCCTCGTCATC\n->433|0|FW|1\n-GCAGCCCGCTCTGCCTCGTCATCGGC\n->435|0|FW|1\n-AGCCCGCTCTGCCTCGTCATCGGCT\n->435|0|FW|1\n-AGCCCGCTCTGCCTCGTCATCGGC\n->437|0|FW|1\n-CCCGCTCTGCCTCGTCATCGGCTG\n->439|0|FW|3\n-CGCTCTGCCTCGTCATCGGCTGC\n->441|0|FW|1\n-CTCTGCCTCGTCATCGGCTGCACCCG\n->442|0|FW|10\n-TCTGCCTCGTCATCGGCTGCACCCGC\n >442|0|FW|1\n-TCTGCCTCGTCATCGGCTGCACCCG\n->442|0|FW|2\n TCTGCCTCGTCATCGGCTGCACCC\n->442|0|FW|2\n-TCTGCCTCGTCATCGGCTGCACC\n->448|0|FW|1\n-TCGTCATCGGCTGCACCCGCTCAC\n->451|0|FW|1\n-TCATCGGCTGCACCCGCTCACGGTC\n->451|0|FW|1\n-TCATCGGCTGCACCCGCTCACGGT\n->451|0|FW|1\n-TCATCGGCTGCACCCGCTCACGG\n->454|0|FW|1\n-TCGGCTGCACCCGCTCACGGTCTGAC\n->455|0|FW|1\n-CGGCTGCACCCGCTCACGGTCTG\n->456|0|FW|2\n+>456|0|FW|1\n GGCTGCACCCGCTCACGGTCTGAC\n->500|0|FW|1\n-CGCTAGCAATAAACGGTACTGCT\n->509|0|FW|1\n-TAAACGGTACTGCTGCACTGCCAG\n->511|0|FW|1\n-AACGGTACTGCTGCACTGCCAGCA\n->568|0|FW|1\n-TCGACCTGGCAGACTGGAATGGACC\n->568|0|FW|1\n-TCGACCTGGCAGACTGGAATGGAC\n->571|0|FW|3\n-ACCTGGCAGACTGGAATGGACCGC\n->571|0|FW|1\n-ACCTGGCAGACTGGAATGGACCG\n+>547|0|FW|1\n+AACGTAAACAAAAAAGCTGGGTC\n >572|0|FW|1\n-CCTGGCAGACTGGAATGGACCGCT\n->572|0|FW|2\n CCTGGCAGACTGGAATGGACCGC\n->574|0|FW|1\n-TGGCAGACTGGAATGGACCGCTAC\n >631|0|FW|1\n TCAGATTTGGGAAACAAGCCGAAA\n->651|0|FW|1\n-GAAAAATACACGCGACAACTCTACC\n->653|0|FW|1\n-AAAATACACGCGACAACTCTACCTT\n->657|0|FW|1\n-TACACGCGACAACTCTACCTTGA\n->672|0|FW|1\n-TACCTTGATCAAAAATGTAGCCCC\n->713|0|FW|1\n-TTGCCTTGCTGGTAGATACCGCTGA\n->718|0|FW|1\n-TTGCTGGTAGATACCGCTGAGGA\n->719|0|FW|1\n-TGCTGGTAGATACCGCTGAGGACG\n->725|0|FW|2\n-TAGATACCGCTGAGGACGTGCCGCT\n+>673|0|FW|1\n+ACCTTGATCAAAAATGTAGCCCCTGC\n >725|0|FW|1\n TAGATACCGCTGAGGACGTGCCGC\n >729|0|FW|1\n-TACCGCTGAGGACGTGCCGCTGGGA\n->729|0|FW|2\n TACCGCTGAGGACGTGCCGCTGGG\n->729|0|FW|1\n-TACCGCTGAGGACGTGCCGCTGG\n->744|0|FW|1\n-GCCGCTGGGATCCGTTGATATCGA\n->762|0|FW|2\n+>762|0|FW|1\n TATCGAACCGAAGAAAACAAAGCC\n->821|0|FW|6\n-GTCTTGTAAATACTTTGATTGGCCT\n >821|0|FW|1\n GTCTTGTAAATACTTTGATTGGCC\n->822|0|FW|74\n+>822|0|FW|12\n TCTTGTAAATACTTTGATTGGCCT\n->822|0|FW|4\n-TCTTGTAAATACTTTGATTGGCC\n->823|0|FW|3\n-CTTGTAAATACTTTGATTGGCCT\n->824|0|FW|1\n-TTGTAAATACTTTGATTGGCCTTAT\n >824|0|FW|1\n TTGTAAATACTTTGATTGGCCTT\n->918|0|FW|1\n-AACGGAGGACGACTACAGAAAAGT\n->1007|0|FW|1\n-TGCAAGTAGTCCTGAAGGGCATTG\n->1027|0|FW|1\n-ATTGAGTCTGATGTTACGCCCGA\n->1048|0|FW|3\n-GAAGAGATAACTGAGGCGCTAAAG\n->1064|0|FW|2\n-CGCTAAAGGAAAAGGGATTTTACGCC\n->1067|0|FW|1\n-TAAAGGAAAAGGGATTTTACGCC\n->1141|0|FW|1\n-AAGATTGAGCTTGAACCAGAAAACA\n->1189|0|FW|1\n-CACCCAATTTACAAACTCCAGCTC\n->1214|0|FW|2\n-TTTTGCACCGTAGGATCACGGTAGAA\n->1214|0|FW|1\n-TTTTGCACCGTAGGATCACGGTAGA\n->1217|0|FW|2\n-TGCACCGTAGGATCACGGTAGAAGAG\n->1221|0|FW|4\n-CCGTAGGATCACGGTAGAAGAGCC\n->1221|0|FW|1\n-CCGTAGGATCACGGTAGAAGAGC\n->1223|0|FW|1\n-GTAGGATCACGGTAGAAGAGCCGC\n->1224|0|FW|1\n-TAGGATCACGGTAGAAGAGCCGC\n->1235|0|FW|1\n-TAGAAGAGCCGCACAAACGCAACGCT\n->1242|0|FW|1\n-GCCGCACAAACGCAACGCTCCTGT\n->1272|0|FW|1\n-TACAAACTGCCAAGAGTATGGCC\n+>1033|0|FW|3\n+TCTGATGTTACGCCCGAAGAGATAAC\n+>1033|0|FW|4\n+TCTGATGTTACGCCCGAAGAGATAA\n+>1033|0|FW|1\n+TCTGATGTTACGCCCGAAGAGATA\n+>1033|0|FW|2\n+TCTGATGTTACGCCCGAAGAGAT\n+>1192|0|FW|1\n+CCAATTTACAAACTCCAGCTCCT\n+>1244|0|FW|1\n+CGCACAAACGCAACGCTCCTGTA\n+>1293|0|FW|1\n+CCACACGAGGTCATATTGTACACTT\n >1303|0|FW|1\n TCATATTGTACACTTCGCCCGGT\n->1309|0|FW|1\n-TGTACACTTCGCCCGGTGTGCGTAGT\n->1322|0|FW|1\n-CGGTGTGCGTAGTCTGTGGAGATC\n->1323|0|FW|1\n-GGTGTGCGTAGTCTGTGGAGATCTC\n->1323|0|FW|1\n-GGTGTGCGTAGTCTGTGGAGATCT\n->1325|0|FW|1\n-TGTGCGTAGTCTGTGGAGATCTCCACGA\n->1325|0|FW|1\n-TGTGCGTAGTCTGTGGAGATCTCCACG\n->1325|0|FW|1\n'..b'GA\n->3755|0|FW|3\n+>3755|0|FW|1\n TGTTCATACAATTGAGGCTGGAGTC\n->3755|0|FW|7\n-TGTTCATACAATTGAGGCTGGAGT\n->3755|0|FW|5\n+>3755|0|FW|1\n TGTTCATACAATTGAGGCTGGAG\n->3757|0|FW|3\n-TTCATACAATTGAGGCTGGAGTCCC\n->3759|0|FW|1\n-CATACAATTGAGGCTGGAGTCCC\n >3836|0|FW|1\n TACAAATAGTCGCTTAACGGTATC\n->3901|0|FW|1\n-CCCCTATCCAAGCTACAGCACAGT\n->3901|0|FW|1\n-CCCCTATCCAAGCTACAGCACAG\n->3907|0|FW|1\n-TCCAAGCTACAGCACAGTTGGCACTG\n->3909|0|FW|1\n-CAAGCTACAGCACAGTTGGCACTG\n->3910|0|FW|2\n-AAGCTACAGCACAGTTGGCACTG\n >3912|0|FW|1\n GCTACAGCACAGTTGGCACTGTACCT\n->3912|0|FW|1\n-GCTACAGCACAGTTGGCACTGTACC\n->3912|0|FW|1\n-GCTACAGCACAGTTGGCACTGTAC\n->3925|0|FW|9\n+>3925|0|FW|2\n TGGCACTGTACCTCACCGACATTGA\n->3927|0|FW|1\n-GCACTGTACCTCACCGACATTGA\n->3943|0|FW|1\n-ACATTGAGAAGTGGCTCTCTGACT\n->3960|0|FW|1\n-TCTGACTGGCGAATAAAAGTAAAC\n->3962|0|FW|1\n-TGACTGGCGAATAAAAGTAAACGAGC\n->4008|0|FW|1\n-TTTACGCTAAACAGACAAGACTGTC\n->4010|0|FW|2\n-TACGCTAAACAGACAAGACTGTCCT\n->4012|0|FW|1\n-CGCTAAACAGACAAGACTGTCCT\n->4015|0|FW|1\n-TAAACAGACAAGACTGTCCTCCGCT\n->4016|0|FW|1\n-AAACAGACAAGACTGTCCTCCGCTCT\n->4018|0|FW|1\n-ACAGACAAGACTGTCCTCCGCTCT\n >4040|0|FW|1\n CTTGTTGAACAGCATACCACTCCCGA\n->4045|0|FW|1\n-TGAACAGCATACCACTCCCGAAAGC\n->4045|0|FW|1\n-TGAACAGCATACCACTCCCGAAA\n->4046|0|FW|1\n-GAACAGCATACCACTCCCGAAAG\n->4049|0|FW|1\n-CAGCATACCACTCCCGAAAGCAGAC\n->4093|0|FW|1\n-TACACCTTGACAGAAGACTCACATGG\n->4099|0|FW|1\n-TTGACAGAAGACTCACATGGCGC\n->4103|0|FW|1\n-CAGAAGACTCACATGGCGCAGGCACA\n->4103|0|FW|1\n-CAGAAGACTCACATGGCGCAGGCAC\n->4103|0|FW|1\n-CAGAAGACTCACATGGCGCAGGCA\n->4105|0|FW|1\n-GAAGACTCACATGGCGCAGGCACA\n->4164|0|FW|1\n-AACAACTTACACTGGCTCATCAACTC\n->4166|0|FW|1\n-CAACTTACACTGGCTCATCAACTC\n->4169|0|FW|1\n-CTTACACTGGCTCATCAACTCTGGT\n->4170|0|FW|1\n-TTACACTGGCTCATCAACTCTGG\n->4183|0|FW|1\n-TCAACTCTGGTTCTCCGCTCAGCCTA\n->4188|0|FW|1\n-TCTGGTTCTCCGCTCAGCCTAGAT\n->4196|0|FW|2\n-TCCGCTCAGCCTAGATCACAAGGTC\n->4233|0|FW|1\n-TCTATATTGAAACCAATCTGGACC\n->4234|0|FW|1\n-CTATATTGAAACCAATCTGGACCT\n->4235|0|FW|1\n-TATATTGAAACCAATCTGGACCT\n->4239|0|FW|1\n-TTGAAACCAATCTGGACCTATGGCTC\n->4240|0|FW|1\n-TGAAACCAATCTGGACCTATGGCT\n->4240|0|FW|1\n-TGAAACCAATCTGGACCTATGGC\n->4242|0|FW|3\n-AAACCAATCTGGACCTATGGCTC\n->4244|0|FW|1\n-ACCAATCTGGACCTATGGCTCACAGT\n->4246|0|FW|1\n-CAATCTGGACCTATGGCTCACAGT\n->4295|0|FW|1\n-TATTGACATCATTCAGCGAGCAC\n->4309|0|FW|1\n-AGCGAGCACAATCAAAGATTCTG\n->4314|0|FW|1\n-GCACAATCAAAGATTCTGAGAACCA\n->4319|0|FW|2\n-ATCAAAGATTCTGAGAACCATCACT\n->4320|0|FW|1\n-TCAAAGATTCTGAGAACCATCACTGG\n->4320|0|FW|3\n+>4042|0|FW|1\n+TGTTGAACAGCATACCACTCCCGAAA\n+>4098|0|FW|1\n+CTTGACAGAAGACTCACATGGCGCA\n+>4104|0|FW|1\n+AGAAGACTCACATGGCGCAGGCAC\n+>4104|0|FW|1\n+AGAAGACTCACATGGCGCAGGCA\n+>4106|0|FW|2\n+AAGACTCACATGGCGCAGGCACA\n+>4320|0|FW|2\n TCAAAGATTCTGAGAACCATCACT\n->4321|0|FW|2\n-CAAAGATTCTGAGAACCATCACTGG\n->4321|0|FW|1\n-CAAAGATTCTGAGAACCATCACT\n->4322|0|FW|1\n-AAAGATTCTGAGAACCATCACTGGGG\n->4322|0|FW|5\n-AAAGATTCTGAGAACCATCACTGG\n->4347|0|FW|1\n-GCACCGTGGTACGTTCGGAGTGA\n+>4329|0|FW|1\n+CTGAGAACCATCACTGGGGCACCGT\n >4348|0|FW|1\n CACCGTGGTACGTTCGGAGTGAAAAC\n->4348|0|FW|4\n+>4348|0|FW|1\n CACCGTGGTACGTTCGGAGTGAAAA\n->4348|0|FW|8\n-CACCGTGGTACGTTCGGAGTGAAA\n->4348|0|FW|6\n+>4348|0|FW|2\n CACCGTGGTACGTTCGGAGTGAA\n->4349|0|FW|2\n-ACCGTGGTACGTTCGGAGTGAAAACA\n->4349|0|FW|9\n-ACCGTGGTACGTTCGGAGTGAAAAC\n->4349|0|FW|3\n+>4349|0|FW|1\n ACCGTGGTACGTTCGGAGTGAAAA\n->4349|0|FW|1\n-ACCGTGGTACGTTCGGAGTGAAA\n->4352|0|FW|2\n-GTGGTACGTTCGGAGTGAAAACATC\n >4352|0|FW|1\n GTGGTACGTTCGGAGTGAAAACA\n->4353|0|FW|2\n-TGGTACGTTCGGAGTGAAAACATC\n->4396|0|FW|1\n-CATCAGTTACCAACGCAATCACGGA\n->4414|0|FW|1\n-TCACGGAACTTAAGGAAAAATACC\n >4415|0|FW|1\n CACGGAACTTAAGGAAAAATACC\n->4434|0|FW|1\n-TACCATAGCAAGCTTCACACGCACCC\n->4464|0|FW|1\n-CACCTAGCGCGAGGTCTAATCCAGC\n->4468|0|FW|1\n-TAGCGCGAGGTCTAATCCAGCTC\n->4495|0|FW|4\n-GCCGTTCCCGTCTCCGGCGAAAGGACC\n->4496|0|FW|1\n-CCGTTCCCGTCTCCGGCGAAAGGAC\n->4498|0|FW|5\n-GTTCCCGTCTCCGGCGAAAGGAC\n->4541|0|FW|1\n-TTATTAGGGCCGTTTAAACATAGAA\n->4545|0|FW|1\n-TAGGGCCGTTTAAACATAGAACAGT\n->4551|0|FW|13\n+>4497|0|FW|1\n+CGTTCCCGTCTCCGGCGAAAGGACC\n+>4500|0|FW|1\n+TCCCGTCTCCGGCGAAAGGACCTACC\n+>4505|0|FW|2\n+TCTCCGGCGAAAGGACCTACCAAC\n+>4507|0|FW|2\n+TCCGGCGAAAGGACCTACCAACCCAGC\n+>4551|0|FW|1\n CGTTTAAACATAGAACAGTTGGAA\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,578 +1,58 @@\n->254|0|FW|1\n-CGTACTTCTCCTACGTCTCACCG\n->281|0|FW|2\n-TCCCAAACGCAGACATCGAGCGGTC\n->281|0|FW|1\n-TCCCAAACGCAGACATCGAGCGGT\n->281|0|FW|1\n-TCCCAAACGCAGACATCGAGCGG\n >282|0|FW|1\n-CCCAAACGCAGACATCGAGCGGTCAA\n->282|0|FW|1\n-CCCAAACGCAGACATCGAGCGGTCA\n->282|0|FW|7\n CCCAAACGCAGACATCGAGCGGTC\n->290|0|FW|1\n-CAGACATCGAGCGGTCAATAACCCA\n->290|0|FW|2\n-CAGACATCGAGCGGTCAATAACC\n >383|0|FW|1\n CTCCGACAGAAGCCCCGCTACCTC\n->436|0|FW|1\n-GCCCGCTCTGCCTCGTCATCGGCTGC\n->436|0|FW|5\n-GCCCGCTCTGCCTCGTCATCGGCTG\n->436|0|FW|1\n-GCCCGCTCTGCCTCGTCATCGGC\n->447|0|FW|1\n-CTCGTCATCGGCTGCACCCGCTCAC\n->453|0|FW|1\n-ATCGGCTGCACCCGCTCACGGTCT\n->461|0|FW|1\n-CACCCGCTCACGGTCTGACTAAGTC\n->501|0|FW|5\n-GCTAGCAATAAACGGTACTGCTGC\n->501|0|FW|2\n-GCTAGCAATAAACGGTACTGCTG\n->547|0|FW|1\n-AACGTAAACAAAAAAGCTGGGTCGAC\n->547|0|FW|9\n-AACGTAAACAAAAAAGCTGGGTCG\n->547|0|FW|6\n-AACGTAAACAAAAAAGCTGGGTC\n->627|0|FW|1\n-AAATTCAGATTTGGGAAACAAGC\n->673|0|FW|1\n-ACCTTGATCAAAAATGTAGCCCCTGC\n->673|0|FW|1\n-ACCTTGATCAAAAATGTAGCCCCTG\n->673|0|FW|3\n-ACCTTGATCAAAAATGTAGCCCCT\n->673|0|FW|5\n-ACCTTGATCAAAAATGTAGCCCC\n->674|0|FW|1\n-CCTTGATCAAAAATGTAGCCCCTGC\n->677|0|FW|2\n-TGATCAAAAATGTAGCCCCTGCAAA\n->702|0|FW|1\n-TACCAACAGATTTGCCTTGCTGG\n->712|0|FW|1\n-TTTGCCTTGCTGGTAGATACCGCTG\n->721|0|FW|2\n-CTGGTAGATACCGCTGAGGACGTGC\n->721|0|FW|1\n-CTGGTAGATACCGCTGAGGACGTG\n->754|0|FW|1\n-TCCGTTGATATCGAACCGAAGAAAA\n >829|0|FW|1\n-AATACTTTGATTGGCCTTATTGGGA\n->829|0|FW|2\n AATACTTTGATTGGCCTTATTGGG\n->829|0|FW|1\n-AATACTTTGATTGGCCTTATTGG\n->902|0|FW|3\n+>902|0|FW|1\n TCAAACTTCAGACGAAAACGGAG\n->908|0|FW|1\n-TTCAGACGAAAACGGAGGACGACT\n->908|0|FW|1\n-TTCAGACGAAAACGGAGGACGAC\n->915|0|FW|1\n-GAAAACGGAGGACGACTACAGAAAAG\n->957|0|FW|1\n-CGCACAAAAAATAGGCTTCTACACCT\n->957|0|FW|13\n-CGCACAAAAAATAGGCTTCTACACC\n->982|0|FW|7\n-TACCAGCTTAAAAGCAGCAAGGGC\n->984|0|FW|1\n-CCAGCTTAAAAGCAGCAAGGGCCTG\n->985|0|FW|1\n-CAGCTTAAAAGCAGCAAGGGCCT\n->1028|0|FW|1\n-TTGAGTCTGATGTTACGCCCGAAGA\n->1033|0|FW|3\n-TCTGATGTTACGCCCGAAGAGATAACT\n->1033|0|FW|40\n-TCTGATGTTACGCCCGAAGAGATAAC\n->1033|0|FW|20\n-TCTGATGTTACGCCCGAAGAGATAA\n->1033|0|FW|15\n-TCTGATGTTACGCCCGAAGAGATA\n->1033|0|FW|22\n-TCTGATGTTACGCCCGAAGAGAT\n->1152|0|FW|3\n-TGAACCAGAAAACAAGCCTCCTAGAA\n->1152|0|FW|9\n+>1152|0|FW|1\n TGAACCAGAAAACAAGCCTCCTAGA\n->1152|0|FW|2\n-TGAACCAGAAAACAAGCCTCCTAG\n->1192|0|FW|4\n-CCAATTTACAAACTCCAGCTCCT\n->1193|0|FW|1\n-CAATTTACAAACTCCAGCTCCTTT\n->1197|0|FW|2\n-TTACAAACTCCAGCTCCTTTTGCACC\n->1216|0|FW|3\n-TTGCACCGTAGGATCACGGTAGAAGA\n->1219|0|FW|1\n-CACCGTAGGATCACGGTAGAAGAGC\n->1244|0|FW|1\n-CGCACAAACGCAACGCTCCTGTA\n->1293|0|FW|1\n-CCACACGAGGTCATATTGTACACTT\n >1296|0|FW|1\n CACGAGGTCATATTGTACACTTCGCC\n->1296|0|FW|8\n+>1296|0|FW|1\n CACGAGGTCATATTGTACACTTC\n->1426|0|FW|1\n-GCAAACTACAGAGGCTGTCCAATCTAC\n->1426|0|FW|1\n-GCAAACTACAGAGGCTGTCCAATCT\n->1426|0|FW|1\n-GCAAACTACAGAGGCTGTCCAATC\n->1551|0|FW|1\n-TTTCTCGAAAGCAGCTAGTTTCGCTC\n->1614|0|FW|9\n-TAACGTTTTAAAATCAGGTATGACG\n->1614|0|FW|3\n-TAACGTTTTAAAATCAGGTATGAC\n->1689|0|FW|2\n-CACACAACAAAACTATCACCCAGCTG\n->1852|0|FW|1\n-CAATCAAATAAATAATGGCTACC\n->1908|0|FW|1\n-TCACAGCGCAAACTTGAGCTAGCTC\n->1952|0|FW|4\n+>1952|0|FW|1\n TATCGACGTAATGCTTCTTTCGGA\n->1967|0|FW|1\n-TCTTTCGGAAACTCATCTCACAAGC\n->2000|0|FW|1\n-TTTTCAAATAAGAGACTACCATTTC\n->2000|0|FW|1\n-TTTTCAAATAAGAGACTACCATT\n->2024|0|FW|1\n-CTACGGTACAAATCATCCCGACGGA\n->2025|0|FW|3\n-TACGGTACAAATCATCCCGACGGA\n->2029|0|FW|1\n-GTACAAATCATCCCGACGGAAAAGC\n->2040|0|FW|1\n-CCCGACGGAAAAGCACACGGTGG\n->2041|0|FW|1\n-CCGACGGAAAAGCACACGGTGGCACC\n->2042|0|FW|1\n-CGACGGAAAAGCACACGGTGGCAC\n->2045|0|FW|1\n-CGGAAAAGCACACGGTGGCACCGC\n->2097|0|FW|2\n-CACTTTTACAAAGAATTTGCGGAAA\n->2097|0|FW|2\n-CACTTTTACAAAGAATTTGCGGA\n->2133|0|FW|3\n-GCCACATCTATCAACATTCAGCTG\n->2167|0|FW|1\n-CTCTCCTTACACTAGCGGCCGTATAC\n->2167|0|FW|3\n-CTCTCCTTACACTAGCGGCCGTA\n->2171|0|FW|1\n-CCTTACACTAGCGGCCGTATACTGCC\n->2171|0|FW|1\n-CCTTACACTAGCGGCCGTATACTG\n->2281|0|FW|1\n-ACGCTAAACATACTCACTGGGGA\n->2286|0|FW|1\n-AAACATACTCACTGGGGATCGCGAC\n->2287|0|FW|2\n-AACATACTCACTGGGGATCGCGACT\n->2287|0|FW|2\n-AACATACTCACTGGGGATCGCGAC\n->2389|0|FW|1\n-GTCCTACATACTGGCCATCAGACCT\n->2389|0|FW|1\n-GTCCTACATACTGGCCATCAGACC\n->2393|0|FW|1\n-TACATACTGGCCATCAGACCTCAATAA\n->2398|0|FW|1\n-ACTGGCCATCAGACCTCAATA'..b'CCACACAGTCGCTT\n->3367|0|FW|4\n-CTGGTAAGAACCACACAGTCGCT\n->3410|0|FW|3\n-TCTACTCTCATGCATTTCGAAACT\n->3470|0|FW|2\n-TCTGATATACCACAATATAATCCCAG\n->3470|0|FW|1\n-TCTGATATACCACAATATAATCCCA\n->3470|0|FW|4\n-TCTGATATACCACAATATAATCCC\n->3470|0|FW|1\n-TCTGATATACCACAATATAATCC\n->3535|0|FW|1\n-AACAGGTGAATCGTATTACAACGGA\n->3540|0|FW|1\n-GTGAATCGTATTACAACGGAAATAA\n->3540|0|FW|7\n-GTGAATCGTATTACAACGGAAATA\n->3569|0|FW|3\n+>3569|0|FW|1\n TGCATTTGAACATCGCGAATACT\n->3614|0|FW|1\n-ATCCCAAGCATTCGACAAAGTCTG\n->3618|0|FW|6\n+>3618|0|FW|1\n CAAGCATTCGACAAAGTCTGGCTC\n->3618|0|FW|21\n+>3618|0|FW|5\n CAAGCATTCGACAAAGTCTGGCT\n->3623|0|FW|2\n+>3623|0|FW|1\n ATTCGACAAAGTCTGGCTCGACGG\n->3703|0|FW|2\n-CTTACCTCTATGACAGAAAGTTTG\n->3758|0|FW|1\n-TCATACAATTGAGGCTGGAGTCCCGC\n->3815|0|FW|1\n-CATCTATACAGCCGACATCCCTAC\n->3857|0|FW|1\n-ATCCACATTTGCCGACGATACAG\n->3913|0|FW|3\n+>3913|0|FW|2\n CTACAGCACAGTTGGCACTGTACCT\n->3913|0|FW|8\n-CTACAGCACAGTTGGCACTGTACC\n->3913|0|FW|9\n+>3913|0|FW|2\n CTACAGCACAGTTGGCACTGTAC\n->3914|0|FW|1\n-TACAGCACAGTTGGCACTGTACCT\n->3914|0|FW|1\n-TACAGCACAGTTGGCACTGTACC\n->3965|0|FW|4\n-CTGGCGAATAAAAGTAAACGAGC\n->3983|0|FW|1\n-CGAGCAAAAATGCAAGCACGTGA\n >4011|0|FW|1\n-ACGCTAAACAGACAAGACTGTCCTCCG\n->4011|0|FW|6\n-ACGCTAAACAGACAAGACTGTCCTCC\n->4011|0|FW|4\n ACGCTAAACAGACAAGACTGTCCTC\n->4011|0|FW|25\n+>4011|0|FW|2\n ACGCTAAACAGACAAGACTGTCCT\n->4011|0|FW|15\n+>4011|0|FW|3\n ACGCTAAACAGACAAGACTGTCC\n->4036|0|FW|1\n-CGCTCTTGTTGAACAGCATACCACT\n->4038|0|FW|1\n-CTCTTGTTGAACAGCATACCACTCC\n->4039|0|FW|1\n-TCTTGTTGAACAGCATACCACTCCCGA\n->4039|0|FW|1\n-TCTTGTTGAACAGCATACCACTCCCG\n->4039|0|FW|1\n-TCTTGTTGAACAGCATACCACTCCC\n->4039|0|FW|2\n-TCTTGTTGAACAGCATACCACTCC\n->4042|0|FW|6\n-TGTTGAACAGCATACCACTCCCGAAA\n->4044|0|FW|1\n-TTGAACAGCATACCACTCCCGAAAGC\n->4098|0|FW|1\n-CTTGACAGAAGACTCACATGGCGCA\n->4098|0|FW|2\n-CTTGACAGAAGACTCACATGGCGC\n->4100|0|FW|1\n-TGACAGAAGACTCACATGGCGCAG\n->4104|0|FW|1\n-AGAAGACTCACATGGCGCAGGCACAT\n->4104|0|FW|8\n-AGAAGACTCACATGGCGCAGGCACA\n->4104|0|FW|10\n-AGAAGACTCACATGGCGCAGGCAC\n->4104|0|FW|1\n-AGAAGACTCACATGGCGCAGGCA\n->4106|0|FW|2\n-AAGACTCACATGGCGCAGGCACATT\n->4106|0|FW|4\n-AAGACTCACATGGCGCAGGCACAT\n->4106|0|FW|20\n-AAGACTCACATGGCGCAGGCACA\n->4148|0|FW|1\n-ACTTAAACTCAAAGCCAACAACT\n->4163|0|FW|4\n-CAACAACTTACACTGGCTCATCAAC\n->4199|0|FW|1\n-GCTCAGCCTAGATCACAAGGTCT\n->4232|0|FW|1\n-TTCTATATTGAAACCAATCTGGACC\n->4241|0|FW|4\n-GAAACCAATCTGGACCTATGGCTC\n->4323|0|FW|6\n-AAGATTCTGAGAACCATCACTGGGGC\n->4323|0|FW|35\n+>4323|0|FW|4\n AAGATTCTGAGAACCATCACTGGGG\n->4323|0|FW|5\n+>4323|0|FW|2\n AAGATTCTGAGAACCATCACTGGG\n->4323|0|FW|17\n+>4323|0|FW|3\n AAGATTCTGAGAACCATCACTGG\n->4324|0|FW|2\n+>4324|0|FW|1\n AGATTCTGAGAACCATCACTGGGGC\n->4324|0|FW|1\n-AGATTCTGAGAACCATCACTGGG\n->4325|0|FW|1\n-GATTCTGAGAACCATCACTGGGGC\n->4326|0|FW|2\n-ATTCTGAGAACCATCACTGGGGCAC\n->4326|0|FW|1\n-ATTCTGAGAACCATCACTGGGGCA\n->4326|0|FW|3\n-ATTCTGAGAACCATCACTGGGGC\n->4327|0|FW|1\n-TTCTGAGAACCATCACTGGGGCACC\n->4328|0|FW|1\n-TCTGAGAACCATCACTGGGGCACC\n->4329|0|FW|1\n-CTGAGAACCATCACTGGGGCACCGT\n->4356|0|FW|3\n-TACGTTCGGAGTGAAAACATCCAAA\n->4356|0|FW|4\n-TACGTTCGGAGTGAAAACATCCAA\n->4380|0|FW|1\n-AGAGACTTAAATATCCCATCAGTTACC\n->4380|0|FW|4\n-AGAGACTTAAATATCCCATCAGT\n->4473|0|FW|1\n-CGAGGTCTAATCCAGCTCAGCAGC\n->4485|0|FW|2\n-CAGCTCAGCAGCCGTTCCCGTCTC\n->4485|0|FW|1\n-CAGCTCAGCAGCCGTTCCCGTCT\n->4489|0|FW|1\n-TCAGCAGCCGTTCCCGTCTCCGG\n->4497|0|FW|6\n-CGTTCCCGTCTCCGGCGAAAGGACC\n->4497|0|FW|7\n-CGTTCCCGTCTCCGGCGAAAGGAC\n->4497|0|FW|1\n-CGTTCCCGTCTCCGGCGAAAGGA\n->4499|0|FW|1\n-TTCCCGTCTCCGGCGAAAGGACC\n->4500|0|FW|8\n-TCCCGTCTCCGGCGAAAGGACCTACC\n->4505|0|FW|1\n-TCTCCGGCGAAAGGACCTACCAACCC\n->4505|0|FW|10\n-TCTCCGGCGAAAGGACCTACCAACC\n->4505|0|FW|7\n-TCTCCGGCGAAAGGACCTACCAAC\n->4505|0|FW|1\n-TCTCCGGCGAAAGGACCTACCAA\n >4506|0|FW|1\n-CTCCGGCGAAAGGACCTACCAACCC\n->4506|0|FW|2\n CTCCGGCGAAAGGACCTACCAACC\n >4506|0|FW|1\n CTCCGGCGAAAGGACCTACCAAC\n->4507|0|FW|20\n-TCCGGCGAAAGGACCTACCAACCCAGC\n->4507|0|FW|4\n-TCCGGCGAAAGGACCTACCAACCCA\n->4507|0|FW|4\n-TCCGGCGAAAGGACCTACCAACCC\n->4507|0|FW|3\n-TCCGGCGAAAGGACCTACCAACC\n->4508|0|FW|2\n-CCGGCGAAAGGACCTACCAACCCAGC\n->4508|0|FW|2\n+>4508|0|FW|1\n CCGGCGAAAGGACCTACCAACCC\n->4516|0|FW|1\n-AGGACCTACCAACCCAGCGAATAAAT\n >4530|0|FW|1\n CAGCGAATAAATTATTAGGGCCGT\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,268 +1,64 @@ ->1160|16|G6_DM|1 -TCCAGGAAGCAGTAACGCTGTGTAT ->1161|16|G6_DM|1 -TTCCAGGAAGCAGTAACGCTGTGTA ->1172|16|G6_DM|2 -TACACATCGGTATTCCAGGAAGCAGT ->1176|16|G6_DM|1 -TTACACATCGGTATTCCAGGAAG ->1213|16|G6_DM|1 -TCTTCTCACATGCCCTCGATTCGTG ->1227|16|G6_DM|1 -TTGTCGTCCTCCCTCTTCTCACAT ->1241|16|G6_DM|1 -GTGGAAGCAGCACGCTTTGTCGTCCT ->1242|16|G6_DM|2 -GTGGAAGCAGCACGCTTTGTCGTCC ->1242|16|G6_DM|2 -AGTGGAAGCAGCACGCTTTGTCGTCC >1243|16|G6_DM|1 GTGGAAGCAGCACGCTTTGTCGTC ->1243|16|G6_DM|3 -AGTGGAAGCAGCACGCTTTGTCGTC ->1243|16|G6_DM|3 -CAGTGGAAGCAGCACGCTTTGTCGTC ->1243|16|G6_DM|1 -GCAGTGGAAGCAGCACGCTTTGTCGTC ->1244|16|G6_DM|1 -AGTGGAAGCAGCACGCTTTGTCGT ->1248|16|G6_DM|2 -TGGCAGTGGAAGCAGCACGCTTTG ->1261|16|G6_DM|1 -CAGGATGGTCCGCCTGGCAGTGGAA >1268|16|G6_DM|1 TGAAAGACGCAGGATGGTCCGCCTGGC ->1270|16|G6_DM|1 -AAAGACGCAGGATGGTCCGCCTG ->1270|16|G6_DM|1 -GAAAGACGCAGGATGGTCCGCCTG ->1270|16|G6_DM|223 +>1270|16|G6_DM|19 TGAAAGACGCAGGATGGTCCGCCTG ->1271|16|G6_DM|226 +>1271|16|G6_DM|23 TGAAAGACGCAGGATGGTCCGCCT ->1272|16|G6_DM|20 +>1272|16|G6_DM|3 TGAAAGACGCAGGATGGTCCGCC >1272|16|G6_DM|1 -CTTGAAAGACGCAGGATGGTCCGCC ->1272|16|G6_DM|4 CCTTGAAAGACGCAGGATGGTCCGCC ->1315|16|G6_DM|30 +>1315|16|G6_DM|5 TCGGAGCAGCGAGTGCTTTGGCCCT ->1315|16|G6_DM|18 +>1315|16|G6_DM|1 TTCGGAGCAGCGAGTGCTTTGGCCCT ->1316|16|G6_DM|1 -TCGGAGCAGCGAGTGCTTTGGCCC ->1316|16|G6_DM|16 +>1316|16|G6_DM|5 TTCGGAGCAGCGAGTGCTTTGGCCC ->1331|16|G6_DM|3 +>1331|16|G6_DM|2 GACGGGCCTTGTTTTCGGAGCAG ->1333|16|G6_DM|1 -TAGCGACGGGCCTTGTTTTCGGAGC ->1334|16|G6_DM|1 -TAGCGACGGGCCTTGTTTTCGGAG ->1335|16|G6_DM|1 -TTAGCGACGGGCCTTGTTTTCGGA ->1343|16|G6_DM|2 -TGTTAGCATTAGCGACGGGCCTTG ->1343|16|G6_DM|3 +>1343|16|G6_DM|1 TTGTTAGCATTAGCGACGGGCCTTG ->1349|16|G6_DM|1 -CGCCTTGTTAGCATTAGCGACGG ->1357|16|G6_DM|1 -CACGGGCGGCGCCTTGTTAGCATT ->1385|16|G6_DM|1 -CTCCTGCCAGAGGTGACGTTTGGTG ->1393|16|G6_DM|3 -TCGGTAGCTCCTGCCAGAGGTGAC ->1393|16|G6_DM|1 -TCTCGGTAGCTCCTGCCAGAGGTGAC >1394|16|G6_DM|1 TCGGTAGCTCCTGCCAGAGGTGA ->1395|16|G6_DM|1 -TCTCGGTAGCTCCTGCCAGAGGTG ->1396|16|G6_DM|1 -TCTCGGTAGCTCCTGCCAGAGGT ->1401|16|G6_DM|1 -TGAGGGCGTCTCGGTAGCTCCTGCCA >1402|16|G6_DM|1 -GAGGGCGTCTCGGTAGCTCCTGCC ->1402|16|G6_DM|4 TGAGGGCGTCTCGGTAGCTCCTGCC ->1406|16|G6_DM|4 -TCCGTTGAGGGCGTCTCGGTAGCTCC ->1408|16|G6_DM|1 -TCCGTTGAGGGCGTCTCGGTAGCT ->1409|16|G6_DM|1 -CTCCGTTGAGGGCGTCTCGGTAGC ->1410|16|G6_DM|2 -CACTCCGTTGAGGGCGTCTCGGTAG ->1411|16|G6_DM|1 -TGCACTCCGTTGAGGGCGTCTCGGTA >1418|16|G6_DM|1 TGCTGCGTGCACTCCGTTGAGGGCGT ->1426|16|G6_DM|1 -TGCGGTGCTGCGTGCACTCCGTT ->1429|16|G6_DM|1 -TTCTGCGGTGCTGCGTGCACTCC ->1430|16|G6_DM|1 -GATTCTGCGGTGCTGCGTGCACTC ->1431|16|G6_DM|2 -TGTGGGATTCTGCGGTGCTGCGTGCACT ->1433|16|G6_DM|1 -GTGGGATTCTGCGGTGCTGCGTGCA ->1433|16|G6_DM|1 -TGTGGGATTCTGCGGTGCTGCGTGCA ->1435|16|G6_DM|22 +>1435|16|G6_DM|2 TGTGGGATTCTGCGGTGCTGCGTG ->1435|16|G6_DM|2 -TTGTGGGATTCTGCGGTGCTGCGTG ->1436|16|G6_DM|32 +>1436|16|G6_DM|1 TGTGGGATTCTGCGGTGCTGCGT ->1436|16|G6_DM|11 +>1436|16|G6_DM|3 TTGTGGGATTCTGCGGTGCTGCGT ->1437|16|G6_DM|5 -TTGTGGGATTCTGCGGTGCTGCG ->1453|16|G6_DM|1 -TTGGGTTTGGACTGGGGTTGTGGG ->1454|16|G6_DM|1 -TTGGGTTTGGACTGGGGTTGTGG ->1459|16|G6_DM|2 -TCTGTTTGGGTTTGGACTGGGGT ->1459|16|G6_DM|3 +>1459|16|G6_DM|1 TTCTGTTTGGGTTTGGACTGGGGT ->1460|16|G6_DM|2 -TTCTGTTTGGGTTTGGACTGGGG ->1484|16|G6_DM|1 -TTCTATCTGACCGGAGTGTGGGG ->1488|16|G6_DM|8 +>1488|16|G6_DM|2 CATCGCTTCTATCTGACCGGAGTGT ->1489|16|G6_DM|6 -CATCGCTTCTATCTGACCGGAGTG ->1489|16|G6_DM|1 -AACATCGCTTCTATCTGACCGGAGTG ->1490|16|G6_DM|2 -CATCGCTTCTATCTGACCGGAGT ->1492|16|G6_DM|1 -AACATCGCTTCTATCTGACCGGA ->1492|16|G6_DM|1 -GAACATCGCTTCTATCTGACCGGA ->1493|16|G6_DM|1 -GAACATCGCTTCTATCTGACCGG ->1550|16|G6_DM|6 +>1550|16|G6_DM|2 TGTGTCATCTGGGTGAACATGCGCT ->1551|16|G6_DM|1 -TGTGTCATCTGGGTGAACATGCGC ->1554|16|G6_DM|1 -GCTGTGTCATCTGGGTGAACATG ->1556|16|G6_DM|1 -CAGCTGTGTCATCTGGGTGAACA ->1564|16|G6_DM|6 +>1564|16|G6_DM|1 TGGTGGCCACCAGCTGTGTCATCTG ->1566|16|G6_DM|1 -TGGTGGCCACCAGCTGTGTCATC ->1573|16|G6_DM|6 +>1573|16|G6_DM|1 TGTTGAGAATGGTGGCCACCAGCTG ->1575|16|G6_DM|1 -TGCTGTTGAGAATGGTGGCCACCAGC ->1575|16|G6_DM|1 -TTGCTGTTGAGAATGGTGGCCACCAGC ->1576|16|G6_DM|1 -TGCTGTTGAGAATGGTGGCCACCAG ->1578|16|G6_DM|3 +>1578|16|G6_DM|1 TGCTGTTGAGAATGGTGGCCACC >1578|16|G6_DM|1 TTGCTGTTGAGAATGGTGGCCACC ->1587|16|G6_DM|2 +>1587|16|G6_DM|1 TGCATGACTTGCTGTTGAGAATG ->1587|16|G6_DM|1 -TTGCATGACTTGCTGTTGAGAATG ->1601|16|G6_DM|1 -TAGGTGGAGCTTTAATTGCATGACT ->1616|16|G6_DM|1 -CGCATTCCAGACGACTAGGTGGAGC ->1622|16|G6_DM|1 -CCGTTCGCATTCCAGACGACTAGG ->1627|16|G6_DM|1 -TGCAGGCCGTTCGCATTCCAGACGA ->1628|16|G6_DM|1 -TGCAGGCCGTTCGCATTCCAGACG ->1628|16|G6_DM|1 -TCTGCAGGCCGTTCGCATTCCAGACG ->1629|16|G6_DM|1 -TGCAGGCCGTTCGCATTCCAGAC ->1635|16|G6_DM|18 +>1635|16|G6_DM|4 TGCTGTTCTGCAGGCCGTTCGCATT ->1635|16|G6_DM|1 -TTGCTGTTCTGCAGGCCGTTCGCATT ->1636|16|G6_DM|4 -TGCTGTTCTGCAGGCCGTTCGCAT ->1654|16|G6_DM|1 -TGGTGCTCGACTATGGCCTTGCTGT ->1655|16|G6_DM|2 -TGGTGCTCGACTATGGCCTTGCTG ->1658|16|G6_DM|1 -GATGGTGCTCGACTATGGCCTTG ->1660|16|G6_DM|22 -TCAGATGGTGCTCGACTATGGCCT ->1660|16|G6_DM|117 +>1660|16|G6_DM|12 TTCAGATGGTGCTCGACTATGGCCT ->1660|16|G6_DM|17 +>1660|16|G6_DM|2 TCTTCAGATGGTGCTCGACTATGGCCT ->1661|16|G6_DM|3 -TCAGATGGTGCTCGACTATGGCC ->1661|16|G6_DM|8 -TTCAGATGGTGCTCGACTATGGCC ->1661|16|G6_DM|1 -TCTTCAGATGGTGCTCGACTATGGCC ->1662|16|G6_DM|1 -TCTTCAGATGGTGCTCGACTATGGC ->1663|16|G6_DM|1 -TCTTCAGATGGTGCTCGACTATGG ->1664|16|G6_DM|2 +>1664|16|G6_DM|1 TCTTCAGATGGTGCTCGACTATG ->1678|16|G6_DM|3 -TATCGATCTGGTGGGTCTTCAGAT ->1679|16|G6_DM|1 -TATCGATCTGGTGGGTCTTCAGA ->1693|16|G6_DM|1 -TCGGCTACGAGTAGGATATCGATCT ->1693|16|G6_DM|2 -TTCGGCTACGAGTAGGATATCGATCT ->1694|16|G6_DM|2 -TTCGGCTACGAGTAGGATATCGATC ->1694|16|G6_DM|3 -TTTCGGCTACGAGTAGGATATCGATC ->1696|16|G6_DM|1 -TTCGGCTACGAGTAGGATATCGA ->1696|16|G6_DM|5 -TTTCGGCTACGAGTAGGATATCGA ->1696|16|G6_DM|1 -GTTTCGGCTACGAGTAGGATATCGA ->1714|16|G6_DM|1 -TCTGGGGGAGAAGTGGGTTTCGG ->1885|16|G6_DM|2 -TTGTGGAAGATCGAGAGGGTGTCT ->1886|16|G6_DM|2 +>1691|16|G6_DM|1 +CTACGAGTAGGATATCGATCTGG +>1886|16|G6_DM|1 TTGTGGAAGATCGAGAGGGTGTC ->1887|16|G6_DM|1 -TGTTGTGGAAGATCGAGAGGGTGT ->1888|16|G6_DM|4 -TGTTGTGGAAGATCGAGAGGGTG ->1890|16|G6_DM|1 -TATTGTTGTGGAAGATCGAGAGGG ->1892|16|G6_DM|1 -TCTATTGTTGTGGAAGATCGAGAG ->1893|16|G6_DM|2 -TGTCTATTGTTGTGGAAGATCGAGA ->1894|16|G6_DM|2 -TGTCTATTGTTGTGGAAGATCGAG ->1895|16|G6_DM|3 +>1895|16|G6_DM|1 TGTCTATTGTTGTGGAAGATCGA ->1897|16|G6_DM|1 -GTTGTCTATTGTTGTGGAAGATC ->1899|16|G6_DM|1 -TGTGTTGTCTATTGTTGTGGAAGA ->1901|16|G6_DM|1 -TATGTGTTGTCTATTGTTGTGGAA ->1905|16|G6_DM|1 -TTTTATATGTGTTGTCTATTGTTGT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,48 +1,10 @@ ->1164|16|G6_DM|3 -TATTCCAGGAAGCAGTAACGCTGT ->1165|16|G6_DM|11 -TATTCCAGGAAGCAGTAACGCTG ->1199|16|G6_DM|1 -TCGATTCGTGAGGGCCTCCACACT ->1316|16|G6_DM|5 -TTTCGGAGCAGCGAGTGCTTTGGCCC ->1316|16|G6_DM|5 -TTTTCGGAGCAGCGAGTGCTTTGGCCC ->1317|16|G6_DM|1 -TTTTCGGAGCAGCGAGTGCTTTGGCC ->1318|16|G6_DM|1 -TTTTCGGAGCAGCGAGTGCTTTGGC ->1321|16|G6_DM|7 -TGTTTTCGGAGCAGCGAGTGCTTT ->1322|16|G6_DM|12 -TGTTTTCGGAGCAGCGAGTGCTT ->1322|16|G6_DM|2 -TTGTTTTCGGAGCAGCGAGTGCTT ->1369|16|G6_DM|1 -TTTGGTGATGCCACGGGCGGCGC ->1459|16|G6_DM|3 +>1459|16|G6_DM|1 TTTCTGTTTGGGTTTGGACTGGGGT ->1460|16|G6_DM|25 +>1460|16|G6_DM|3 TTTCTGTTTGGGTTTGGACTGGGG ->1461|16|G6_DM|25 +>1461|16|G6_DM|2 TTTCTGTTTGGGTTTGGACTGGG ->1479|16|G6_DM|1 -ATCTGACCGGAGTGTGGGGTTTCT ->1489|16|G6_DM|1 -ATCGCTTCTATCTGACCGGAGTG ->1633|16|G6_DM|1 -TGTTCTGCAGGCCGTTCGCATTCC ->1652|16|G6_DM|1 -TGCTCGACTATGGCCTTGCTGTTC ->1688|16|G6_DM|13 -TACGAGTAGGATATCGATCTGGTGG ->1689|16|G6_DM|43 +>1689|16|G6_DM|3 TACGAGTAGGATATCGATCTGGTG ->1689|16|G6_DM|4 -CTACGAGTAGGATATCGATCTGGTG ->1690|16|G6_DM|65 +>1690|16|G6_DM|8 TACGAGTAGGATATCGATCTGGT ->1690|16|G6_DM|15 -CTACGAGTAGGATATCGATCTGGT ->1691|16|G6_DM|8 -CTACGAGTAGGATATCGATCTGG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number -1 1 0.09 -2 30 2.77 -3 17 1.57 -4 14 1.29 -5 69 6.37 -6 87 8.03 -7 27 2.49 -8 64 5.90 -9 27 2.49 -10 129 11.90 -11 81 7.47 -12 21 1.94 -13 44 4.06 -14 28 2.58 -15 36 3.32 -16 56 5.17 -17 56 5.17 -18 59 5.44 -19 49 4.52 -20 53 4.89 -21 80 7.38 -22 17 1.57 -23 39 3.60 +1 0 0.00 +2 0 0.00 +3 0 0.00 +4 1 1.72 +5 10 17.24 +6 16 27.59 +7 0 0.00 +8 0 0.00 +9 1 1.72 +10 9 15.52 +11 3 5.17 +12 0 0.00 +13 2 3.45 +14 1 1.72 +15 0 0.00 +16 2 3.45 +17 0 0.00 +18 2 3.45 +19 6 10.34 +20 1 1.72 +21 2 3.45 +22 0 0.00 +23 2 3.45 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,186 +1,50 @@ ->1186|0|G6_DM|2 +>1186|0|G6_DM|1 TACCGATGTGTAAAGTGTGGAGGC ->1186|0|G6_DM|2 -TACCGATGTGTAAAGTGTGGAGGCC >1190|0|G6_DM|1 GATGTGTAAAGTGTGGAGGCCCTC >1196|0|G6_DM|1 TAAAGTGTGGAGGCCCTCACGAAT ->1212|0|G6_DM|1 -TCACGAATCGAGGGCATGTGAGAA ->1219|0|G6_DM|5 +>1219|0|G6_DM|1 TCGAGGGCATGTGAGAAGAGGGA ->1219|0|G6_DM|2 -TCGAGGGCATGTGAGAAGAGGGAG ->1221|0|G6_DM|1 -GAGGGCATGTGAGAAGAGGGAGGA ->1226|0|G6_DM|1 -CATGTGAGAAGAGGGAGGACGAC ->1251|0|G6_DM|1 -AGCGTGCTGCTTCCACTGCCAGGCG ->1255|0|G6_DM|5 -TGCTGCTTCCACTGCCAGGCGGACC ->1305|0|G6_DM|1 -TGCATACAAAAGGGCCAAAGCACTC ->1309|0|G6_DM|1 -TACAAAAGGGCCAAAGCACTCGC ->1309|0|G6_DM|3 -TACAAAAGGGCCAAAGCACTCGCT ->1309|0|G6_DM|1 -TACAAAAGGGCCAAAGCACTCGCTG ->1309|0|G6_DM|4 -TACAAAAGGGCCAAAGCACTCGCTGC ->1309|0|G6_DM|2 -TACAAAAGGGCCAAAGCACTCGCTGCT ->1311|0|G6_DM|1 -CAAAAGGGCCAAAGCACTCGCTG ->1311|0|G6_DM|1 -CAAAAGGGCCAAAGCACTCGCTGC ->1311|0|G6_DM|10 -CAAAAGGGCCAAAGCACTCGCTGCT ->1311|0|G6_DM|1 -CAAAAGGGCCAAAGCACTCGCTGCTC ->1312|0|G6_DM|1 -AAAAGGGCCAAAGCACTCGCTGCTCC ->1313|0|G6_DM|1 -AAAGGGCCAAAGCACTCGCTGCTC ->1315|0|G6_DM|1 -AGGGCCAAAGCACTCGCTGCTCCGA ->1324|0|G6_DM|1 -GCACTCGCTGCTCCGAAAACAAGGCCC ->1325|0|G6_DM|1 -CACTCGCTGCTCCGAAAACAAGGCCC ->1327|0|G6_DM|1 -CTCGCTGCTCCGAAAACAAGGCCC ->1327|0|G6_DM|1 -CTCGCTGCTCCGAAAACAAGGCCCG ->1329|0|G6_DM|1 -CGCTGCTCCGAAAACAAGGCCCGT ->1329|0|G6_DM|1 -CGCTGCTCCGAAAACAAGGCCCGTC ->1334|0|G6_DM|1 -CTCCGAAAACAAGGCCCGTCGCTAA ->1337|0|G6_DM|1 -CGAAAACAAGGCCCGTCGCTAATGC ->1338|0|G6_DM|1 -GAAAACAAGGCCCGTCGCTAATGC ->1384|0|G6_DM|1 -TCACCAAACGTCACCTCTGGCAGG ->1384|0|G6_DM|31 +>1335|0|G6_DM|6 +TCCGAAAACAAGGCCCGTCGCTA +>1335|0|G6_DM|1 +TCCGAAAACAAGGCCCGTCGCTAA +>1335|0|G6_DM|3 +TCCGAAAACAAGGCCCGTCGCTAAT +>1335|0|G6_DM|1 +TCCGAAAACAAGGCCCGTCGCTAATG +>1384|0|G6_DM|5 TCACCAAACGTCACCTCTGGCAGGA >1384|0|G6_DM|3 -TCACCAAACGTCACCTCTGGCAGGAG ->1384|0|G6_DM|5 TCACCAAACGTCACCTCTGGCAGGAGC ->1385|0|G6_DM|3 -CACCAAACGTCACCTCTGGCAGGAGC ->1386|0|G6_DM|8 +>1386|0|G6_DM|1 ACCAAACGTCACCTCTGGCAGGA >1386|0|G6_DM|1 ACCAAACGTCACCTCTGGCAGGAG ->1386|0|G6_DM|6 -ACCAAACGTCACCTCTGGCAGGAGC ->1387|0|G6_DM|1 -CCAAACGTCACCTCTGGCAGGAGC ->1389|0|G6_DM|1 -AAACGTCACCTCTGGCAGGAGCT ->1389|0|G6_DM|1 -AAACGTCACCTCTGGCAGGAGCTAC ->1389|0|G6_DM|1 -AAACGTCACCTCTGGCAGGAGCTACC ->1393|0|G6_DM|1 -GTCACCTCTGGCAGGAGCTACCGAG ->1394|0|G6_DM|2 -TCACCTCTGGCAGGAGCTACCGAGA ->1398|0|G6_DM|1 -CTCTGGCAGGAGCTACCGAGACGCCCT +>1399|0|G6_DM|2 +TCTGGCAGGAGCTACCGAGACGCC >1399|0|G6_DM|1 -TCTGGCAGGAGCTACCGAGACGC ->1399|0|G6_DM|3 -TCTGGCAGGAGCTACCGAGACGCC ->1399|0|G6_DM|7 -TCTGGCAGGAGCTACCGAGACGCCC ->1399|0|G6_DM|4 TCTGGCAGGAGCTACCGAGACGCCCT >1401|0|G6_DM|1 TGGCAGGAGCTACCGAGACGCCCTC ->1411|0|G6_DM|4 -TACCGAGACGCCCTCAACGGAGTG ->1484|0|G6_DM|1 -CCCCACACTCCGGTCAGATAGAAG ->1487|0|G6_DM|1 -CACACTCCGGTCAGATAGAAGCGA ->1487|0|G6_DM|1 -CACACTCCGGTCAGATAGAAGCGAT ->1489|0|G6_DM|1 -CACTCCGGTCAGATAGAAGCGATG ->1492|0|G6_DM|6 +>1492|0|G6_DM|1 TCCGGTCAGATAGAAGCGATGTTCGC +>1493|0|G6_DM|1 +CCGGTCAGATAGAAGCGATGTTCGC >1532|0|G6_DM|1 TGATGGAAAGGATGATGGAGCGCAT ->1534|0|G6_DM|9 +>1534|0|G6_DM|1 ATGGAAAGGATGATGGAGCGCAT ->1537|0|G6_DM|2 -GAAAGGATGATGGAGCGCATGTTCA ->1539|0|G6_DM|1 -AAGGATGATGGAGCGCATGTTCACC ->1540|0|G6_DM|1 -AGGATGATGGAGCGCATGTTCACCC ->1618|0|G6_DM|1 -TCCACCTAGTCGTCTGGAATGCGAACG ->1619|0|G6_DM|1 -CCACCTAGTCGTCTGGAATGCGAA ->1620|0|G6_DM|1 -CACCTAGTCGTCTGGAATGCGAAC >1620|0|G6_DM|1 CACCTAGTCGTCTGGAATGCGAACGG ->1621|0|G6_DM|1 -ACCTAGTCGTCTGGAATGCGAACGG ->1624|0|G6_DM|1 -TAGTCGTCTGGAATGCGAACGGC ->1624|0|G6_DM|8 -TAGTCGTCTGGAATGCGAACGGCCT ->1630|0|G6_DM|1 -TCTGGAATGCGAACGGCCTGCAGAAC ->1634|0|G6_DM|1 -GAATGCGAACGGCCTGCAGAACAGC ->1637|0|G6_DM|2 -TGCGAACGGCCTGCAGAACAGCA ->1637|0|G6_DM|1 -TGCGAACGGCCTGCAGAACAGCAAGG ->1637|0|G6_DM|1 -TGCGAACGGCCTGCAGAACAGCAAGGC ->1639|0|G6_DM|1 -CGAACGGCCTGCAGAACAGCAAGGC >1649|0|G6_DM|1 GCAGAACAGCAAGGCCATAGTCGAG ->1663|0|G6_DM|1 -CCATAGTCGAGCACCATCTGAAGAC ->1664|0|G6_DM|2 -CATAGTCGAGCACCATCTGAAGA >1664|0|G6_DM|1 CATAGTCGAGCACCATCTGAAGACC ->1668|0|G6_DM|1 -GTCGAGCACCATCTGAAGACCCACCA ->1670|0|G6_DM|1 -CGAGCACCATCTGAAGACCCACCA ->1679|0|G6_DM|4 -TCTGAAGACCCACCAGATCGATATC ->1679|0|G6_DM|3 -TCTGAAGACCCACCAGATCGATATCC ->1679|0|G6_DM|1 -TCTGAAGACCCACCAGATCGATATCCT ->1681|0|G6_DM|2 +>1681|0|G6_DM|1 TGAAGACCCACCAGATCGATATCC ->1685|0|G6_DM|3 -GACCCACCAGATCGATATCCTACTCG ->1689|0|G6_DM|1 -CACCAGATCGATATCCTACTCGTAG >1700|0|G6_DM|1 TATCCTACTCGTAGCCGAAACCCA ->1700|0|G6_DM|1 -TATCCTACTCGTAGCCGAAACCCAC >1893|0|G6_DM|1 TCTCGATCTTCCACAACAATAGAC ->1893|0|G6_DM|1 -TCTCGATCTTCCACAACAATAGACAA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,50 +1,6 @@ ->1178|0|G6_DM|2 -TCCTGGAATACCGATGTGTAAAGTG ->1213|0|G6_DM|3 -CACGAATCGAGGGCATGTGAGAA ->1332|0|G6_DM|1 -TGCTCCGAAAACAAGGCCCGTCGCT ->1333|0|G6_DM|1 -GCTCCGAAAACAAGGCCCGTCGCTAA ->1335|0|G6_DM|62 -TCCGAAAACAAGGCCCGTCGCTA ->1335|0|G6_DM|1 -TCCGAAAACAAGGCCCGTCGCTAA ->1335|0|G6_DM|5 -TCCGAAAACAAGGCCCGTCGCTAAT ->1335|0|G6_DM|1 -TCCGAAAACAAGGCCCGTCGCTAATG ->1336|0|G6_DM|1 -CCGAAAACAAGGCCCGTCGCTAA ->1382|0|G6_DM|1 -CATCACCAAACGTCACCTCTGGC ->1382|0|G6_DM|1 -CATCACCAAACGTCACCTCTGGCA ->1382|0|G6_DM|1 -CATCACCAAACGTCACCTCTGGCAGG ->1382|0|G6_DM|1 -CATCACCAAACGTCACCTCTGGCAGGA ->1474|0|G6_DM|3 +>1474|0|G6_DM|1 CAAACAGAAACCCCACACTCCGGTC ->1493|0|G6_DM|8 -CCGGTCAGATAGAAGCGATGTTCGC ->1502|0|G6_DM|1 -TAGAAGCGATGTTCGCTCGCATGGAAG ->1647|0|G6_DM|1 -CTGCAGAACAGCAAGGCCATAGT ->1666|0|G6_DM|1 -TAGTCGAGCACCATCTGAAGACCC ->1666|0|G6_DM|3 -TAGTCGAGCACCATCTGAAGACCCA ->1666|0|G6_DM|4 -TAGTCGAGCACCATCTGAAGACCCAC ->1666|0|G6_DM|1 -TAGTCGAGCACCATCTGAAGACCCACC ->1703|0|G6_DM|9 +>1703|0|G6_DM|2 CCTACTCGTAGCCGAAACCCACT ->1703|0|G6_DM|5 -CCTACTCGTAGCCGAAACCCACTT ->1703|0|G6_DM|6 +>1703|0|G6_DM|1 CCTACTCGTAGCCGAAACCCACTTC ->1704|0|G6_DM|2 -CTACTCGTAGCCGAAACCCACTTC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,68 +1,18 @@ ->55|16|Gypsy2-LTR_DM|1 -TTGGTCAGCATTTTGGGCACTCGTG ->62|16|Gypsy2-LTR_DM|1 -TGCAGACCTTTGGTCAGCATTTTGGGC >75|16|Gypsy2-LTR_DM|1 AGCGGAAAGAATGCAGACCTTTGGT ->80|16|Gypsy2-LTR_DM|2 +>80|16|Gypsy2-LTR_DM|1 TTGACAGCGGAAAGAATGCAGACCT ->80|16|Gypsy2-LTR_DM|1 -TGACAGCGGAAAGAATGCAGACCT ->93|16|Gypsy2-LTR_DM|1 -TTTTAGCTGGTCGTTGACAGCGGAA ->94|16|Gypsy2-LTR_DM|1 -CACTTTTAGCTGGTCGTTGACAGCGGA ->94|16|Gypsy2-LTR_DM|2 -CTTTTAGCTGGTCGTTGACAGCGGA ->95|16|Gypsy2-LTR_DM|1 -CACTTTTAGCTGGTCGTTGACAGCGG ->97|16|Gypsy2-LTR_DM|4 +>97|16|Gypsy2-LTR_DM|2 TCGCACTTTTAGCTGGTCGTTGACAGC >97|16|Gypsy2-LTR_DM|1 CGCACTTTTAGCTGGTCGTTGACAGC ->97|16|Gypsy2-LTR_DM|2 +>97|16|Gypsy2-LTR_DM|1 GCACTTTTAGCTGGTCGTTGACAGC ->97|16|Gypsy2-LTR_DM|1 -CACTTTTAGCTGGTCGTTGACAGC ->98|16|Gypsy2-LTR_DM|1 -TCGCACTTTTAGCTGGTCGTTGACAG ->98|16|Gypsy2-LTR_DM|1 -CGCACTTTTAGCTGGTCGTTGACAG ->98|16|Gypsy2-LTR_DM|1 -GCACTTTTAGCTGGTCGTTGACAG ->108|16|Gypsy2-LTR_DM|2 -GCAGATGATCGCACTTTTAGCTGG ->109|16|Gypsy2-LTR_DM|1 -TGCAGATGATCGCACTTTTAGCTG ->109|16|Gypsy2-LTR_DM|1 -GCAGATGATCGCACTTTTAGCTG ->120|16|Gypsy2-LTR_DM|1 -CGGCGGAGAAGTGCAGATGATCGC ->146|16|Gypsy2-LTR_DM|1 -AGCGAATCAGTGGTCGTCAGCGGCTA ->148|16|Gypsy2-LTR_DM|4 +>140|16|Gypsy2-LTR_DM|3 +TCAGTGGTCGTCAGCGGCTACGCGGC +>141|16|Gypsy2-LTR_DM|1 +GAATCAGTGGTCGTCAGCGGCTACGCGG +>148|16|Gypsy2-LTR_DM|1 AGCGAATCAGTGGTCGTCAGCGGC ->151|16|Gypsy2-LTR_DM|1 -TCGGCAGCGAATCAGTGGTCGTCAGC ->151|16|Gypsy2-LTR_DM|7 -GGCAGCGAATCAGTGGTCGTCAGC ->154|16|Gypsy2-LTR_DM|1 -TCGGCAGCGAATCAGTGGTCGTC ->159|16|Gypsy2-LTR_DM|2 -GCAGGCGTCGGCAGCGAATCAGTGG ->161|16|Gypsy2-LTR_DM|2 -GCAGGCGTCGGCAGCGAATCAGT ->165|16|Gypsy2-LTR_DM|2 -TCGCAGCAGGCGTCGGCAGCGAAT ->167|16|Gypsy2-LTR_DM|1 -AGCGTCGCAGCAGGCGTCGGCAGCGA ->169|16|Gypsy2-LTR_DM|1 -AGCGTCGCAGCAGGCGTCGGCAGC ->172|16|Gypsy2-LTR_DM|1 -AGCAGCGTCGCAGCAGGCGTCGGC ->172|16|Gypsy2-LTR_DM|1 -GCAGCGTCGCAGCAGGCGTCGGC ->245|16|Gypsy2-LTR_DM|1 -TGTAATTGTTCATTTGAAACTAAAGC ->250|16|Gypsy2-LTR_DM|1 -TTATTGTAATTGTTCATTTGAAACT +>193|16|Gypsy2-LTR_DM|1 +TAGCAATCAAGTGTGGGCGTCAGC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,28 +0,0 @@ ->71|16|Gypsy2-LTR_DM|1 -GCGGAAAGAATGCAGACCTTTGGTCAGC ->73|16|Gypsy2-LTR_DM|1 -GCGGAAAGAATGCAGACCTTTGGTCA ->73|16|Gypsy2-LTR_DM|1 -CGGAAAGAATGCAGACCTTTGGTCA ->76|16|Gypsy2-LTR_DM|2 -GCGGAAAGAATGCAGACCTTTGG ->94|16|Gypsy2-LTR_DM|1 -ACTTTTAGCTGGTCGTTGACAGCGGA ->121|16|Gypsy2-LTR_DM|1 -GCGGCGGAGAAGTGCAGATGATCG ->123|16|Gypsy2-LTR_DM|1 -TACGCGGCGGAGAAGTGCAGATGAT ->140|16|Gypsy2-LTR_DM|20 -TCAGTGGTCGTCAGCGGCTACGCGGC ->141|16|Gypsy2-LTR_DM|1 -GAATCAGTGGTCGTCAGCGGCTACGCGG ->146|16|Gypsy2-LTR_DM|1 -GAATCAGTGGTCGTCAGCGGCTA ->193|16|Gypsy2-LTR_DM|1 -TAGCAATCAAGTGTGGGCGTCAGC ->250|16|Gypsy2-LTR_DM|1 -TTTATTGTAATTGTTCATTTGAAACT ->250|16|Gypsy2-LTR_DM|2 -TATTGTAATTGTTCATTTGAAACT ->274|16|Gypsy2-LTR_DM|1 -ATTTTGTAGATCGCAAGCGACCGTT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number -1 4 2.35 -2 3 1.76 -3 1 0.59 -4 5 2.94 -5 5 2.94 -6 3 1.76 -7 10 5.88 -8 11 6.47 -9 11 6.47 -10 20 11.76 -11 15 8.82 -12 7 4.12 -13 11 6.47 -14 9 5.29 -15 6 3.53 -16 12 7.06 -17 5 2.94 -18 4 2.35 -19 8 4.71 -20 5 2.94 -21 6 3.53 -22 4 2.35 -23 5 2.94 +1 0 0.00 +2 0 0.00 +3 0 0.00 +4 0 0.00 +5 0 0.00 +6 0 0.00 +7 0 0.00 +8 1 33.33 +9 0 0.00 +10 0 0.00 +11 1 33.33 +12 0 0.00 +13 0 0.00 +14 1 33.33 +15 0 0.00 +16 0 0.00 +17 0 0.00 +18 0 0.00 +19 0 0.00 +20 0 0.00 +21 0 0.00 +22 0 0.00 +23 0 0.00 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,48 +1,8 @@ >59|0|Gypsy2-LTR_DM|1 AGTGCCCAAAATGCTGACCAAAGGTCT ->61|0|Gypsy2-LTR_DM|2 -TGCCCAAAATGCTGACCAAAGGTCTG ->62|0|Gypsy2-LTR_DM|2 -GCCCAAAATGCTGACCAAAGGTCTG ->85|0|Gypsy2-LTR_DM|1 -TGCATTCTTTCCGCTGTCAACGAC ->127|0|Gypsy2-LTR_DM|5 -TCTGCACTTCTCCGCCGCGTAGCCGC ->133|0|Gypsy2-LTR_DM|1 -CTTCTCCGCCGCGTAGCCGCTGACGA ->137|0|Gypsy2-LTR_DM|1 -TCCGCCGCGTAGCCGCTGACGACC ->145|0|Gypsy2-LTR_DM|1 -GTAGCCGCTGACGACCACTGATTCG ->146|0|Gypsy2-LTR_DM|2 -TAGCCGCTGACGACCACTGATTCGC ->146|0|Gypsy2-LTR_DM|1 -TAGCCGCTGACGACCACTGATTCG ->146|0|Gypsy2-LTR_DM|1 -TAGCCGCTGACGACCACTGATTC ->150|0|Gypsy2-LTR_DM|1 -CGCTGACGACCACTGATTCGCTG ->158|0|Gypsy2-LTR_DM|2 +>158|0|Gypsy2-LTR_DM|1 ACCACTGATTCGCTGCCGACGCCTG ->168|0|Gypsy2-LTR_DM|1 -CGCTGCCGACGCCTGCTGCGACGC ->206|0|Gypsy2-LTR_DM|1 -CTTGATTGCTAGGGACTTAGGGAA ->208|0|Gypsy2-LTR_DM|1 -TGATTGCTAGGGACTTAGGGAAA ->223|0|Gypsy2-LTR_DM|1 -TAGGGAAATATTTTGTATCTTAGCTT ->259|0|Gypsy2-LTR_DM|2 -TGAACAATTACAATAAACGGTCGCT ->260|0|Gypsy2-LTR_DM|1 -GAACAATTACAATAAACGGTCGCT ->263|0|Gypsy2-LTR_DM|1 -CAATTACAATAAACGGTCGCTTGC ->267|0|Gypsy2-LTR_DM|6 -TACAATAAACGGTCGCTTGCGATC +>266|0|Gypsy2-LTR_DM|2 +TTACAATAAACGGTCGCTTGCGATC >267|0|Gypsy2-LTR_DM|1 TACAATAAACGGTCGCTTGCGAT ->291|0|Gypsy2-LTR_DM|1 -TACAAAATAAAAATCAATAAACTGT ->298|0|Gypsy2-LTR_DM|1 -TAAAAATCAATAAACTGTAATTAT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,30 +0,0 @@ ->88|0|Gypsy2-LTR_DM|1 -ATTCTTTCCGCTGTCAACGACCAG ->89|0|Gypsy2-LTR_DM|1 -TTCTTTCCGCTGTCAACGACCAG ->110|0|Gypsy2-LTR_DM|1 -AGCTAAAAGTGCGATCATCTGCACT ->135|0|Gypsy2-LTR_DM|1 -TCTCCGCCGCGTAGCCGCTGACGACC ->135|0|Gypsy2-LTR_DM|1 -TCTCCGCCGCGTAGCCGCTGACGA ->138|0|Gypsy2-LTR_DM|1 -CCGCCGCGTAGCCGCTGACGACCA ->138|0|Gypsy2-LTR_DM|1 -CCGCCGCGTAGCCGCTGACGACC ->156|0|Gypsy2-LTR_DM|2 -CGACCACTGATTCGCTGCCGACGCC ->159|0|Gypsy2-LTR_DM|2 -CCACTGATTCGCTGCCGACGCCTG ->207|0|Gypsy2-LTR_DM|1 -TTGATTGCTAGGGACTTAGGGAAAT ->207|0|Gypsy2-LTR_DM|1 -TTGATTGCTAGGGACTTAGGGAA ->264|0|Gypsy2-LTR_DM|2 -AATTACAATAAACGGTCGCTTGCGA ->266|0|Gypsy2-LTR_DM|4 -TTACAATAAACGGTCGCTTGCGATC ->266|0|Gypsy2-LTR_DM|1 -TTACAATAAACGGTCGCTTGCGA ->289|0|Gypsy2-LTR_DM|1 -TCTACAAAATAAAAATCAATAAACTG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM.html --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM.html Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,295 +0,0 @@\n-\n- <!DOCTYPE html>\n- <html lang="en">\n- <head>\n- <meta charset="utf-8">\n- <title>pipeline</title>\n- <meta name="viewport" content="width=device-width, initial-scale=1.0">\n- <meta name="description" content="">\n- <meta name="author" content="">\n- <!-- Le styles -->\n- <link href="css/bootstrap.css" rel="stylesheet">\n- <link href="css/bootstrap-table.css" rel="stylesheet">\n- <style type="text/css">\n- body {\n- padding-top: 60px;\n- padding-bottom: 40px;\n- }\n- div#page {\n- width: 940px;\n- background-color: #fff;\n- margin: 0 auto;\n- text-align: left;\n- border-color: #fff;\n- border-style: none solid solid;\n- border-width: medium 1px 1px;\n- }\n-\n- div.content {\n- \tdisplay: none;\n-\t float: right;\n-\t width: 550px;\n- }\n- div.content a, div.navigation a {\n- text-decoration: none;\n- \tcolor: #777;\n- }\n- div.content a:focus, div.content a:hover, div.content a:active {\n- text-decoration: underline;\n- }\n- \n- div.controls {\n- margin-top: 5px;\n-\t height: 23px;\n- }\n- \n- div.controls a {\n-\t padding: 5px;\n- }\n- div.ss-controls {\n-\t float: left;\n- }\n- div.nav-controls {\n-\t float: right;\n- }\n- div.slideshow-container {\n-\t position: relative;\n-\t clear: both;\n-\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- }\n- div.loader {\n- \tposition: absolute;\n- \ttop: 0;\n- \tleft: 0;\n- background-image: url(\'loader.gif\');\n- background-repeat: no-repeat;\n- background-position: center;\n- \twidth: 550px;\n- \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- }\n- div.slideshow {\n- \n- }\n- \n- div.slideshow span.image-wrapper {\n-\t display: block;\n-\t position: absolute;\n-\t top: 0;\n-\t left: 0;\n- }\n- div.slideshow a.advance-link {\n-\t display: block;\n- \t width: 550px;\n- height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n- text-align: center;\n- }\n- div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n- text-decoration: none;\n- }\n- div.slideshow img {\n- vertical-align: middle;\n-\tborder: 1px solid #ccc;\n- }\n-\n- div.image-title {\n- font-weight: bold;\n- font-size: 1.4em;\n- }\n-\n- div.image-desc {\n- line-height: 1.3em;\n- padding-top: 12px;\n- }\n- div.navigation {\n-\n- }\n- ul.thumbs {\n-\tclear: both;\n-\tmargin: 0;\n-\tpadding: 0;\n- }\n- ul.thumbs li {\n-\tfloat: none;\n-\tpadding: 0;\n-\tmargin: 0;\n- list-style: none;\n- }\n- a.thumb {\n-\tpadding: 0;\n-\tdisplay: inline;\n-\tborder: none;\n- }\n- ul.thumbs li.selected a.thumb {\n-\tcolor: #000;\n- font-weight: bold;\n- }\n- a.thumb:focus {\n-\toutline: none;\n- }\n- ul.thumbs img {\n-\tborder: none;\n-\tdisplay: block;\n- }\n- div.pagination {\n-\tclear: both;\n- }\n- div.navigation div.top {\n- margin-bottom: 12px;\n-\theight: 11px;\n- }\n- div.navigation div.bottom {\n- margin-top: 12px;\n- }\n- div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n-\tdisplay: block;\n-\tfloat: left;\n- margin-right: 2px;\n-\tpadding: 4px 7px 2px 7px;\n-\tborder: 1px solid #ccc;\n- }\n- div.pagination a:hover {\n- background-color: #eee;\n- text-decoration: none;\n- }\n- div.pagination span.current {\n- font-weight: bold;\n- background-color: #000;\n- border-color: #000;\n-\tcolor: #fff;\n- }\n- div.pagination span.ellipsis {\n-\tborder: none;\n-\tpadding: 5px 0 3px 2px;\n- }\n- \n- div.download {\n-\tfloat: right;\n- }\n- \n- div.caption-container {\n-\tposition: relative;\n-\tclear: left;\n-\theight: 75px;\n- }\n- span.image-caption {\n-\tdisplay: block;\n-\tposition: absolute;\n-\twidth: 550px;\n-\ttop: 0;\n-\tleft: 0;\n- }\n- div.caption {\n-\tpadding: 12px;\n- }\n-\n- /* Featurettes\n- ------------------------- */\n-\n- .featurette {\n- padding-top: 20px; /* Vertica'..b'w: hidden; /* Vertically center images part 2: clear their floats. */\n- text-align: center;\n- }\n-\n- .featurette-p\n- {\n- text-align: left;\n- }\n-\n- .featurette-image {\n- margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n- width: 450px;\n- height: auto;\n- }\n-\n- </style>\n- <link href="css/bootstrap-responsive.css" rel="stylesheet">\n- </head>\n- <body>\n- \n-\t\t\t\t\t<div align="center">\n-\t\t\t\t\t<h2>I_DM</h2>\n-\t\t\t\t\t<p> <img class="featurette-image" src="I_DM/histogram.png"/></p>\n-\t\t\t\t\t<p><a href="I_DM/overlap_size.txt">ping pong signature</a></p>\n-\t\t\t\t\t<p><a href="I_DM/sensPPP.txt">sense reads with PPP</a></p>\n-\t\t\t\t\t<p><a href="I_DM/antisensPPP.txt">reverse reads with PPP</a></p>\n-\t\t\t\t\t<p><a href="I_DM/sens.txt">sense reads without PPP</a></p>\n-\t\t\t\t\t<p><a href="I_DM/antisens.txt">reverse reads without PPP</a></p>\n-\t\t\t\t\t</div>\n- <!-- FOOTER -->\n- <div class="container">\n- <footer>\n- \n- </footer>\n- </div>\n- <!-- Le javascript\n- ================================================== -->\n- <!-- Placed at the end of the document so the pages load faster -->\n- <script type="text/javascript" src="js/filter.js"></script>\n- <script type="text/javascript" src="js/jquery.js"></script>\n- <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n- <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n- <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n- <script type="text/javascript" src="js/bootstrap-table.js"></script>\n- <script type="text/javascript" src="js/bootstrap.min.js"></script>\n- <script type="text/javascript">\n- jQuery(document).ready(function($) {\n- // We only want these styles applied when javascript is enabled\n- $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n- $(\'div.content\').css(\'display\', \'block\');\n- \n- $(".each-gallery").each(function(i){\n- // Initially set opacity on thumbs and add\n- // additional styling for hover effect on thumbs\n- var onMouseOutOpacity = 0.67;\n- $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n- mouseOutOpacity: onMouseOutOpacity,\n- mouseOverOpacity: 1.0,\n- fadeSpeed: \'fast\',\n- exemptionSelector: \'.selected\'\n- });\n- \n- // Initialize Advanced Galleriffic Gallery\n- var gallery = $(\'#thumbs\'+i).galleriffic({\n- delay: 2500,\n- numThumbs: 22,\n- preloadAhead: 10,\n- enableTopPager: true,\n- enableBottomPager: true,\n- maxPagesToShow: 7,\n- imageContainerSel: \'#slideshow\'+ i,\n- controlsContainerSel: \'#controls\' + i,\n- captionContainerSel: \'#caption\' + i,\n- loadingContainerSel: \'#loading\' + i,\n- renderSSControls: true,\n- renderNavControls: true,\n- playLinkText: \'Play\',\n- pauseLinkText: \'Pause\',\n- prevLinkText: \'‹ Previous\',\n- nextLinkText: \'Next ›\',\n- nextPageLinkText: \'Next ›\',\n- prevPageLinkText: \'‹ Prev\',\n- enableHistory: false,\n- autoStart: false,\n- syncTransitions: true,\n- defaultTransitionDuration: 900,\n- onSlideChange: function(prevIndex, nextIndex) {\n- // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n- this.find(\'ul.thumbs\').children()\n- .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n- .eq(nextIndex).fadeTo(\'fast\', 1.0);\n- },\n- onPageTransitionOut: function(callback) {\n- this.fadeTo(\'fast\', 0.0, callback);\n- },\n- onPageTransitionIn: function() {\n- this.fadeTo(\'fast\', 1.0);\n- }\n- });\n- });\n- });\n- </script>\n- </body>\n- </html>\n- \n\\ No newline at end of file\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,32 +0,0 @@ ->1256|16|I_DM|3 -TCCATGTCTTCAAGTTTGTCGTAGC ->1487|16|I_DM|1 -TAACTTAAAGGTAGTGTTAACGGA ->1659|16|I_DM|1 -TATTGAGGTTGGAATGTTATTAGT ->2966|16|I_DM|1 -TTGTGGTATGTGTCTATTGGATATT ->2980|16|I_DM|1 -TGTTTTGTAGGCTTGTGGTATGT ->2997|16|I_DM|1 -ATTGGGATGATTAGACTTGTTTT ->3007|16|I_DM|1 -TTCGGCTTGAGGATTGGGATGATTA ->4286|16|I_DM|1 -TTATGGATTCTGAGTGATGTGTCT ->4289|16|I_DM|1 -TCTTATGGATTCTGAGTGATGTG ->4425|16|I_DM|1 -TGTATGTTTCCGTTGTAATGGCGAA ->4748|16|I_DM|1 -TTTATGTTTGGGGTGAGGATAACT ->4985|16|I_DM|1 -GTTGGTATTGAATTTGGATTTAGG ->5007|16|I_DM|1 -TATCAACTTAGCAAAACGGACAAGT ->5103|16|I_DM|1 -TTTGCTAAGAAGGTCTAGAGGGTT ->5115|16|I_DM|1 -TTATTGGATTGGGTTTGCTAAGAAG ->5344|16|I_DM|1 -TATTTATTATGATAGATAGGATAGT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ ->3202|16|I_DM|2 -TTATGAGATAGTCTACATAGAGTA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -size number percentage of the total overlap number -1 0 0.00 -2 0 0.00 -3 0 0.00 -4 0 0.00 -5 0 0.00 -6 0 0.00 -7 0 0.00 -8 0 0.00 -9 0 0.00 -10 1 50.00 -11 0 0.00 -12 0 0.00 -13 0 0.00 -14 0 0.00 -15 0 0.00 -16 0 0.00 -17 0 0.00 -18 0 0.00 -19 0 0.00 -20 0 0.00 -21 0 0.00 -22 1 50.00 -23 0 0.00 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ ->903|0|I_DM|1 -CCAACAGAGCCCAATTGACCGCAAATG ->1428|0|I_DM|1 -AAACAAGCACACTAACTACAGCGAC ->1721|0|I_DM|1 -TGGGGGCGTAGCATTACTAGTGC ->3191|0|I_DM|3 -TTCGGACTTTCTACTCTATGTAGAC ->3236|0|I_DM|1 -AATGCACACCTCCCTCGTCACTCTTG ->3238|0|I_DM|1 -TGCACACCTCCCTCGTCACTCTTGA ->4624|0|I_DM|1 -TATGAATACGATCGCTAATAACG ->4826|0|I_DM|1 -AAACATAATAAACTGCAGTCAATG ->4913|0|I_DM|1 -TTGGACCAGACTCGACCAAATAAAAAT ->5105|0|I_DM|1 -CCCTCTAGACCTTCTTAGCAAACC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ ->3216|0|I_DM|1 -TATCTCATAACGAAGTCAAAAATG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,40 +1,12 @@ ->35|16|MAX_I|1 -TCTTGATTTTTCCGCAAGGAGCGCT ->68|16|MAX_I|2 -CACGGACGGAATAAGATTTAAAGC ->85|16|MAX_I|1 -AAAAACGAAAATGGCGACCACGGAC ->92|16|MAX_I|1 -GTTGGAAAAACGAAAATGGCGAC ->94|16|MAX_I|1 -CCGTTGGAAAAACGAAAATGGCG ->105|16|MAX_I|1 -AAGAATAAACGCCGTTGGAAAAAC ->115|16|MAX_I|1 -GATGGACGGAAAGAATAAACGCCG ->116|16|MAX_I|1 -CGGATGGACGGAAAGAATAAACGCC ->126|16|MAX_I|7 +>106|16|MAX_I|2 +AAAGAATAAACGCCGTTGGAAAAA +>106|16|MAX_I|2 +GAAAGAATAAACGCCGTTGGAAAAA +>107|16|MAX_I|2 +GAAAGAATAAACGCCGTTGGAAAA +>126|16|MAX_I|2 TCACTTGATACGGATGGACGGAAAG ->127|16|MAX_I|1 -CACTTGATACGGATGGACGGAAA ->127|16|MAX_I|10 -TCACTTGATACGGATGGACGGAAA >128|16|MAX_I|1 TCACTTGATACGGATGGACGGAA ->130|16|MAX_I|1 -TTTCACTTGATACGGATGGACGG ->131|16|MAX_I|1 -TTTTCACTTGATACGGATGGACG ->171|16|MAX_I|1 -TAATCACGGCGGCTGGGCGCATG ->236|16|MAX_I|1 -CACCGTGAGACGAATTAGGGGGC >236|16|MAX_I|1 TCACCGTGAGACGAATTAGGGGGC ->251|16|MAX_I|1 -GCTTGGATACCAGCGGATCACCGTGA ->263|16|MAX_I|1 -TATGTATATGCGCTTGGATACCAGC ->310|16|MAX_I|1 -TAGCAGCGGACGATAATAGTGAATT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,14 +0,0 @@ ->106|16|MAX_I|2 -AAAGAATAAACGCCGTTGGAAAAA ->106|16|MAX_I|14 -GAAAGAATAAACGCCGTTGGAAAAA ->107|16|MAX_I|3 -AAAGAATAAACGCCGTTGGAAAA ->107|16|MAX_I|10 -GAAAGAATAAACGCCGTTGGAAAA ->108|16|MAX_I|1 -GAAAGAATAAACGCCGTTGGAAA ->301|16|MAX_I|1 -GACGATAATAGTGAATTTTGGACAGT ->303|16|MAX_I|3 -GACGATAATAGTGAATTTTGGACA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number -1 2 3.70 -2 2 3.70 -3 3 5.56 -4 1 1.85 -5 1 1.85 -6 2 3.70 +1 0 0.00 +2 0 0.00 +3 0 0.00 +4 0 0.00 +5 0 0.00 +6 0 0.00 7 0 0.00 -8 2 3.70 -9 3 5.56 -10 11 20.37 -11 5 9.26 +8 0 0.00 +9 0 0.00 +10 0 0.00 +11 0 0.00 12 0 0.00 -13 1 1.85 +13 0 0.00 14 0 0.00 15 0 0.00 16 0 0.00 -17 1 1.85 -18 3 5.56 -19 1 1.85 -20 3 5.56 -21 4 7.41 -22 6 11.11 -23 3 5.56 +17 0 0.00 +18 0 0.00 +19 0 0.00 +20 0 0.00 +21 1 100.00 +22 0 0.00 +23 0 0.00 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,20 +1,2 @@ ->54|0|MAX_I|1 -TCAAGATAAGTACGGCTTTAAATCT ->55|0|MAX_I|1 -CAAGATAAGTACGGCTTTAAATC ->60|0|MAX_I|2 -TAAGTACGGCTTTAAATCTTATTCC ->81|0|MAX_I|1 -TTCCGTCCGTGGTCGCCATTTTCG ->88|0|MAX_I|1 -CGTGGTCGCCATTTTCGTTTTTCC ->93|0|MAX_I|1 -TCGCCATTTTCGTTTTTCCAACGGC ->109|0|MAX_I|1 -TTCCAACGGCGTTTATTCTTTCC ->128|0|MAX_I|1 -TTCCGTCCATCCGTATCAAGTGAA ->231|0|MAX_I|1 -TACCGGCCCCCTAATTCGTCTCAC >239|0|MAX_I|1 CCCTAATTCGTCTCACGGTGATCCG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,8 +0,0 @@ ->120|0|MAX_I|1 -TTTATTCTTTCCGTCCATCCGTA ->121|0|MAX_I|1 -TTATTCTTTCCGTCCATCCGTATC ->317|0|MAX_I|2 -TATTATCGTCCGCTGCTAAACTAC ->317|0|MAX_I|2 -TATTATCGTCCGCTGCTAAACTACTG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,36 +1,10 @@ ->5|16|MAX_LTR|9 +>5|16|MAX_LTR|1 TCAACTGTTTGCGCCCTTCTGGCGTG >14|16|MAX_LTR|1 TGCCGCTCAACTGTTTGCGCCCT ->14|16|MAX_LTR|3 -CACTGCCGCTCAACTGTTTGCGCCCT ->15|16|MAX_LTR|6 -CACTGCCGCTCAACTGTTTGCGCCC ->16|16|MAX_LTR|6 -CACTGCCGCTCAACTGTTTGCGCC ->17|16|MAX_LTR|1 -TACACTGCCGCTCAACTGTTTGCGC ->53|16|MAX_LTR|1 -CCGTGGAGGAGCTTTGAGTACAAG >85|16|MAX_LTR|1 AGAGAAGGAGAGCGCGAGCAGCGGTG ->89|16|MAX_LTR|1 -GGAGAGAAGGAGAGCGCGAGCAGC ->95|16|MAX_LTR|1 -CGAGAGGAGAGAAGGAGAGCGCG >134|16|MAX_LTR|1 -ACCGCGGAGTGGTGAATACCTTG ->134|16|MAX_LTR|2 GGACCGCGGAGTGGTGAATACCTTG ->152|16|MAX_LTR|2 -CATTGGAAATACCGCGGGACCGC ->152|16|MAX_LTR|1 -AACATTGGAAATACCGCGGGACCGC ->153|16|MAX_LTR|1 -ACATTGGAAATACCGCGGGACCG >153|16|MAX_LTR|1 AACATTGGAAATACCGCGGGACCG ->154|16|MAX_LTR|3 -TAACATTGGAAATACCGCGGGACC ->155|16|MAX_LTR|1 -TAACATTGGAAATACCGCGGGAC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -7,18 +7,18 @@ 6 0 0.00 7 0 0.00 8 0 0.00 -9 2 12.50 +9 0 0.00 10 0 0.00 11 0 0.00 12 0 0.00 13 0 0.00 14 0 0.00 -15 1 6.25 +15 0 0.00 16 0 0.00 17 0 0.00 -18 8 50.00 +18 0 0.00 19 0 0.00 -20 3 18.75 +20 1 100.00 21 0 0.00 -22 2 12.50 +22 0 0.00 23 0 0.00 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,22 +1,6 @@ ->13|0|MAX_LTR|1 -AAGGGCGCAAACAGTTGAGCGGCA ->22|0|MAX_LTR|2 -AACAGTTGAGCGGCAGTGTAAGC >49|0|MAX_LTR|1 AATGCTTGTACTCAAAGCTCCTCC ->53|0|MAX_LTR|1 -CTTGTACTCAAAGCTCCTCCACG ->53|0|MAX_LTR|1 -CTTGTACTCAAAGCTCCTCCACGG ->53|0|MAX_LTR|2 -CTTGTACTCAAAGCTCCTCCACGGC ->53|0|MAX_LTR|1 -CTTGTACTCAAAGCTCCTCCACGGCT ->81|0|MAX_LTR|5 +>81|0|MAX_LTR|2 CAAGCACCGCTGCTCGCGCTCTCCT ->89|0|MAX_LTR|1 -GCTGCTCGCGCTCTCCTTCTCTCCT ->135|0|MAX_LTR|2 -AAGGTATTCACCACTCCGCGGTCCC ->139|0|MAX_LTR|6 +>139|0|MAX_LTR|1 TATTCACCACTCCGCGGTCCCGC |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,110 +1,20 @@ ->120|16|PROTOP|1 -GCTGTCTGCTGTAGCGCTCTCCG ->223|16|PROTOP|1 -TAAGAACTTCTGAGGTGAAGGGC >223|16|PROTOP|1 TCTAAGAACTTCTGAGGTGAAGGGC ->225|16|PROTOP|3 -TCTAAGAACTTCTGAGGTGAAGG ->226|16|PROTOP|2 -GTCTAAGAACTTCTGAGGTGAAG ->466|16|PROTOP|1 -GGCACGAAGTGCGGACACAAGCCCT ->504|16|PROTOP|1 -TGTTATTCTAGTGTCTTTGGTTT ->2349|16|PROTOP|1 -TAGTGAGGTACATTTTCTATTGTT ->2445|16|PROTOP|1 -TATTCCTATAGACTTGAAAAGATG ->2489|16|PROTOP|1 -TCAACTAGTCCGTCAGGGGTTGCT ->2492|16|PROTOP|1 -AAAGTCAACTAGTCCGTCAGGGGTT >2493|16|PROTOP|2 -AAAGTCAACTAGTCCGTCAGGGGT ->2493|16|PROTOP|2 -CAAAGTCAACTAGTCCGTCAGGGGT ->2493|16|PROTOP|14 TCAAAGTCAACTAGTCCGTCAGGGGT ->2494|16|PROTOP|1 -TCAAAGTCAACTAGTCCGTCAGGGG ->2508|16|PROTOP|1 -AACCTCTCGAATGAAATCAAAGTCAAC ->2535|16|PROTOP|2 -TTACTGATCCATGATGTAATTCGTA ->2553|16|PROTOP|1 -TAATTTAGTCATTCTCGTTACTGA ->2580|16|PROTOP|2 -TCTAGTTGGATTAACGTGACTCCT ->2592|16|PROTOP|6 -CATTAGCTCAAATCTAGTTGGATT ->2593|16|PROTOP|1 -CATTAGCTCAAATCTAGTTGGAT ->2686|16|PROTOP|1 -TCGGAACTATTTCGATGTAATTGCT ->2692|16|PROTOP|1 -TGCAACTTCGGAACTATTTCGATGTA >2707|16|PROTOP|1 -AACCGTAGAAGCTGCAACTTCGG ->2707|16|PROTOP|2 TGCAACCGTAGAAGCTGCAACTTCGG ->2711|16|PROTOP|2 +>2711|16|PROTOP|1 TAATGCAACCGTAGAAGCTGCAACT ->2718|16|PROTOP|2 -TTTGGACTAATGCAACCGTAGAAGC ->2720|16|PROTOP|2 -TTTTGGACTAATGCAACCGTAGAA ->2720|16|PROTOP|3 -TTTTTGGACTAATGCAACCGTAGAA ->2725|16|PROTOP|1 -TAACTTTTTGGACTAATGCAACCG ->2731|16|PROTOP|1 -TAATCATTAACTTTTTGGACTAATG ->2736|16|PROTOP|1 -CAAAGTAATCATTAACTTTTTGGAC >2756|16|PROTOP|1 TACTCTGCTATTCAGGCAATCAAAG ->2853|16|PROTOP|1 -TATTTAACGCTTTTTAAGTATTCCTG +>2760|16|PROTOP|1 +TAATACTCTGCTATTCAGGCAATC >3060|16|PROTOP|1 TTAAATTCGTTAACTGTAAGACT ->3060|16|PROTOP|2 -TATTAAATTCGTTAACTGTAAGACT ->3091|16|PROTOP|1 -TGTGTAGAGATATGAGCATGGCAA ->3161|16|PROTOP|1 -TCGAATCAAACTCTATTGACAAAATA ->3190|16|PROTOP|1 -TATTTTTTAATGCAAGGCTGATATA >3222|16|PROTOP|1 TATACGGAGTATTCTTGCTGCTG ->3272|16|PROTOP|3 +>3272|16|PROTOP|1 TTGCATATTTTGGTCAAAGTACCTC ->3371|16|PROTOP|1 -TTATCGATCTGCATTTATCGCATCTC ->3373|16|PROTOP|2 -TTATCGATCTGCATTTATCGCATC ->3382|16|PROTOP|1 -TCTTTTAAAATTATCGATCTGCATT ->3408|16|PROTOP|2 -TGATGGAGCTGTTAAATTCTCGGT ->3408|16|PROTOP|1 -TCTGATGGAGCTGTTAAATTCTCGGT ->3449|16|PROTOP|1 -TCAGAGTCTATTGAGTAGTTTTTC ->3479|16|PROTOP|1 -TAAATCAGATGGTGCCTTTAGTTTC ->3490|16|PROTOP|1 -TATTAAAAAAATAAATCAGATGGTG ->4354|16|PROTOP|1 -CCCGCTGAGAGCATAAGAAATCTAA ->4371|16|PROTOP|1 -CTCTTTCCGCTCGCTCCCGCTGA ->4372|16|PROTOP|2 -TCTCTTTCCGCTCGCTCCCGCTG ->4389|16|PROTOP|1 -TAGTGACGGCCAAAATTGCTCTCTT ->4393|16|PROTOP|1 -TTTTTAGTGACGGCCAAAATTGCTC >4426|16|PROTOP|1 TAACATACATTGGTTTGGCACTATG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,4 @@ ->2334|16|PROTOP|1 -TTCTATTGTTACCTCCTTAATCGTA ->2428|16|PROTOP|7 +>2428|16|PROTOP|1 AAAAGATGCGGAATGTCATAAAACA ->2429|16|PROTOP|3 +>2429|16|PROTOP|1 AAAAGATGCGGAATGTCATAAAAC ->2684|16|PROTOP|1 -AACTATTTCGATGTAATTGCTTG ->2759|16|PROTOP|1 -TAATACTCTGCTATTCAGGCAATCA ->2760|16|PROTOP|1 -TAATACTCTGCTATTCAGGCAATC ->3384|16|PROTOP|3 -TTCTTTTAAAATTATCGATCTGCA ->4372|16|PROTOP|1 -TGCTCTCTTTCCGCTCGCTCCCGCTG ->4375|16|PROTOP|3 -TGCTCTCTTTCCGCTCGCTCCCG |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/histogram.png has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/overlap_size.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/overlap_size.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/overlap_size.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,24 +1,24 @@ size number percentage of the total overlap number -1 3 6.12 -2 4 8.16 +1 0 0.00 +2 0 0.00 3 0 0.00 4 0 0.00 -5 1 2.04 -6 4 8.16 -7 3 6.12 +5 0 0.00 +6 0 0.00 +7 0 0.00 8 0 0.00 -9 3 6.12 -10 11 22.45 +9 0 0.00 +10 2 66.67 11 0 0.00 12 0 0.00 -13 2 4.08 -14 1 2.04 -15 2 4.08 -16 1 2.04 -17 1 2.04 -18 3 6.12 -19 3 6.12 -20 2 4.08 -21 3 6.12 +13 0 0.00 +14 0 0.00 +15 0 0.00 +16 0 0.00 +17 0 0.00 +18 0 0.00 +19 0 0.00 +20 0 0.00 +21 0 0.00 22 0 0.00 -23 2 4.08 +23 1 33.33 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sens.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sens.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sens.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,62 +1,10 @@ ->15|0|PROTOP|1 -TAACAAGATACGTAACGCCATACC ->60|0|PROTOP|1 -TCGCCTTGGCTCTAGAGGTGGCTC ->65|0|PROTOP|2 -TTGGCTCTAGAGGTGGCTCCAGGC ->104|0|PROTOP|1 -TTAGAGAGCGAGAGAGCGGAGAGC ->104|0|PROTOP|2 -TTAGAGAGCGAGAGAGCGGAGAGCGC ->105|0|PROTOP|1 -TAGAGAGCGAGAGAGCGGAGAGCGC ->161|0|PROTOP|1 -TGATAGCAGACAATTTTATGTGTG ->210|0|PROTOP|7 +>210|0|PROTOP|2 TTTGACAAAATATGCCCTTCACCTC ->210|0|PROTOP|3 -TTTGACAAAATATGCCCTTCACCTCA >225|0|PROTOP|1 CCTTCACCTCAGAAGTTCTTAGACTT ->446|0|PROTOP|1 -TAATAAGGCAATGATTGTTGAGG ->450|0|PROTOP|1 -AAGGCAATGATTGTTGAGGGCTT ->2375|0|PROTOP|1 -TGAAGTCACCCATGAGAAACCTTAC ->2541|0|PROTOP|1 -TTACATCATGGATCAGTAACGAGAA ->2616|0|PROTOP|2 -CGCGTATGTTTGGAAACTCAAACACT ->2648|0|PROTOP|1 -CACTGTTGCAGCGGCAATTAAGACT ->2649|0|PROTOP|1 -ACTGTTGCAGCGGCAATTAAGACT ->2654|0|PROTOP|2 +>2654|0|PROTOP|1 TGCAGCGGCAATTAAGACTTGTAAC ->2690|0|PROTOP|1 -ATTACATCGAAATAGTTCCGAAGTT ->2691|0|PROTOP|1 -TTACATCGAAATAGTTCCGAAGTTG ->2743|0|PROTOP|1 -AAGTTAATGATTACTTTGATTGCC ->2743|0|PROTOP|6 -AAGTTAATGATTACTTTGATTGCCT ->3328|0|PROTOP|1 -TAACTTCCAGTAGATATTTTGCT ->3453|0|PROTOP|1 -AACTACTCAATAGACTCTGACTTCGG ->4136|0|PROTOP|3 -TCTAAAAATATAATAGTCAGGGCGC ->4308|0|PROTOP|1 -GTTCTCGTCTCTTGTTTTCACTCACA ->4309|0|PROTOP|1 -TTCTCGTCTCTTGTTTTCACTCACA >4361|0|PROTOP|1 TCTTATGCTCTCAGCGGGAGCGAG ->4389|0|PROTOP|1 -AAGAGAGCAATTTTGGCCGTCACTA ->4399|0|PROTOP|1 -TTTTGGCCGTCACTAAAAAATTGG ->4399|0|PROTOP|1 -TTTTGGCCGTCACTAAAAAATTGGC +>4388|0|PROTOP|1 +AAAGAGAGCAATTTTGGCCGTCACT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sensPPP.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sensPPP.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sensPPP.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,12 +1,2 @@ ->2349|0|PROTOP|1 -AACAATAGAAAATGTACCTCACTACT >2443|0|PROTOP|1 CGCATCTTTTCAAGTCTATAGGA ->2697|0|PROTOP|1 -CGAAATAGTTCCGAAGTTGCAGC ->2774|0|PROTOP|1 -CAGAGTATTAACGACAAAAACCC ->3398|0|PROTOP|1 -TTTAAAAGAAACCGAGAATTTAACA ->4388|0|PROTOP|5 -AAAGAGAGCAATTTTGGCCGTCACT |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/ppp.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/ppp.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/ppp.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,17 +1,17 @@ -BATUMI_I 92 22 4 6.26931797136554 2.87112570812537 0.00204506417965455 -BATUMI_LTR 13 1 0.565217391304348 0.824941998304795 0.52704627669473 0.299080726341764 -BS2 4418 610 192.086956521739 94.6508058457982 4.41531416181612 5.04316992888665e-06 +BATUMI_I 0 0 0 0 NA NA +BATUMI_LTR 0 0 0 0 NA NA +BS2 185 51 8.04347826086956 9.6028902391509 4.47329092276793 3.85124343149634e-06 COPIA_DM_I 0 0 0 0 NA NA COPIA_DM_LTR 0 0 0 0 NA NA -DMCR1A 109 30 4.73913043478261 6.40799359023961 3.94208720865353 4.03877968415678e-05 -DMRT1B 299 13 13 10.8266980794861 0 0.5 -FW 9995 1042 434.565217391304 141.421610207381 4.29520482561295 8.7266059448643e-06 -G6_DM 1084 129 47.1304347826087 28.7512636362392 2.84751189558847 0.0022031223713177 +DMCR1A 8 1 0.347826086956522 0.560178205509788 1.1642257885595 0.122166260952844 +DMRT1B 13 1 0.565217391304348 0.711769806249778 0.610847221781526 0.270650364023612 +FW 369 54 16.0434782608696 9.77342564156839 3.88364562551062 5.14509267872665e-05 +G6_DM 58 9 2.52173913043478 3.95484914478846 1.63805511471961 0.0507050985511251 Gypsy2-I_DM 0 0 0 0 NA NA -Gypsy2-LTR_DM 170 20 7.39130434782609 4.341299449171 2.90435981203315 0.00184002483108026 -I_DM 2 1 0.0869565217391304 0.281771334713385 3.24037034920393 0.000596872722436026 -MAX_I 54 11 2.34782608695652 2.44253424438055 3.5422938011818 0.00019833170283523 -MAX_LTR 16 0 0.695652173913043 1.75535906419012 -0.396301923694456 0.654058845865745 -PROTOP 49 11 2.1304347826087 2.30885531258291 3.84154224348902 6.11318444337927e-05 +Gypsy2-LTR_DM 3 0 0.130434782608696 0.336781160539775 -0.387298334620742 0.650732320848331 +I_DM 0 0 0 0 NA NA +MAX_I 1 0 0.0434782608695652 0.203931119992323 -0.21320071635561 0.584414795229119 +MAX_LTR 1 0 0.0434782608695652 0.203931119992323 -0.21320071635561 0.584414795229119 +PROTOP 3 2 0.130434782608696 0.447636093086391 4.17652920813624 1.47995375637811e-05 ZAM_I 0 0 0 0 NA NA ZAM_LTR 0 0 0 0 NA NA |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err --- a/test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err Thu Jan 24 13:09:46 2019 -0500 |
| [ |
| @@ -1,6 +1,6 @@ -[bwa_aln_core] calculate SA coordinate... 0.95 sec -[bwa_aln_core] write to the disk... 0.01 sec -[bwa_aln_core] 28283 sequences have been processed. +[bwa_aln_core] calculate SA coordinate... 0.14 sec +[bwa_aln_core] write to the disk... 0.00 sec +[bwa_aln_core] 2853 sequences have been processed. [main] Version: 0.7.12-r1039 -[main] CMD: bwa aln -t 8 -n 3 /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq -[main] Real time: 0.204 sec; CPU: 1.004 sec +[main] CMD: bwa aln -t 8 -n 3 /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq +[main] Real time: 0.033 sec; CPU: 0.148 sec |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err --- a/test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err Thu Jan 24 13:09:46 2019 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -[bwa_aln_core] convert to sequence coordinate... 0.07 sec -[bwa_aln_core] refine gapped alignments... 0.01 sec -[bwa_aln_core] print alignments... 0.05 sec -[bwa_aln_core] 28283 sequences have been processed. +[bwa_aln_core] convert to sequence coordinate... 0.01 sec +[bwa_aln_core] refine gapped alignments... 0.00 sec +[bwa_aln_core] print alignments... 0.01 sec +[bwa_aln_core] 2853 sequences have been processed. [main] Version: 0.7.12-r1039 -[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa /dev/stdin /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq -[main] Real time: 0.388 sec; CPU: 0.172 sec +[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa /dev/stdin /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq +[main] Real time: 0.074 sec; CPU: 0.024 sec |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_I.png |
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| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_I.png has changed |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_LTR.png |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BS2.png |
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PROTOP\t3244\t3271\t0\n-PROTOP\t3271\t3296\t76.8443\n-PROTOP\t3296\t3370\t0\n-PROTOP\t3370\t3372\t25.6148\n-PROTOP\t3372\t3381\t76.8443\n-PROTOP\t3381\t3383\t102.459\n-PROTOP\t3383\t3396\t179.303\n-PROTOP\t3396\t3406\t102.459\n-PROTOP\t3406\t3431\t76.8443\n-PROTOP\t3431\t3433\t25.6148\n-PROTOP\t3433\t3448\t0\n-PROTOP\t3448\t3464\t25.6148\n-PROTOP\t3464\t3472\t51.2295\n-PROTOP\t3472\t3478\t25.6148\n-PROTOP\t3478\t3485\t76.8443\n-PROTOP\t3485\t3487\t51.2295\n-PROTOP\t3487\t3489\t76.8443\n-PROTOP\t3489\t3499\t102.459\n-PROTOP\t3499\t3503\t76.8443\n-PROTOP\t3503\t3508\t51.2295\n-PROTOP\t3508\t3513\t25.6148\n-PROTOP\t3513\t4353\t0\n-PROTOP\t4353\t4370\t25.6148\n-PROTOP\t4370\t4371\t51.2295\n-PROTOP\t4371\t4374\t128.074\n-PROTOP\t4374\t4378\t204.918\n-PROTOP\t4378\t4388\t179.303\n-PROTOP\t4388\t4392\t204.918\n-PROTOP\t4392\t4393\t230.533\n-PROTOP\t4393\t4394\t204.918\n-PROTOP\t4394\t4397\t153.689\n-PROTOP\t4397\t4413\t51.2295\n-PROTOP\t4413\t4417\t25.6148\n-PROTOP\t4417\t4425\t0\n-PROTOP\t4425\t4450\t25.6148\n+PROTOP\t3271\t3296\t252.016\n+PROTOP\t3296\t4425\t0\n+PROTOP\t4425\t4450\t252.016\n PROTOP\t4450\t4480\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,2914 +1,716 @@\n-BATUMI_I\t0\t1\t25.6148\n-BATUMI_I\t1\t6\t51.2295\n-BATUMI_I\t6\t22\t76.8443\n-BATUMI_I\t22\t26\t51.2295\n-BATUMI_I\t26\t32\t25.6148\n-BATUMI_I\t32\t119\t0\n-BATUMI_I\t119\t123\t51.2295\n-BATUMI_I\t123\t144\t76.8443\n-BATUMI_I\t144\t150\t0\n-BATUMI_I\t150\t159\t25.6148\n-BATUMI_I\t159\t160\t51.2295\n-BATUMI_I\t160\t176\t76.8443\n-BATUMI_I\t176\t179\t51.2295\n-BATUMI_I\t179\t185\t25.6148\n-BATUMI_I\t185\t385\t0\n-BATUMI_I\t385\t386\t25.6148\n-BATUMI_I\t386\t407\t51.2295\n-BATUMI_I\t407\t411\t25.6148\n-BATUMI_I\t411\t417\t0\n-BATUMI_I\t417\t418\t25.6148\n-BATUMI_I\t418\t419\t128.074\n-BATUMI_I\t419\t437\t179.303\n-BATUMI_I\t437\t441\t153.689\n-BATUMI_I\t441\t442\t102.459\n-BATUMI_I\t442\t443\t25.6148\n-BATUMI_I\t443\t7006\t0\n-BATUMI_I\t7006\t7007\t25.6148\n-BATUMI_I\t7007\t7008\t51.2295\n-BATUMI_I\t7008\t7009\t179.303\n-BATUMI_I\t7009\t7010\t486.68\n-BATUMI_I\t7010\t7015\t512.295\n-BATUMI_I\t7015\t7016\t537.91\n-BATUMI_I\t7016\t7017\t1101.43\n-BATUMI_I\t7017\t7018\t2459.02\n-BATUMI_I\t7018\t7030\t4123.98\n-BATUMI_I\t7030\t7031\t4021.52\n-BATUMI_I\t7031\t7033\t3765.37\n-BATUMI_I\t7033\t7034\t3739.75\n-BATUMI_I\t7034\t7035\t3611.68\n-BATUMI_I\t7035\t7036\t3560.45\n-BATUMI_I\t7036\t7037\t3073.77\n-BATUMI_I\t7037\t7038\t3022.54\n-BATUMI_I\t7038\t7039\t2715.16\n-BATUMI_I\t7039\t7040\t1716.19\n-BATUMI_I\t7040\t7041\t1511.27\n-BATUMI_I\t7041\t7042\t281.762\n-BATUMI_I\t7042\t7043\t25.6148\n-BATUMI_I\t7043\t7963\t0\n-BATUMI_LTR\t0\t32\t0\n-BATUMI_LTR\t32\t57\t25.6148\n-BATUMI_LTR\t57\t118\t0\n-BATUMI_LTR\t118\t142\t25.6148\n-BATUMI_LTR\t142\t192\t0\n-BATUMI_LTR\t192\t195\t25.6148\n-BATUMI_LTR\t195\t213\t51.2295\n-BATUMI_LTR\t213\t218\t25.6148\n-BATUMI_LTR\t218\t272\t0\n-BS2\t0\t21\t0\n-BS2\t21\t42\t51.2295\n-BS2\t42\t45\t76.8443\n-BS2\t45\t68\t25.6148\n-BS2\t68\t69\t384.221\n-BS2\t69\t72\t435.451\n-BS2\t72\t77\t486.68\n-BS2\t77\t79\t512.295\n-BS2\t79\t80\t537.91\n-BS2\t80\t81\t563.525\n-BS2\t81\t82\t717.213\n-BS2\t82\t91\t742.828\n-BS2\t91\t93\t717.213\n-BS2\t93\t94\t384.221\n-BS2\t94\t97\t307.377\n-BS2\t97\t98\t281.762\n-BS2\t98\t102\t256.148\n-BS2\t102\t106\t230.533\n-BS2\t106\t107\t102.459\n-BS2\t107\t108\t51.2295\n-BS2\t108\t186\t0\n-BS2\t186\t187\t25.6148\n-BS2\t187\t188\t76.8443\n-BS2\t188\t192\t128.074\n-BS2\t192\t193\t204.918\n-BS2\t193\t194\t230.533\n-BS2\t194\t195\t358.607\n-BS2\t195\t196\t384.221\n-BS2\t196\t208\t409.836\n-BS2\t208\t211\t384.221\n-BS2\t211\t213\t332.992\n-BS2\t213\t215\t307.377\n-BS2\t215\t219\t281.762\n-BS2\t219\t220\t230.533\n-BS2\t220\t221\t204.918\n-BS2\t221\t222\t179.303\n-BS2\t222\t223\t230.533\n-BS2\t223\t224\t256.148\n-BS2\t224\t225\t537.91\n-BS2\t225\t235\t563.525\n-BS2\t235\t237\t537.91\n-BS2\t237\t238\t486.68\n-BS2\t238\t241\t461.066\n-BS2\t241\t246\t435.451\n-BS2\t246\t248\t332.992\n-BS2\t248\t276\t0\n-BS2\t276\t277\t76.8443\n-BS2\t277\t284\t102.459\n-BS2\t284\t285\t128.074\n-BS2\t285\t297\t179.303\n-BS2\t297\t298\t128.074\n-BS2\t298\t303\t76.8443\n-BS2\t303\t304\t102.459\n-BS2\t304\t308\t128.074\n-BS2\t308\t329\t51.2295\n-BS2\t329\t335\t25.6148\n-BS2\t335\t338\t51.2295\n-BS2\t338\t339\t281.762\n-BS2\t339\t341\t409.836\n-BS2\t341\t344\t435.451\n-BS2\t344\t350\t537.91\n-BS2\t350\t353\t589.139\n-BS2\t353\t362\t563.525\n-BS2\t362\t363\t435.451\n-BS2\t363\t364\t256.148\n-BS2\t364\t365\t153.689\n-BS2\t365\t367\t179.303\n-BS2\t367\t368\t153.689\n-BS2\t368\t372\t128.074\n-BS2\t372\t374\t102.459\n-BS2\t374\t386\t76.8443\n-BS2\t386\t390\t25.6148\n-BS2\t390\t430\t0\n-BS2\t430\t440\t25.6148\n-BS2\t440\t454\t76.8443\n-BS2\t454\t455\t51.2295\n-BS2\t455\t456\t76.8443\n-BS2\t456\t457\t230.533\n-BS2\t457\t463\t256.148\n-BS2\t463\t465\t230.533\n-BS2\t465\t471\t204.918\n-BS2\t471\t474\t230.533\n-BS2\t474\t475\t256.148\n-BS2\t475\t480\t281.762\n-BS2\t480\t484\t102.459\n-BS2\t484\t490\t153.689\n-BS2\t490\t492\t179.303\n-BS2\t492\t493\t204.918\n-BS2\t493\t495\t281.762\n-BS2\t495\t496\t307.377\n-BS2\t496\t499\t281.762\n-BS2\t499\t501\t332.992\n-BS2\t501\t503\t307.377\n-BS2\t503\t504\t358.607\n-BS2\t504\t506\t307.377\n-BS2\t506\t509\t332.992\n-BS2\t509\t511\t358.607\n-BS2\t511\t512\t537.91\n-BS2\t512\t513\t512.295\n-BS2\t513\t516\t486.68\n-BS2\t516\t518\t461.066\n-BS2\t518\t519\t435.451\n-BS2\t519\t522\t409.836\n-BS2\t522\t528\t332.992\n-BS2\t528\t530\t281.762\n-BS2\t530\t533\t256.148\n-BS2\t533\t534\t230.533\n-BS2\t534\t535\t76.8443\n-BS2\t535\t537\t25.6148\n-BS2\t537\t562\t0\n-BS2\t562\t566\t102.459\n-BS2\t566\t576\t179.303\n-BS2\t576\t582\t204.918\n-BS2\t582\t586\t230.533\n-BS2\t586\t587\t204.918\n-BS2\t587\t588\t281.762\n-BS2\t588\t589\t230.533\n-BS2\t589\t591\t256.148\n-BS2\t591\t592\t230.533\n-BS2\t592\t593\t281.762\n-BS2\t593\t601\t307.377\n-BS2\t601\t607\t281.762\n-BS2\t607\t608\t256.148\n-BS2\t6'..b'\n-MAX_I\t140\t142\t128.074\n-MAX_I\t142\t144\t51.2295\n-MAX_I\t144\t151\t25.6148\n-MAX_I\t151\t230\t0\n-MAX_I\t230\t237\t25.6148\n-MAX_I\t237\t238\t51.2295\n-MAX_I\t238\t254\t76.8443\n-MAX_I\t254\t257\t51.2295\n-MAX_I\t257\t263\t25.6148\n-MAX_I\t263\t316\t0\n-MAX_I\t316\t338\t128.074\n-MAX_I\t338\t340\t102.459\n-MAX_I\t340\t342\t51.2295\n-MAX_I\t342\t4085\t0\n-MAX_I\t4085\t4103\t51.2295\n+Gypsy2-LTR_DM\t58\t85\t252.016\n+Gypsy2-LTR_DM\t85\t157\t0\n+Gypsy2-LTR_DM\t157\t182\t252.016\n+Gypsy2-LTR_DM\t182\t258\t0\n+Gypsy2-LTR_DM\t258\t265\t252.016\n+Gypsy2-LTR_DM\t265\t266\t756.048\n+Gypsy2-LTR_DM\t266\t279\t1008.06\n+Gypsy2-LTR_DM\t279\t289\t756.048\n+Gypsy2-LTR_DM\t289\t290\t504.032\n+Gypsy2-LTR_DM\t290\t338\t0\n+I_DM\t0\t1619\t0\n+I_DM\t1619\t1641\t252.016\n+I_DM\t1641\t3237\t0\n+I_DM\t3237\t3262\t252.016\n+I_DM\t3262\t4912\t0\n+I_DM\t4912\t4939\t252.016\n+I_DM\t4939\t5374\t0\n+MAX_I\t0\t238\t0\n+MAX_I\t238\t263\t252.016\n+MAX_I\t263\t4085\t0\n+MAX_I\t4085\t4103\t252.016\n MAX_I\t4103\t7914\t0\n-MAX_LTR\t0\t12\t25.6148\n-MAX_LTR\t12\t15\t51.2295\n-MAX_LTR\t15\t18\t76.8443\n-MAX_LTR\t18\t21\t51.2295\n-MAX_LTR\t21\t22\t102.459\n-MAX_LTR\t22\t23\t128.074\n-MAX_LTR\t23\t35\t153.689\n-MAX_LTR\t35\t36\t128.074\n-MAX_LTR\t36\t44\t102.459\n-MAX_LTR\t44\t45\t25.6148\n+MAX_LTR\t0\t23\t0\n+MAX_LTR\t23\t45\t252.016\n MAX_LTR\t45\t48\t0\n-MAX_LTR\t48\t52\t51.2295\n-MAX_LTR\t52\t70\t230.533\n-MAX_LTR\t70\t72\t204.918\n-MAX_LTR\t72\t74\t153.689\n-MAX_LTR\t74\t75\t128.074\n-MAX_LTR\t75\t76\t102.459\n-MAX_LTR\t76\t77\t76.8443\n-MAX_LTR\t77\t78\t25.6148\n-MAX_LTR\t78\t80\t0\n-MAX_LTR\t80\t84\t153.689\n-MAX_LTR\t84\t88\t204.918\n-MAX_LTR\t88\t100\t230.533\n-MAX_LTR\t100\t105\t204.918\n-MAX_LTR\t105\t113\t25.6148\n-MAX_LTR\t113\t134\t0\n-MAX_LTR\t134\t138\t51.2295\n-MAX_LTR\t138\t159\t230.533\n-MAX_LTR\t159\t161\t153.689\n+MAX_LTR\t48\t72\t252.016\n+MAX_LTR\t72\t80\t0\n+MAX_LTR\t80\t84\t504.032\n+MAX_LTR\t84\t105\t756.048\n+MAX_LTR\t105\t138\t0\n+MAX_LTR\t138\t161\t252.016\n MAX_LTR\t161\t321\t0\n-PROTOP\t0\t14\t0\n-PROTOP\t14\t38\t25.6148\n-PROTOP\t38\t59\t0\n-PROTOP\t59\t64\t25.6148\n-PROTOP\t64\t83\t102.459\n-PROTOP\t83\t86\t76.8443\n-PROTOP\t86\t88\t51.2295\n-PROTOP\t88\t103\t0\n-PROTOP\t103\t104\t76.8443\n-PROTOP\t104\t106\t102.459\n-PROTOP\t106\t108\t128.074\n-PROTOP\t108\t125\t153.689\n-PROTOP\t125\t126\t128.074\n-PROTOP\t126\t127\t102.459\n-PROTOP\t127\t129\t76.8443\n-PROTOP\t129\t160\t0\n-PROTOP\t160\t179\t51.2295\n-PROTOP\t179\t184\t25.6148\n-PROTOP\t184\t209\t0\n-PROTOP\t209\t224\t256.148\n-PROTOP\t224\t234\t281.762\n-PROTOP\t234\t235\t102.459\n-PROTOP\t235\t250\t25.6148\n-PROTOP\t250\t445\t0\n-PROTOP\t445\t449\t25.6148\n-PROTOP\t449\t468\t128.074\n-PROTOP\t468\t469\t102.459\n-PROTOP\t469\t470\t51.2295\n-PROTOP\t470\t472\t25.6148\n-PROTOP\t472\t2348\t0\n-PROTOP\t2348\t2399\t25.6148\n-PROTOP\t2399\t2442\t0\n-PROTOP\t2442\t2465\t25.6148\n-PROTOP\t2465\t2499\t0\n-PROTOP\t2499\t2520\t25.6148\n-PROTOP\t2520\t2540\t0\n-PROTOP\t2540\t2565\t25.6148\n-PROTOP\t2565\t2615\t0\n-PROTOP\t2615\t2641\t51.2295\n-PROTOP\t2641\t2647\t0\n-PROTOP\t2647\t2648\t25.6148\n-PROTOP\t2648\t2653\t51.2295\n-PROTOP\t2653\t2672\t102.459\n-PROTOP\t2672\t2678\t51.2295\n-PROTOP\t2678\t2689\t0\n-PROTOP\t2689\t2690\t25.6148\n-PROTOP\t2690\t2696\t51.2295\n-PROTOP\t2696\t2714\t128.074\n-PROTOP\t2714\t2715\t102.459\n-PROTOP\t2715\t2718\t76.8443\n-PROTOP\t2718\t2719\t25.6148\n-PROTOP\t2719\t2742\t0\n-PROTOP\t2742\t2745\t179.303\n-PROTOP\t2745\t2746\t256.148\n-PROTOP\t2746\t2749\t332.992\n-PROTOP\t2749\t2752\t358.607\n-PROTOP\t2752\t2766\t384.221\n-PROTOP\t2766\t2767\t307.377\n-PROTOP\t2767\t2785\t25.6148\n-PROTOP\t2785\t2786\t0\n-PROTOP\t2786\t2797\t25.6148\n-PROTOP\t2797\t3258\t0\n-PROTOP\t3258\t3279\t51.2295\n-PROTOP\t3279\t3327\t0\n-PROTOP\t3327\t3350\t25.6148\n-PROTOP\t3350\t3397\t0\n-PROTOP\t3397\t3422\t25.6148\n-PROTOP\t3422\t3452\t0\n-PROTOP\t3452\t3462\t25.6148\n-PROTOP\t3462\t3478\t51.2295\n-PROTOP\t3478\t3484\t25.6148\n-PROTOP\t3484\t4135\t0\n-PROTOP\t4135\t4160\t76.8443\n-PROTOP\t4160\t4307\t0\n-PROTOP\t4307\t4308\t25.6148\n-PROTOP\t4308\t4333\t51.2295\n-PROTOP\t4333\t4360\t0\n-PROTOP\t4360\t4384\t25.6148\n+PROTOP\t0\t209\t0\n+PROTOP\t209\t224\t504.032\n+PROTOP\t224\t234\t756.048\n+PROTOP\t234\t250\t252.016\n+PROTOP\t250\t2442\t0\n+PROTOP\t2442\t2465\t252.016\n+PROTOP\t2465\t2653\t0\n+PROTOP\t2653\t2678\t252.016\n+PROTOP\t2678\t4360\t0\n+PROTOP\t4360\t4384\t252.016\n PROTOP\t4384\t4387\t0\n-PROTOP\t4387\t4388\t128.074\n-PROTOP\t4388\t4398\t153.689\n-PROTOP\t4398\t4412\t204.918\n-PROTOP\t4412\t4413\t76.8443\n-PROTOP\t4413\t4422\t51.2295\n-PROTOP\t4422\t4423\t25.6148\n-PROTOP\t4423\t4480\t0\n+PROTOP\t4387\t4412\t252.016\n+PROTOP\t4412\t4480\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 333 1071.17 14443.10 5285714.29 10907.30 179 154 94.413407821229 38.5474860335196 42.2077922077922 20.7792207792208 -BATUMI_LTR 102 9605.53 4424.01 1619047.62 3340.98 4 98 75 0 2.04081632653061 40.8163265306122 -BS2 7237 39265.83 313887.93 114873015.87 237045.53 1487 5750 44.7209145931406 40.2824478816409 15.7913043478261 31.5130434782609 +BATUMI_I 32 1012.75 13698.63 3555555.56 10389.61 11 21 90.9090909090909 63.6363636363636 61.9047619047619 14.2857142857143 +BATUMI_LTR 8 7412.24 3424.66 888888.89 2597.40 0 8 0 0 0 0 +BS2 757 40410.13 324058.22 84111111.11 245779.22 151 606 43.7086092715232 42.3841059602649 14.5214521452145 32.013201320132 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 393 2252.04 17045.45 6238095.24 12872.58 93 300 52.6881720430108 51.6129032258064 20.6666666666667 32.3333333333333 -DMRT1B 377 1863.16 16351.49 5984126.98 12348.51 199 178 40.2010050251256 37.1859296482412 4.49438202247191 18.5393258426966 -FW 15168 82805.75 657876.47 240761904.76 496822.80 2680 12488 40.1492537313433 57.3880597014925 14.9263292761051 26.0009609224856 -G6_DM 2055 25777.83 89130.81 32619047.62 67310.84 427 1628 54.8009367681499 49.1803278688525 2.08845208845209 29.8525798525799 +DMCR1A 52 2931.73 22260.27 5777777.78 16883.12 12 40 50 58.3333333333333 20 45 +DMRT1B 39 1896.32 16695.21 4333333.33 12662.34 20 19 30 35 0 15.7894736842105 +FW 1510 81104.93 646404.11 167777777.78 490259.74 279 1231 38.7096774193548 63.0824372759857 14.9471974004874 27.4573517465475 +G6_DM 204 25176.93 87328.77 22666666.67 66233.77 53 151 62.2641509433962 54.7169811320755 1.98675496688742 33.112582781457 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 195 14777.74 8457.67 3095238.10 6387.16 82 113 54.8780487804878 31.7073170731707 9.73451327433628 18.5840707964602 -I_DM 48 228.79 2081.89 761904.76 1572.22 18 30 50 33.3333333333333 23.3333333333333 43.3333333333333 -MAX_I 120 388.40 5204.72 1904761.90 3930.56 30 90 73.3333333333333 6.66666666666667 62.2222222222222 17.7777777777778 -MAX_LTR 102 8139.27 4424.01 1619047.62 3340.98 34 68 23.5294117647059 38.2352941176471 4.41176470588235 29.4117647058824 -PROTOP 210 1200.69 9108.26 3333333.33 6878.48 81 129 58.0246913580247 64.1975308641975 23.2558139534884 29.4573643410853 +Gypsy2-LTR_DM 22 16403.42 9417.81 2444444.44 7142.86 6 16 66.6666666666667 66.6666666666667 0 6.25 +I_DM 5 234.48 2140.41 555555.56 1623.38 3 2 66.6666666666667 66.6666666666667 0 0 +MAX_I 13 413.98 5565.07 1444444.44 4220.78 2 11 0 0 72.7272727272727 0 +MAX_LTR 16 12561.55 6849.32 1777777.78 5194.81 6 10 16.6666666666667 16.6666666666667 10 20 +PROTOP 20 1125.07 8561.64 2222222.22 6493.51 7 13 57.1428571428571 57.1428571428571 7.69230769230769 23.0769230769231 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_mismatches.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_mismatches.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_mismatches.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 274 881.38 11884.11 4349206.35 8974.78 169 105 96.4497041420118 39.6449704142012 41.9047619047619 23.8095238095238 -BATUMI_LTR 96 9040.50 4163.78 1523809.52 3144.45 3 93 66.6666666666667 0 2.1505376344086 39.7849462365591 -BS2 227 1231.64 9845.59 3603174.60 7435.31 57 170 59.6491228070175 35.0877192982456 7.05882352941176 37.6470588235294 +BATUMI_I 21 664.62 8989.73 2333333.33 6818.18 10 11 100 70 63.6363636363636 9.09090909090909 +BATUMI_LTR 8 7412.24 3424.66 888888.89 2597.40 0 8 0 0 0 0 +BS2 25 1334.55 10702.05 2777777.78 8116.88 5 20 60 40 15 30 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 78 446.97 3383.07 1238095.24 2554.86 7 71 85.7142857142857 42.8571428571429 23.943661971831 26.7605633802817 -DMRT1B 216 1067.49 9368.49 3428571.43 7075.01 132 84 48.4848484848485 48.4848484848485 8.33333333333333 32.1428571428571 -FW 91 496.79 3946.91 1444444.44 2980.67 31 60 70.9677419354839 80.6451612903226 8.33333333333333 31.6666666666667 +DMCR1A 7 394.66 2996.58 777777.78 2272.73 1 6 100 100 33.3333333333333 0 +DMRT1B 23 1118.34 9845.89 2555555.56 7467.53 11 12 27.2727272727273 45.4545454545455 0 25 +FW 8 429.70 3424.66 888888.89 2597.40 5 3 80 100 0 66.6666666666667 G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 4 303.13 173.49 63492.06 131.02 0 4 0 0 0 25 -I_DM 38 181.12 1648.16 603174.60 1244.68 12 26 50 33.3333333333333 19.2307692307692 50 -MAX_I 36 116.52 1561.42 571428.57 1179.17 15 21 60 6.66666666666667 23.8095238095238 23.8095238095238 -MAX_LTR 45 3590.85 1951.77 714285.71 1473.96 12 33 0 91.6666666666667 9.09090909090909 3.03030303030303 -PROTOP 127 726.13 5508.33 2015873.02 4159.84 55 72 65.4545454545455 63.6363636363636 27.7777777777778 23.6111111111111 +Gypsy2-LTR_DM 1 745.61 428.08 111111.11 324.68 0 1 0 0 0 0 +I_DM 3 140.69 1284.25 333333.33 974.03 1 2 0 100 0 0 +MAX_I 3 95.53 1284.25 333333.33 974.03 2 1 0 0 0 0 +MAX_LTR 5 3925.48 2140.41 555555.56 1623.38 1 4 0 100 25 0 +PROTOP 13 731.30 5565.07 1444444.44 4220.78 6 7 50 50 0 14.2857142857143 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_nomismatches.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_nomismatches.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_nomismatches.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 59 189.79 2558.99 936507.94 1932.53 10 49 60 20 42.8571428571429 14.2857142857143 -BATUMI_LTR 6 565.03 260.24 95238.10 196.53 1 5 100 0 0 60 -BS2 7010 38034.19 304042.33 111269841.27 229610.22 1430 5580 44.1258741258741 40.4895104895105 16.0573476702509 31.326164874552 +BATUMI_I 11 348.13 4708.90 1222222.22 3571.43 1 10 0 0 60 20 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 732 39075.58 313356.16 81333333.33 237662.34 146 586 43.1506849315069 42.4657534246575 14.5051194539249 32.0819112627986 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 315 1805.07 13662.39 5000000.00 10317.72 86 229 50 52.3255813953488 19.6506550218341 34.061135371179 -DMRT1B 161 795.67 6983.00 2555555.56 5273.50 67 94 23.8805970149254 14.9253731343284 1.06382978723404 6.38297872340426 -FW 15077 82308.96 653929.56 239317460.32 493842.12 2649 12428 39.7885994714987 57.115892789732 14.9581589958159 25.9736079819762 -G6_DM 2055 25777.83 89130.81 32619047.62 67310.84 427 1628 54.8009367681499 49.1803278688525 2.08845208845209 29.8525798525799 +DMCR1A 45 2537.08 19263.70 5000000.00 14610.39 11 34 45.4545454545455 54.5454545454545 17.6470588235294 52.9411764705882 +DMRT1B 16 777.98 6849.32 1777777.78 5194.81 9 7 33.3333333333333 22.2222222222222 0 0 +FW 1502 80675.24 642979.45 166888888.89 487662.34 274 1228 37.956204379562 62.4087591240876 14.9837133550489 27.3615635179153 +G6_DM 204 25176.93 87328.77 22666666.67 66233.77 53 151 62.2641509433962 54.7169811320755 1.98675496688742 33.112582781457 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 191 14474.61 8284.18 3031746.03 6256.14 82 109 54.8780487804878 31.7073170731707 10.0917431192661 18.348623853211 -I_DM 10 47.66 433.73 158730.16 327.55 6 4 50 33.3333333333333 50 0 -MAX_I 84 271.88 3643.30 1333333.33 2751.39 15 69 86.6666666666667 6.66666666666667 73.9130434782609 15.9420289855072 -MAX_LTR 57 4548.41 2472.24 904761.90 1867.02 22 35 36.3636363636364 9.09090909090909 0 54.2857142857143 -PROTOP 83 474.56 3599.93 1317460.32 2718.64 26 57 42.3076923076923 65.3846153846154 17.5438596491228 36.8421052631579 +Gypsy2-LTR_DM 21 15657.81 8989.73 2333333.33 6818.18 6 15 66.6666666666667 66.6666666666667 0 6.66666666666667 +I_DM 2 93.79 856.16 222222.22 649.35 2 0 100 50 0 0 +MAX_I 10 318.44 4280.82 1111111.11 3246.75 0 10 0 0 80 0 +MAX_LTR 11 8636.07 4708.90 1222222.22 3571.43 5 6 20 0 0 33.3333333333333 +PROTOP 7 393.78 2996.58 777777.78 2272.73 1 6 100 100 16.6666666666667 33.3333333333333 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_unique_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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chrom_5\t0\t450\t0\n-chrom_5\t450\t468\t51.2295\n+chrom_5\t450\t468\t252.016\n chrom_5\t468\t1999\t0\n-chrom_6\t0\t3076\t0\n-chrom_6\t3076\t3096\t25.6148\n-chrom_6\t3096\t3999\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
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chrom_5\t1803\t1999\t0\n chrom_6\t0\t440\t0\n-chrom_6\t440\t464\t25.6148\n-chrom_6\t464\t885\t0\n-chrom_6\t885\t905\t51.2295\n-chrom_6\t905\t906\t25.6148\n-chrom_6\t906\t1038\t0\n-chrom_6\t1038\t1060\t25.6148\n-chrom_6\t1060\t1109\t0\n-chrom_6\t1109\t1110\t25.6148\n-chrom_6\t1110\t1115\t51.2295\n-chrom_6\t1115\t1117\t102.459\n-chrom_6\t1117\t1125\t128.074\n-chrom_6\t1125\t1130\t153.689\n-chrom_6\t1130\t1133\t102.459\n-chrom_6\t1133\t1136\t76.8443\n-chrom_6\t1136\t1142\t51.2295\n-chrom_6\t1142\t1143\t25.6148\n-chrom_6\t1143\t3002\t0\n-chrom_6\t3002\t3027\t25.6148\n-chrom_6\t3027\t3999\t0\n+chrom_6\t440\t464\t252.016\n+chrom_6\t464\t3999\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
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chrom_5\t0\t450\t0\n-chrom_5\t450\t468\t51.2295\n+chrom_5\t450\t468\t252.016\n chrom_5\t468\t1999\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
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chrom_1\t84969\t85094\t0\n-chrom_1\t85094\t85115\t51.2295\n-chrom_1\t85115\t85355\t0\n-chrom_1\t85355\t85376\t25.6148\n-chrom_1\t85376\t85397\t0\n-chrom_1\t85397\t85407\t25.6148\n-chrom_1\t85407\t85422\t51.2295\n-chrom_1\t85422\t85428\t25.6148\n-chrom_1\t85428\t85513\t0\n-chrom_1\t85513\t85534\t25.6148\n-chrom_1\t85534\t85980\t0\n-chrom_1\t85980\t86005\t25.6148\n-chrom_1\t86005\t86344\t0\n-chrom_1\t86344\t86354\t51.2295\n-chrom_1\t86354\t86362\t76.8443\n-chrom_1\t86362\t86365\t102.459\n-chrom_1\t86365\t86376\t51.2295\n-chrom_1\t86376\t86383\t25.6148\n-chrom_1\t86383\t86432\t0\n-chrom_1\t86432\t86453\t25.6148\n-chrom_1\t86453\t86950\t0\n-chrom_1\t86950\t86971\t25.6148\n-chrom_1\t86971\t87113\t0\n-chrom_1\t87113\t87134\t25.6148\n-chrom_1\t87134\t87255\t0\n-chrom_1\t87255\t87278\t25.6148\n-chrom_1\t87278\t88301\t0\n-chrom_1\t88301\t88325\t25.6148\n-chrom_1\t88325\t88633\t0\n-chrom_1\t88633\t88654\t25.6148\n-chrom_1\t88654\t88989\t0\n-chrom_1\t88989\t89015\t25.6148\n-chrom_1\t89015\t89111\t0\n-chrom_1\t89111\t89137\t25.6148\n-chrom_1\t89137\t89597\t0\n-chrom_1\t89597\t89618\t25.6148\n-chrom_1\t89618\t89999\t0\n-chrom_2\t0\t41979\t0\n-chrom_2\t41979\t42001\t51.2295\n-chrom_2\t42001\t49999\t0\n-chrom_4\t0\t1047\t0\n-chrom_4\t1047\t1066\t76.8443\n-chrom_4\t1066\t1067\t51.2295\n-chrom_4\t1067\t1071\t25.6148\n-chrom_4\t1071\t1151\t0\n-chrom_4\t1151\t1172\t25.6148\n-chrom_4\t1172\t1208\t0\n-chrom_4\t1208\t1212\t76.8443\n-chrom_4\t1212\t1230\t102.459\n+chrom_1\t85094\t85115\t252.016\n+chrom_1\t85115\t86344\t0\n+chrom_1\t86344\t86365\t252.016\n+chrom_1\t86365\t89999\t0\n+chrom_4\t0\t1208\t0\n+chrom_4\t1208\t1230\t252.016\n chrom_4\t1230\t2000\t0\n-chrom_5\t0\t1648\t0\n-chrom_5\t1648\t1669\t25.6148\n-chrom_5\t1669\t1782\t0\n-chrom_5\t1782\t1803\t25.6148\n+chrom_5\t0\t1782\t0\n+chrom_5\t1782\t1803\t252.016\n chrom_5\t1803\t1999\t0\n chrom_6\t0\t440\t0\n-chrom_6\t440\t464\t25.6148\n-chrom_6\t464\t885\t0\n-chrom_6\t885\t905\t51.2295\n-chrom_6\t905\t906\t25.6148\n-chrom_6\t906\t1038\t0\n-chrom_6\t1038\t1060\t25.6148\n-chrom_6\t1060\t1109\t0\n-chrom_6\t1109\t1110\t25.6148\n-chrom_6\t1110\t1115\t51.2295\n-chrom_6\t1115\t1117\t102.459\n-chrom_6\t1117\t1125\t128.074\n-chrom_6\t1125\t1130\t153.689\n-chrom_6\t1130\t1133\t102.459\n-chrom_6\t1133\t1136\t76.8443\n-chrom_6\t1136\t1142\t51.2295\n-chrom_6\t1142\t1143\t25.6148\n-chrom_6\t1143\t3999\t0\n+chrom_6\t440\t464\t252.016\n+chrom_6\t464\t3999\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_reads_counts.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_reads_counts.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_reads_counts.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,14 +1,14 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -FBtr0073689 195 1316.17 8457.67 3095238.10 6387.16 84 111 90.4761904761905 78.5714285714286 7.20720720720721 15.3153153153153 -FBtr0078666 307 3241.44 13315.41 4873015.87 10055.68 143 164 94.4055944055944 75.5244755244755 14.6341463414634 9.14634146341463 -FBtr0086080 142 918.74 6158.92 2253968.25 4651.16 73 69 69.8630136986301 31.5068493150685 0 24.6376811594203 -FBtr0089125 146 517.18 6332.41 2317460.32 4782.18 6 140 83.3333333333333 50 57.8571428571429 11.4285714285714 -FBtr0089196 450 2634.06 19517.70 7142857.14 14739.60 316 134 98.1012658227848 60.4430379746835 11.1940298507463 33.5820895522388 -FBtr0113825 91 797.45 3946.91 1444444.44 2980.67 73 18 84.9315068493151 68.4931506849315 5.55555555555556 27.7777777777778 -FBtr0114365 29 116.12 1257.81 460317.46 949.89 16 13 37.5 18.75 0 7.69230769230769 -FBtr0310270 52 434.01 2255.38 825396.83 1703.24 1 51 0 100 5.88235294117647 15.6862745098039 -FBtr0332656 30 220.63 1301.18 476190.48 982.64 30 0 100 46.6666666666667 0 0 -FBtr0345361 59 1172.44 2558.99 936507.94 1932.53 59 0 98.3050847457627 67.7966101694915 0 0 -FBtr0345575 294 2545.03 12751.56 4666666.67 9629.87 66 228 81.8181818181818 60.6060606060606 61.8421052631579 7.45614035087719 -FBtr0345650 377 1167.40 16351.49 5984126.98 12348.51 261 116 55.9386973180077 6.13026819923372 4.31034482758621 6.89655172413793 -FBtr0346343 74 303.62 3209.58 1174603.17 2423.85 72 2 97.2222222222222 4.16666666666667 50 50 +FBtr0073689 23 1527.37 9845.89 2555555.56 7467.53 10 13 100 100 0 0 +FBtr0078666 33 3428.08 14126.71 3666666.67 10714.29 14 19 92.8571428571429 64.2857142857143 15.7894736842105 0 +FBtr0086080 19 1209.47 8133.56 2111111.11 6168.83 13 6 69.2307692307692 23.0769230769231 0 33.3333333333333 +FBtr0089125 15 522.78 6421.23 1666666.67 4870.13 0 15 0 0 60 20 +FBtr0089196 37 2130.85 15839.04 4111111.11 12012.99 23 14 95.6521739130435 73.9130434782609 0 28.5714285714286 +FBtr0113825 7 603.53 2996.58 777777.78 2272.73 7 0 100 85.7142857142857 0 0 +FBtr0114365 2 78.79 856.16 222222.22 649.35 1 1 0 100 0 0 +FBtr0310270 7 574.82 2996.58 777777.78 2272.73 0 7 0 0 0 14.2857142857143 +FBtr0332656 2 144.71 856.16 222222.22 649.35 2 0 100 0 0 0 +FBtr0345361 7 1368.59 2996.58 777777.78 2272.73 6 1 100 83.3333333333333 0 0 +FBtr0345575 28 2384.74 11986.30 3111111.11 9090.91 6 22 66.6666666666667 66.6666666666667 54.5454545454545 4.54545454545455 +FBtr0345650 42 1279.58 17979.45 4666666.67 13636.36 26 16 53.8461538461538 3.84615384615385 6.25 6.25 +FBtr0346343 5 201.84 2140.41 555555.56 1623.38 5 0 100 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_unique_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err --- a/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err Thu Jan 24 13:09:46 2019 -0500 |
| [ |
| @@ -1,6 +1,6 @@ -[bwa_aln_core] calculate SA coordinate... 0.26 sec +[bwa_aln_core] calculate SA coordinate... 0.08 sec [bwa_aln_core] write to the disk... 0.00 sec -[bwa_aln_core] 39040 sequences have been processed. +[bwa_aln_core] 3968 sequences have been processed. [main] Version: 0.7.12-r1039 -[main] CMD: bwa aln -t 8 -n 0 /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa fastq_dir/reads-sample-small.fastq_all_mappers.fastq -[main] Real time: 0.135 sec; CPU: 0.316 sec +[main] CMD: bwa aln -t 8 -n 0 /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35116.dat_symlink.fa fastq_dir/reads-sample-small.fastq_all_mappers.fastq +[main] Real time: 0.022 sec; CPU: 0.084 sec |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err --- a/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err Thu Jan 24 13:09:46 2019 -0500 |
| [ |
| @@ -1,7 +1,7 @@ [bwa_aln_core] convert to sequence coordinate... 0.00 sec [bwa_aln_core] refine gapped alignments... 0.00 sec -[bwa_aln_core] print alignments... 0.02 sec -[bwa_aln_core] 39040 sequences have been processed. +[bwa_aln_core] print alignments... 0.00 sec +[bwa_aln_core] 3968 sequences have been processed. [main] Version: 0.7.12-r1039 -[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa /dev/stdin fastq_dir/reads-sample-small.fastq_all_mappers.fastq -[main] Real time: 0.295 sec; CPU: 0.080 sec +[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35116.dat_symlink.fa /dev/stdin fastq_dir/reads-sample-small.fastq_all_mappers.fastq +[main] Real time: 0.051 sec; CPU: 0.016 sec |
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| @@ -1,16 +1,8 @@ chrom_3 0 643 0 -chrom_3 643 663 461.066 -chrom_3 663 665 179.303 -chrom_3 665 682 0 -chrom_3 682 704 102.459 +chrom_3 643 663 252.016 +chrom_3 663 682 0 +chrom_3 682 704 252.016 chrom_3 704 1041 0 -chrom_3 1041 1042 896.516 -chrom_3 1042 1062 922.131 -chrom_3 1062 1063 870.902 -chrom_3 1063 1064 51.2295 -chrom_3 1064 1065 25.6148 -chrom_3 1065 1078 0 -chrom_3 1078 1079 25.6148 -chrom_3 1079 1080 51.2295 -chrom_3 1080 1101 128.074 -chrom_3 1101 1499 0 +chrom_3 1041 1063 1764.11 +chrom_3 1063 1065 252.016 +chrom_3 1065 1499 0 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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| @@ -1,16 +1,8 @@ chrom_3 0 643 0 -chrom_3 643 663 461.066 -chrom_3 663 665 179.303 -chrom_3 665 682 0 -chrom_3 682 704 102.459 +chrom_3 643 663 252.016 +chrom_3 663 682 0 +chrom_3 682 704 252.016 chrom_3 704 1041 0 -chrom_3 1041 1042 896.516 -chrom_3 1042 1062 922.131 -chrom_3 1062 1063 870.902 -chrom_3 1063 1064 51.2295 -chrom_3 1064 1065 25.6148 -chrom_3 1065 1078 0 -chrom_3 1078 1079 25.6148 -chrom_3 1079 1080 51.2295 -chrom_3 1080 1101 128.074 -chrom_3 1101 1499 0 +chrom_3 1041 1063 1764.11 +chrom_3 1063 1065 252.016 +chrom_3 1065 1499 0 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs_reads_counts.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs_reads_counts.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs_reads_counts.txt Thu Jan 24 13:09:46 2019 -0500 |
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| @@ -11,7 +11,7 @@ dme-mir-1007_MI0005868 0 0.00 0.00 0.00 0.00 dme-mir-1008_MI0005869 0 0.00 0.00 0.00 0.00 dme-mir-1009_MI0005870 0 0.00 0.00 0.00 0.00 -dme-mir-100_MI0000378 22 5635.25 954.20 349206.35 720.60 +dme-mir-100_MI0000378 2 5040.32 856.16 222222.22 649.35 dme-mir-1010_MI0005871 0 0.00 0.00 0.00 0.00 dme-mir-1011_MI0005872 0 0.00 0.00 0.00 0.00 dme-mir-1012_MI0005873 0 0.00 0.00 0.00 0.00 @@ -23,7 +23,7 @@ dme-mir-10_MI0000130 0 0.00 0.00 0.00 0.00 dme-mir-11_MI0000131 0 0.00 0.00 0.00 0.00 dme-mir-124_MI0000373 0 0.00 0.00 0.00 0.00 -dme-mir-125_MI0000417 41 9547.32 1778.28 650793.65 1342.94 +dme-mir-125_MI0000417 7 16037.39 2996.58 777777.78 2272.73 dme-mir-12_MI0000132 0 0.00 0.00 0.00 0.00 dme-mir-133_MI0000362 0 0.00 0.00 0.00 0.00 dme-mir-137_MI0005849 0 0.00 0.00 0.00 0.00 |
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| b |
| b'@@ -1,3960 +1,1275 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PROTOP\t3244\t3271\t0\n-PROTOP\t3271\t3296\t76.8443\n-PROTOP\t3296\t3370\t0\n-PROTOP\t3370\t3372\t25.6148\n-PROTOP\t3372\t3381\t76.8443\n-PROTOP\t3381\t3383\t102.459\n-PROTOP\t3383\t3396\t179.303\n-PROTOP\t3396\t3406\t102.459\n-PROTOP\t3406\t3431\t76.8443\n-PROTOP\t3431\t3433\t25.6148\n-PROTOP\t3433\t3448\t0\n-PROTOP\t3448\t3472\t25.6148\n-PROTOP\t3472\t3478\t0\n-PROTOP\t3478\t3489\t25.6148\n-PROTOP\t3489\t3503\t51.2295\n-PROTOP\t3503\t3513\t25.6148\n-PROTOP\t3513\t4353\t0\n-PROTOP\t4353\t4370\t25.6148\n-PROTOP\t4370\t4371\t51.2295\n-PROTOP\t4371\t4374\t128.074\n-PROTOP\t4374\t4378\t204.918\n-PROTOP\t4378\t4388\t179.303\n-PROTOP\t4388\t4392\t204.918\n-PROTOP\t4392\t4393\t230.533\n-PROTOP\t4393\t4394\t204.918\n-PROTOP\t4394\t4397\t153.689\n-PROTOP\t4397\t4413\t51.2295\n-PROTOP\t4413\t4417\t25.6148\n-PROTOP\t4417\t4425\t0\n-PROTOP\t4425\t4450\t25.6148\n+PROTOP\t3271\t3296\t252.016\n+PROTOP\t3296\t4425\t0\n+PROTOP\t4425\t4450\t252.016\n PROTOP\t4450\t4480\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,2185 +1,538 @@\n-BATUMI_I\t0\t1\t25.6148\n-BATUMI_I\t1\t6\t51.2295\n-BATUMI_I\t6\t22\t76.8443\n-BATUMI_I\t22\t26\t51.2295\n-BATUMI_I\t26\t32\t25.6148\n-BATUMI_I\t32\t119\t0\n-BATUMI_I\t119\t144\t51.2295\n-BATUMI_I\t144\t150\t0\n-BATUMI_I\t150\t160\t25.6148\n-BATUMI_I\t160\t176\t51.2295\n-BATUMI_I\t176\t185\t25.6148\n-BATUMI_I\t185\t386\t0\n-BATUMI_I\t386\t411\t25.6148\n-BATUMI_I\t411\t417\t0\n-BATUMI_I\t417\t418\t25.6148\n-BATUMI_I\t418\t419\t128.074\n-BATUMI_I\t419\t441\t153.689\n-BATUMI_I\t441\t442\t102.459\n-BATUMI_I\t442\t443\t25.6148\n-BATUMI_I\t443\t7006\t0\n-BATUMI_I\t7006\t7007\t25.6148\n-BATUMI_I\t7007\t7008\t51.2295\n-BATUMI_I\t7008\t7009\t128.074\n-BATUMI_I\t7009\t7016\t281.762\n-BATUMI_I\t7016\t7017\t640.369\n-BATUMI_I\t7017\t7018\t1664.96\n-BATUMI_I\t7018\t7031\t3201.84\n-BATUMI_I\t7031\t7033\t3073.77\n-BATUMI_I\t7033\t7034\t3048.16\n-BATUMI_I\t7034\t7038\t2920.08\n-BATUMI_I\t7038\t7039\t2715.16\n-BATUMI_I\t7039\t7040\t1716.19\n-BATUMI_I\t7040\t7041\t1511.27\n-BATUMI_I\t7041\t7042\t281.762\n-BATUMI_I\t7042\t7043\t25.6148\n-BATUMI_I\t7043\t7963\t0\n-BATUMI_LTR\t0\t32\t0\n-BATUMI_LTR\t32\t57\t25.6148\n-BATUMI_LTR\t57\t118\t0\n-BATUMI_LTR\t118\t142\t25.6148\n-BATUMI_LTR\t142\t195\t0\n-BATUMI_LTR\t195\t218\t25.6148\n-BATUMI_LTR\t218\t272\t0\n-BS2\t0\t21\t0\n-BS2\t21\t42\t51.2295\n-BS2\t42\t45\t76.8443\n-BS2\t45\t68\t25.6148\n-BS2\t68\t69\t384.221\n-BS2\t69\t72\t435.451\n-BS2\t72\t77\t486.68\n-BS2\t77\t79\t512.295\n-BS2\t79\t80\t537.91\n-BS2\t80\t81\t563.525\n-BS2\t81\t82\t717.213\n-BS2\t82\t91\t742.828\n-BS2\t91\t93\t717.213\n-BS2\t93\t94\t384.221\n-BS2\t94\t97\t307.377\n-BS2\t97\t98\t281.762\n-BS2\t98\t102\t256.148\n-BS2\t102\t106\t230.533\n-BS2\t106\t107\t102.459\n-BS2\t107\t108\t51.2295\n-BS2\t108\t186\t0\n-BS2\t186\t187\t25.6148\n-BS2\t187\t188\t51.2295\n-BS2\t188\t192\t102.459\n-BS2\t192\t193\t128.074\n-BS2\t193\t194\t153.689\n-BS2\t194\t196\t256.148\n-BS2\t196\t211\t281.762\n-BS2\t211\t213\t256.148\n-BS2\t213\t214\t230.533\n-BS2\t214\t215\t307.377\n-BS2\t215\t219\t281.762\n-BS2\t219\t220\t230.533\n-BS2\t220\t221\t204.918\n-BS2\t221\t222\t179.303\n-BS2\t222\t223\t230.533\n-BS2\t223\t224\t256.148\n-BS2\t224\t235\t537.91\n-BS2\t235\t237\t512.295\n-BS2\t237\t238\t461.066\n-BS2\t238\t241\t435.451\n-BS2\t241\t246\t409.836\n-BS2\t246\t248\t332.992\n-BS2\t248\t284\t0\n-BS2\t284\t285\t25.6148\n-BS2\t285\t303\t76.8443\n-BS2\t303\t304\t102.459\n-BS2\t304\t308\t128.074\n-BS2\t308\t329\t51.2295\n-BS2\t329\t335\t25.6148\n-BS2\t335\t338\t51.2295\n-BS2\t338\t339\t281.762\n-BS2\t339\t341\t409.836\n-BS2\t341\t344\t435.451\n-BS2\t344\t350\t512.295\n-BS2\t350\t353\t537.91\n-BS2\t353\t362\t512.295\n-BS2\t362\t363\t384.221\n-BS2\t363\t364\t204.918\n-BS2\t364\t365\t128.074\n-BS2\t365\t367\t153.689\n-BS2\t367\t368\t128.074\n-BS2\t368\t374\t76.8443\n-BS2\t374\t386\t51.2295\n-BS2\t386\t390\t25.6148\n-BS2\t390\t430\t0\n-BS2\t430\t440\t25.6148\n-BS2\t440\t454\t76.8443\n-BS2\t454\t455\t51.2295\n-BS2\t455\t456\t76.8443\n-BS2\t456\t457\t230.533\n-BS2\t457\t463\t256.148\n-BS2\t463\t465\t230.533\n-BS2\t465\t471\t204.918\n-BS2\t471\t475\t230.533\n-BS2\t475\t480\t256.148\n-BS2\t480\t483\t76.8443\n-BS2\t483\t484\t51.2295\n-BS2\t484\t492\t76.8443\n-BS2\t492\t493\t102.459\n-BS2\t493\t495\t128.074\n-BS2\t495\t499\t153.689\n-BS2\t499\t501\t204.918\n-BS2\t501\t503\t179.303\n-BS2\t503\t506\t230.533\n-BS2\t506\t509\t256.148\n-BS2\t509\t511\t281.762\n-BS2\t511\t516\t461.066\n-BS2\t516\t518\t435.451\n-BS2\t518\t519\t409.836\n-BS2\t519\t522\t384.221\n-BS2\t522\t528\t307.377\n-BS2\t528\t530\t256.148\n-BS2\t530\t534\t230.533\n-BS2\t534\t535\t76.8443\n-BS2\t535\t537\t25.6148\n-BS2\t537\t562\t0\n-BS2\t562\t566\t102.459\n-BS2\t566\t576\t153.689\n-BS2\t576\t582\t179.303\n-BS2\t582\t586\t204.918\n-BS2\t586\t588\t179.303\n-BS2\t588\t591\t153.689\n-BS2\t591\t592\t128.074\n-BS2\t592\t593\t179.303\n-BS2\t593\t601\t204.918\n-BS2\t601\t608\t179.303\n-BS2\t608\t612\t153.689\n-BS2\t612\t615\t102.459\n-BS2\t615\t617\t51.2295\n-BS2\t617\t618\t25.6148\n-BS2\t618\t626\t0\n-BS2\t626\t638\t25.6148\n-BS2\t638\t650\t51.2295\n-BS2\t650\t652\t76.8443\n-BS2\t652\t663\t51.2295\n-BS2\t663\t677\t25.6148\n-BS2\t677\t746\t0\n-BS2\t746\t763\t25.6148\n-BS2\t763\t771\t51.2295\n-BS2\t771\t772\t179.303\n-BS2\t772\t788\t204.918\n-BS2\t788\t794\t179.303\n-BS2\t794\t795\t25.6148\n-BS2\t795\t796\t102.459\n-BS2\t796\t797\t128.074\n-BS2\t797\t818\t102.459\n-BS2\t818\t819\t76.8443\n-BS2\t819\t820\t25.6148\n-BS2\t820\t859\t0\n-BS2\t859\t862\t25.6148\n-BS2\t862\t871\t51.2295\n-BS2\t871\t884\t102.459\n-BS2\t884\t885\t76.8443\n-BS2\t885\t895\t51.2295\n-BS2\t895\t898\t0\n-BS2\t898\t899\t1050.2\n-BS2\t899\t901\t2228.48\n-BS2\t901\t902\t2305.33\n-BS2\t902\t921\t2330.94\n-BS2\t921\t922\t2305.33\n-BS2\t922\t923\t2151.64\n-BS2\t9'..b'ypsy2-LTR_DM\t297\t314\t76.8443\n-Gypsy2-LTR_DM\t314\t315\t51.2295\n-Gypsy2-LTR_DM\t315\t321\t25.6148\n-Gypsy2-LTR_DM\t321\t338\t0\n-I_DM\t0\t902\t0\n-I_DM\t902\t929\t25.6148\n-I_DM\t929\t1427\t0\n-I_DM\t1427\t1452\t25.6148\n-I_DM\t1452\t1720\t0\n-I_DM\t1720\t1743\t25.6148\n-I_DM\t1743\t3190\t0\n-I_DM\t3190\t3215\t76.8443\n-I_DM\t3215\t3235\t25.6148\n-I_DM\t3235\t3237\t51.2295\n-I_DM\t3237\t3239\t76.8443\n-I_DM\t3239\t3261\t51.2295\n-I_DM\t3261\t3262\t25.6148\n-I_DM\t3262\t4623\t0\n-I_DM\t4623\t4646\t25.6148\n-I_DM\t4646\t4825\t0\n-I_DM\t4825\t4849\t25.6148\n-I_DM\t4849\t4912\t0\n-I_DM\t4912\t4939\t25.6148\n-I_DM\t4939\t5104\t0\n-I_DM\t5104\t5128\t25.6148\n-I_DM\t5128\t5374\t0\n-MAX_I\t0\t53\t0\n-MAX_I\t53\t54\t25.6148\n-MAX_I\t54\t59\t51.2295\n-MAX_I\t59\t77\t102.459\n-MAX_I\t77\t78\t76.8443\n-MAX_I\t78\t80\t51.2295\n-MAX_I\t80\t84\t76.8443\n-MAX_I\t84\t87\t25.6148\n-MAX_I\t87\t92\t51.2295\n-MAX_I\t92\t104\t76.8443\n-MAX_I\t104\t105\t25.6148\n-MAX_I\t105\t108\t51.2295\n-MAX_I\t108\t111\t76.8443\n-MAX_I\t111\t118\t51.2295\n-MAX_I\t118\t119\t25.6148\n-MAX_I\t119\t120\t51.2295\n-MAX_I\t120\t127\t76.8443\n-MAX_I\t127\t131\t102.459\n-MAX_I\t131\t142\t76.8443\n-MAX_I\t142\t144\t51.2295\n-MAX_I\t144\t151\t25.6148\n-MAX_I\t151\t230\t0\n-MAX_I\t230\t238\t25.6148\n-MAX_I\t238\t254\t51.2295\n-MAX_I\t254\t263\t25.6148\n-MAX_I\t263\t316\t0\n-MAX_I\t316\t340\t102.459\n-MAX_I\t340\t342\t51.2295\n-MAX_I\t342\t7914\t0\n-MAX_LTR\t0\t12\t0\n-MAX_LTR\t12\t21\t25.6148\n-MAX_LTR\t21\t36\t76.8443\n-MAX_LTR\t36\t44\t51.2295\n-MAX_LTR\t44\t48\t0\n-MAX_LTR\t48\t52\t25.6148\n-MAX_LTR\t52\t72\t153.689\n-MAX_LTR\t72\t75\t128.074\n-MAX_LTR\t75\t76\t102.459\n-MAX_LTR\t76\t77\t76.8443\n-MAX_LTR\t77\t78\t25.6148\n-MAX_LTR\t78\t80\t0\n-MAX_LTR\t80\t88\t128.074\n-MAX_LTR\t88\t105\t153.689\n-MAX_LTR\t105\t113\t25.6148\n-MAX_LTR\t113\t134\t0\n-MAX_LTR\t134\t138\t51.2295\n-MAX_LTR\t138\t159\t204.918\n-MAX_LTR\t159\t161\t153.689\n+Gypsy2-LTR_DM\t58\t85\t252.016\n+Gypsy2-LTR_DM\t85\t157\t0\n+Gypsy2-LTR_DM\t157\t182\t252.016\n+Gypsy2-LTR_DM\t182\t265\t0\n+Gypsy2-LTR_DM\t265\t266\t504.032\n+Gypsy2-LTR_DM\t266\t289\t756.048\n+Gypsy2-LTR_DM\t289\t290\t504.032\n+Gypsy2-LTR_DM\t290\t338\t0\n+I_DM\t0\t3237\t0\n+I_DM\t3237\t3262\t252.016\n+I_DM\t3262\t4912\t0\n+I_DM\t4912\t4939\t252.016\n+I_DM\t4939\t5374\t0\n+MAX_I\t0\t238\t0\n+MAX_I\t238\t263\t252.016\n+MAX_I\t263\t7914\t0\n+MAX_LTR\t0\t48\t0\n+MAX_LTR\t48\t72\t252.016\n+MAX_LTR\t72\t80\t0\n+MAX_LTR\t80\t105\t504.032\n+MAX_LTR\t105\t138\t0\n+MAX_LTR\t138\t161\t252.016\n MAX_LTR\t161\t321\t0\n-PROTOP\t0\t14\t0\n-PROTOP\t14\t38\t25.6148\n-PROTOP\t38\t59\t0\n-PROTOP\t59\t64\t25.6148\n-PROTOP\t64\t83\t76.8443\n-PROTOP\t83\t88\t51.2295\n-PROTOP\t88\t103\t0\n-PROTOP\t103\t104\t76.8443\n-PROTOP\t104\t127\t102.459\n-PROTOP\t127\t129\t76.8443\n-PROTOP\t129\t160\t0\n-PROTOP\t160\t184\t25.6148\n-PROTOP\t184\t209\t0\n-PROTOP\t209\t224\t256.148\n-PROTOP\t224\t234\t281.762\n-PROTOP\t234\t235\t102.459\n-PROTOP\t235\t250\t25.6148\n-PROTOP\t250\t445\t0\n-PROTOP\t445\t449\t25.6148\n-PROTOP\t449\t468\t51.2295\n-PROTOP\t468\t472\t25.6148\n-PROTOP\t472\t2348\t0\n-PROTOP\t2348\t2399\t25.6148\n-PROTOP\t2399\t2442\t0\n-PROTOP\t2442\t2465\t25.6148\n-PROTOP\t2465\t2540\t0\n-PROTOP\t2540\t2565\t25.6148\n-PROTOP\t2565\t2615\t0\n-PROTOP\t2615\t2641\t51.2295\n-PROTOP\t2641\t2647\t0\n-PROTOP\t2647\t2648\t25.6148\n-PROTOP\t2648\t2653\t51.2295\n-PROTOP\t2653\t2672\t102.459\n-PROTOP\t2672\t2678\t51.2295\n-PROTOP\t2678\t2689\t0\n-PROTOP\t2689\t2690\t25.6148\n-PROTOP\t2690\t2696\t51.2295\n-PROTOP\t2696\t2714\t76.8443\n-PROTOP\t2714\t2715\t51.2295\n-PROTOP\t2715\t2719\t25.6148\n-PROTOP\t2719\t2742\t0\n-PROTOP\t2742\t2766\t179.303\n-PROTOP\t2766\t2767\t153.689\n-PROTOP\t2767\t2773\t0\n-PROTOP\t2773\t2785\t25.6148\n-PROTOP\t2785\t2786\t0\n-PROTOP\t2786\t2797\t25.6148\n-PROTOP\t2797\t3327\t0\n-PROTOP\t3327\t3350\t25.6148\n-PROTOP\t3350\t3397\t0\n-PROTOP\t3397\t3422\t25.6148\n-PROTOP\t3422\t3452\t0\n-PROTOP\t3452\t3478\t25.6148\n-PROTOP\t3478\t4135\t0\n-PROTOP\t4135\t4160\t76.8443\n-PROTOP\t4160\t4307\t0\n-PROTOP\t4307\t4308\t25.6148\n-PROTOP\t4308\t4333\t51.2295\n-PROTOP\t4333\t4360\t0\n-PROTOP\t4360\t4384\t25.6148\n+PROTOP\t0\t209\t0\n+PROTOP\t209\t224\t504.032\n+PROTOP\t224\t234\t756.048\n+PROTOP\t234\t250\t252.016\n+PROTOP\t250\t2442\t0\n+PROTOP\t2442\t2465\t252.016\n+PROTOP\t2465\t2653\t0\n+PROTOP\t2653\t2678\t252.016\n+PROTOP\t2678\t4360\t0\n+PROTOP\t4360\t4384\t252.016\n PROTOP\t4384\t4387\t0\n-PROTOP\t4387\t4388\t128.074\n-PROTOP\t4388\t4398\t153.689\n-PROTOP\t4398\t4412\t204.918\n-PROTOP\t4412\t4413\t76.8443\n-PROTOP\t4413\t4422\t51.2295\n-PROTOP\t4422\t4423\t25.6148\n-PROTOP\t4423\t4480\t0\n+PROTOP\t4387\t4412\t252.016\n+PROTOP\t4412\t4480\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 262 842.78 11363.64 4158730.16 8581.72 139 123 95.6834532374101 44.6043165467626 37.3983739837398 21.1382113821138 -BATUMI_LTR 89 8381.30 3860.17 1412698.41 2915.17 3 86 100 0 2.32558139534884 39.5348837209302 -BS2 5896 31989.96 255725.19 93587301.59 193121.52 1224 4672 47.3856209150327 39.5424836601307 17.8724315068493 32.7696917808219 +BATUMI_I 25 791.21 10702.05 2777777.78 8116.88 11 14 90.9090909090909 63.6363636363636 64.2857142857143 7.14285714285714 +BATUMI_LTR 8 7412.24 3424.66 888888.89 2597.40 0 8 0 0 0 0 +BS2 625 33363.71 267551.37 69444444.44 202922.08 124 501 48.3870967741936 43.5483870967742 16.3672654690619 32.7345309381238 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 347 1988.44 15050.31 5507936.51 11365.87 81 266 49.3827160493827 58.0246913580247 21.4285714285714 34.5864661654135 -DMRT1B 291 1438.14 12621.44 4619047.62 9531.61 163 128 41.7177914110429 38.0368098159509 2.34375 13.28125 -FW 11088 60532.05 480916.03 176000000.00 363183.75 1669 9419 43.4991012582385 63.0317555422409 16.2437626074955 27.9329015819089 -G6_DM 1586 19894.71 68789.04 25174603.17 51948.90 340 1246 61.7647058823529 45.5882352941176 2.1669341894061 31.7014446227929 +DMCR1A 49 2762.59 20976.03 5444444.44 15909.09 10 39 50 70 20.5128205128205 46.1538461538462 +DMRT1B 31 1507.33 13270.55 3444444.44 10064.94 16 15 31.25 31.25 0 13.3333333333333 +FW 1077 57847.69 461044.52 119666666.67 349675.32 184 893 40.2173913043478 66.304347826087 16.6853303471445 31.2430011198208 +G6_DM 163 20116.86 69777.40 18111111.11 52922.08 43 120 72.0930232558139 51.1627906976744 1.66666666666667 33.3333333333333 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 147 11140.14 6375.78 2333333.33 4814.94 59 88 62.7118644067797 38.9830508474576 11.3636363636364 17.0454545454545 -I_DM 33 157.29 1431.30 523809.52 1080.90 13 20 61.5384615384615 30.7692307692308 25 50 -MAX_I 87 281.59 3773.42 1380952.38 2849.66 17 70 82.3529411764706 0 65.7142857142857 20 -MAX_LTR 65 5186.79 2819.22 1031746.03 2129.05 23 42 26.0869565217391 39.1304347826087 0 47.6190476190476 -PROTOP 173 989.14 7503.47 2746031.75 5666.56 60 113 56.6666666666667 66.6666666666667 23.0088495575221 29.2035398230088 +Gypsy2-LTR_DM 17 12675.37 7277.40 1888888.89 5519.48 5 12 60 60 0 0 +I_DM 3 140.69 1284.25 333333.33 974.03 2 1 100 50 0 0 +MAX_I 11 350.29 4708.90 1222222.22 3571.43 1 10 0 0 70 0 +MAX_LTR 9 7065.87 3852.74 1000000.00 2922.08 4 5 25 25 0 40 +PROTOP 20 1125.07 8561.64 2222222.22 6493.51 7 13 57.1428571428571 57.1428571428571 7.69230769230769 23.0769230769231 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_mismatches.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_mismatches.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_mismatches.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 224 720.55 9715.48 3555555.56 7337.05 135 89 97.037037037037 45.1851851851852 38.2022471910112 23.5955056179775 -BATUMI_LTR 88 8287.13 3816.79 1396825.40 2882.41 2 86 100 0 2.32558139534884 39.5348837209302 -BS2 192 1041.74 8327.55 3047619.05 6288.90 48 144 68.75 29.1666666666667 8.33333333333333 40.2777777777778 +BATUMI_I 17 538.02 7277.40 1888888.89 5519.48 10 7 100 70 71.4285714285714 0 +BATUMI_LTR 8 7412.24 3424.66 888888.89 2597.40 0 8 0 0 0 0 +BS2 23 1227.78 9845.89 2555555.56 7467.53 5 18 60 40 16.6666666666667 33.3333333333333 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 65 372.47 2819.22 1031746.03 2129.05 6 59 100 50 25.4237288135593 28.8135593220339 -DMRT1B 159 785.79 6896.25 2523809.52 5207.99 111 48 50.4504504504504 50.4504504504504 6.25 25 -FW 69 376.69 2992.71 1095238.10 2260.07 24 45 70.8333333333333 83.3333333333333 11.1111111111111 37.7777777777778 +DMCR1A 6 338.28 2568.49 666666.67 1948.05 1 5 100 100 40 0 +DMRT1B 18 875.22 7705.48 2000000.00 5844.16 9 9 33.3333333333333 44.4444444444444 0 22.2222222222222 +FW 7 375.98 2996.58 777777.78 2272.73 4 3 75 100 0 66.6666666666667 G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 3 227.35 130.12 47619.05 98.26 0 3 0 0 0 0 -I_DM 25 119.16 1084.32 396825.40 818.87 8 17 62.5 25 17.6470588235294 58.8235294117647 -MAX_I 25 80.92 1084.32 396825.40 818.87 10 15 80 0 26.6666666666667 20 -MAX_LTR 24 1915.12 1040.94 380952.38 786.11 9 15 0 88.8888888888889 0 6.66666666666667 -PROTOP 108 617.50 4684.25 1714285.71 3537.50 44 64 70.4545454545455 59.0909090909091 25 20.3125 +Gypsy2-LTR_DM 1 745.61 428.08 111111.11 324.68 0 1 0 0 0 0 +I_DM 1 46.90 428.08 111111.11 324.68 0 1 0 0 0 0 +MAX_I 2 63.69 856.16 222222.22 649.35 1 1 0 0 0 0 +MAX_LTR 3 2355.29 1284.25 333333.33 974.03 1 2 0 100 0 0 +PROTOP 13 731.30 5565.07 1444444.44 4220.78 6 7 50 50 0 14.2857142857143 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_nomismatches.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_nomismatches.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_nomismatches.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 38 122.24 1648.16 603174.60 1244.68 4 34 50 25 35.2941176470588 14.7058823529412 -BATUMI_LTR 1 94.17 43.37 15873.02 32.75 1 0 100 0 0 0 -BS2 5704 30948.22 247397.64 90539682.54 186832.62 1176 4528 46.5136054421769 39.9659863945578 18.1757950530035 32.5309187279152 +BATUMI_I 8 253.19 3424.66 888888.89 2597.40 1 7 0 0 57.1428571428571 14.2857142857143 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 602 32135.93 257705.48 66888888.89 195454.55 119 483 47.8991596638655 43.6974789915966 16.3561076604555 32.712215320911 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 282 1615.96 12231.09 4476190.48 9236.82 75 207 45.3333333333333 58.6666666666667 20.2898550724638 36.231884057971 -DMRT1B 132 652.35 5725.19 2095238.10 4323.62 52 80 23.0769230769231 11.5384615384615 0 6.25 -FW 11019 60155.37 477923.32 174904761.90 360923.68 1645 9374 43.1003039513678 62.7355623100304 16.268401962876 27.8856411350544 -G6_DM 1586 19894.71 68789.04 25174603.17 51948.90 340 1246 61.7647058823529 45.5882352941176 2.1669341894061 31.7014446227929 +DMCR1A 43 2424.32 18407.53 4777777.78 13961.04 9 34 44.4444444444444 66.6666666666667 17.6470588235294 52.9411764705882 +DMRT1B 13 632.11 5565.07 1444444.44 4220.78 7 6 28.5714285714286 14.2857142857143 0 0 +FW 1070 57471.71 458047.95 118888888.89 347402.60 180 890 39.4444444444444 65.5555555555556 16.7415730337079 31.123595505618 +G6_DM 163 20116.86 69777.40 18111111.11 52922.08 43 120 72.0930232558139 51.1627906976744 1.66666666666667 33.3333333333333 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 144 10912.79 6245.66 2285714.29 4716.67 59 85 62.7118644067797 38.9830508474576 11.7647058823529 17.6470588235294 -I_DM 8 38.13 346.98 126984.13 262.04 5 3 60 40 66.6666666666667 0 -MAX_I 62 200.67 2689.10 984126.98 2030.79 7 55 85.7142857142857 0 76.3636363636364 20 -MAX_LTR 41 3271.67 1778.28 650793.65 1342.94 14 27 42.8571428571429 7.14285714285714 0 70.3703703703704 -PROTOP 65 371.64 2819.22 1031746.03 2129.05 16 49 18.75 87.5 20.4081632653061 40.8163265306122 +Gypsy2-LTR_DM 16 11929.76 6849.32 1777777.78 5194.81 5 11 60 60 0 0 +I_DM 2 93.79 856.16 222222.22 649.35 2 0 100 50 0 0 +MAX_I 9 286.60 3852.74 1000000.00 2922.08 0 9 0 0 77.7777777777778 0 +MAX_LTR 6 4710.58 2568.49 666666.67 1948.05 3 3 33.3333333333333 0 0 66.6666666666667 +PROTOP 7 393.78 2996.58 777777.78 2272.73 1 6 100 100 16.6666666666667 33.3333333333333 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_unique_sorted.bam |
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| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_unique_sorted.bam has changed |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
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chrom_6\t0\t440\t0\n-chrom_6\t440\t464\t25.6148\n-chrom_6\t464\t1117\t0\n-chrom_6\t1117\t1142\t25.6148\n-chrom_6\t1142\t3002\t0\n-chrom_6\t3002\t3027\t25.6148\n-chrom_6\t3027\t3999\t0\n+chrom_6\t440\t464\t252.016\n+chrom_6\t464\t3999\t0\n' |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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chrom_6\t0\t440\t0\n-chrom_6\t440\t464\t25.6148\n-chrom_6\t464\t1117\t0\n-chrom_6\t1117\t1142\t25.6148\n-chrom_6\t1142\t3999\t0\n+chrom_6\t440\t464\t252.016\n+chrom_6\t464\t3999\t0\n' |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_reads_counts.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_reads_counts.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_reads_counts.txt Thu Jan 24 13:09:46 2019 -0500 |
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| @@ -1,14 +1,14 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -FBtr0073689 162 1093.44 7026.37 2571428.57 5306.26 79 83 92.4050632911392 78.4810126582278 9.63855421686747 15.6626506024096 -FBtr0078666 230 2428.44 9975.71 3650793.65 7533.57 121 109 95.8677685950413 84.297520661157 20.1834862385321 9.1743119266055 -FBtr0086080 98 634.06 4250.52 1555555.56 3209.96 54 44 68.5185185185185 25.9259259259259 0 20.4545454545455 -FBtr0089125 126 446.34 5464.95 2000000.00 4127.09 5 121 80 60 65.2892561983471 0.826446280991736 -FBtr0089196 395 2312.12 17132.20 6269841.27 12938.09 285 110 98.5964912280702 61.7543859649123 10.9090909090909 35.4545454545455 -FBtr0113825 61 534.55 2645.73 968253.97 1998.03 50 11 84 78 9.09090909090909 36.3636363636364 -FBtr0114365 7 28.03 303.61 111111.11 229.28 4 3 25 25 0 0 -FBtr0310270 3 25.04 130.12 47619.05 98.26 0 3 0 0 66.6666666666667 33.3333333333333 -FBtr0332656 20 147.08 867.45 317460.32 655.09 20 0 100 70 0 0 -FBtr0345361 45 894.23 1951.77 714285.71 1473.96 45 0 100 88.8888888888889 0 0 -FBtr0345575 248 2146.83 10756.42 3936507.94 8123.16 49 199 85.7142857142857 73.469387755102 67.8391959798995 4.02010050251256 -FBtr0345650 322 997.09 13966.00 5111111.11 10547.00 217 105 52.9953917050691 6.91244239631336 1.9047619047619 5.71428571428571 -FBtr0346343 67 274.90 2905.97 1063492.06 2194.56 65 2 98.4615384615385 1.53846153846154 50 50 +FBtr0073689 19 1261.74 8133.56 2111111.11 6168.83 10 9 100 100 0 0 +FBtr0078666 25 2597.03 10702.05 2777777.78 8116.88 12 13 91.6666666666667 66.6666666666667 23.0769230769231 0 +FBtr0086080 16 1018.50 6849.32 1777777.78 5194.81 11 5 63.6363636363636 18.1818181818182 0 20 +FBtr0089125 10 348.52 4280.82 1111111.11 3246.75 0 10 0 0 70 0 +FBtr0089196 32 1842.90 13698.63 3555555.56 10389.61 21 11 95.2380952380952 76.1904761904762 0 27.2727272727273 +FBtr0113825 3 258.65 1284.25 333333.33 974.03 3 0 100 100 0 0 +FBtr0114365 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0310270 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0332656 1 72.36 428.08 111111.11 324.68 1 0 100 0 0 0 +FBtr0345361 6 1173.08 2568.49 666666.67 1948.05 5 1 100 100 0 0 +FBtr0345575 27 2299.57 11558.22 3000000.00 8766.23 6 21 66.6666666666667 66.6666666666667 57.1428571428571 0 +FBtr0345650 35 1066.32 14982.88 3888888.89 11363.64 22 13 59.0909090909091 4.54545454545455 7.69230769230769 0 +FBtr0346343 5 201.84 2140.41 555555.56 1623.38 5 0 100 0 0 0 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/pie_chart.png |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/repartition.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/repartition.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/repartition.txt Thu Jan 24 13:09:46 2019 -0500 |
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| @@ -1,8 +1,8 @@ type number percentage -TEs 26344 67.48 -miRNAs 63 0.16 -others 1939 4.97 -rRNAs 8170 20.93 -snRNAs 81 0.21 -tRNAs 196 0.50 -transcripts 2247 5.76 +TEs 2678 67.49 +miRNAs 9 0.23 +others 175 4.41 +rRNAs 850 21.42 +snRNAs 8 0.20 +tRNAs 21 0.53 +transcripts 227 5.72 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_I.png |
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| b'@@ -1,1185 +1,249 @@\n BATUMI_I\t0\t219\t0\n-BATUMI_I\t219\t239\t25.6148\n-BATUMI_I\t239\t353\t0\n-BATUMI_I\t353\t354\t25.6148\n-BATUMI_I\t354\t355\t51.2295\n-BATUMI_I\t355\t357\t76.8443\n-BATUMI_I\t357\t374\t128.074\n-BATUMI_I\t374\t375\t102.459\n-BATUMI_I\t375\t376\t76.8443\n-BATUMI_I\t376\t378\t51.2295\n+BATUMI_I\t219\t239\t252.016\n+BATUMI_I\t239\t355\t0\n+BATUMI_I\t355\t357\t252.016\n+BATUMI_I\t357\t376\t504.032\n+BATUMI_I\t376\t378\t252.016\n BATUMI_I\t378\t7963\t0\n-BATUMI_LTR\t0\t45\t0\n-BATUMI_LTR\t45\t66\t25.6148\n-BATUMI_LTR\t66\t109\t0\n-BATUMI_LTR\t109\t130\t51.2295\n-BATUMI_LTR\t130\t181\t0\n-BATUMI_LTR\t181\t202\t25.6148\n-BATUMI_LTR\t202\t272\t0\n-BS2\t0\t12\t0\n-BS2\t12\t32\t25.6148\n-BS2\t32\t33\t51.2295\n-BS2\t33\t53\t25.6148\n-BS2\t53\t125\t0\n-BS2\t125\t146\t25.6148\n-BS2\t146\t212\t0\n-BS2\t212\t217\t25.6148\n-BS2\t217\t218\t76.8443\n-BS2\t218\t219\t128.074\n-BS2\t219\t233\t179.303\n-BS2\t233\t238\t153.689\n-BS2\t238\t239\t102.459\n-BS2\t239\t240\t51.2295\n-BS2\t240\t272\t0\n-BS2\t272\t273\t51.2295\n-BS2\t273\t293\t76.8443\n-BS2\t293\t294\t25.6148\n-BS2\t294\t500\t0\n-BS2\t500\t521\t461.066\n-BS2\t521\t522\t0\n-BS2\t522\t543\t25.6148\n-BS2\t543\t551\t0\n-BS2\t551\t572\t51.2295\n-BS2\t572\t604\t0\n-BS2\t604\t605\t25.6148\n-BS2\t605\t625\t51.2295\n-BS2\t625\t626\t25.6148\n-BS2\t626\t663\t0\n-BS2\t663\t678\t25.6148\n-BS2\t678\t684\t51.2295\n-BS2\t684\t685\t25.6148\n-BS2\t685\t689\t51.2295\n-BS2\t689\t699\t76.8443\n-BS2\t699\t706\t51.2295\n-BS2\t706\t710\t25.6148\n-BS2\t710\t858\t0\n-BS2\t858\t860\t25.6148\n-BS2\t860\t879\t128.074\n-BS2\t879\t881\t102.459\n-BS2\t881\t910\t0\n-BS2\t910\t930\t25.6148\n-BS2\t930\t931\t51.2295\n-BS2\t931\t933\t25.6148\n-BS2\t933\t936\t76.8443\n-BS2\t936\t937\t102.459\n-BS2\t937\t951\t128.074\n-BS2\t951\t954\t102.459\n-BS2\t954\t957\t51.2295\n-BS2\t957\t958\t25.6148\n-BS2\t958\t994\t0\n-BS2\t994\t1015\t25.6148\n-BS2\t1015\t1016\t0\n-BS2\t1016\t1037\t25.6148\n-BS2\t1037\t1042\t0\n-BS2\t1042\t1063\t51.2295\n-BS2\t1063\t1101\t0\n-BS2\t1101\t1122\t25.6148\n-BS2\t1122\t1173\t0\n-BS2\t1173\t1194\t51.2295\n-BS2\t1194\t1200\t0\n-BS2\t1200\t1221\t25.6148\n-BS2\t1221\t1248\t0\n-BS2\t1248\t1269\t25.6148\n-BS2\t1269\t1271\t0\n-BS2\t1271\t1292\t25.6148\n-BS2\t1292\t1313\t0\n-BS2\t1313\t1314\t25.6148\n-BS2\t1314\t1317\t51.2295\n-BS2\t1317\t1334\t76.8443\n-BS2\t1334\t1335\t51.2295\n-BS2\t1335\t1338\t25.6148\n-BS2\t1338\t1365\t0\n-BS2\t1365\t1386\t25.6148\n-BS2\t1386\t1502\t0\n-BS2\t1502\t1523\t51.2295\n-BS2\t1523\t1528\t0\n-BS2\t1528\t1555\t25.6148\n-BS2\t1555\t1569\t51.2295\n-BS2\t1569\t1570\t76.8443\n-BS2\t1570\t1576\t51.2295\n-BS2\t1576\t1579\t25.6148\n-BS2\t1579\t1585\t51.2295\n-BS2\t1585\t1590\t102.459\n-BS2\t1590\t1600\t76.8443\n-BS2\t1600\t1606\t51.2295\n-BS2\t1606\t1613\t0\n-BS2\t1613\t1630\t25.6148\n-BS2\t1630\t1633\t51.2295\n-BS2\t1633\t1634\t128.074\n-BS2\t1634\t1651\t102.459\n-BS2\t1651\t1652\t76.8443\n-BS2\t1652\t1654\t102.459\n-BS2\t1654\t1673\t25.6148\n-BS2\t1673\t1753\t0\n-BS2\t1753\t1770\t25.6148\n-BS2\t1770\t1774\t51.2295\n-BS2\t1774\t1791\t25.6148\n-BS2\t1791\t1864\t0\n-BS2\t1864\t1885\t25.6148\n-BS2\t1885\t1949\t0\n-BS2\t1949\t1970\t51.2295\n-BS2\t1970\t1983\t0\n-BS2\t1983\t1989\t25.6148\n-BS2\t1989\t2004\t51.2295\n-BS2\t2004\t2010\t25.6148\n-BS2\t2010\t2091\t0\n-BS2\t2091\t2112\t25.6148\n-BS2\t2112\t2144\t0\n-BS2\t2144\t2145\t896.516\n-BS2\t2145\t2146\t922.131\n-BS2\t2146\t2157\t973.361\n-BS2\t2157\t2165\t1024.59\n-BS2\t2165\t2166\t128.074\n-BS2\t2166\t2167\t102.459\n-BS2\t2167\t2178\t51.2295\n-BS2\t2178\t2207\t0\n-BS2\t2207\t2228\t25.6148\n-BS2\t2228\t2371\t0\n-BS2\t2371\t2392\t128.074\n-BS2\t2392\t2396\t0\n-BS2\t2396\t2417\t25.6148\n-BS2\t2417\t2440\t0\n-BS2\t2440\t2461\t25.6148\n-BS2\t2461\t2628\t0\n-BS2\t2628\t2649\t25.6148\n-BS2\t2649\t2670\t51.2295\n-BS2\t2670\t2675\t0\n-BS2\t2675\t2683\t25.6148\n-BS2\t2683\t2685\t51.2295\n-BS2\t2685\t2696\t281.762\n-BS2\t2696\t2704\t256.148\n-BS2\t2704\t2706\t230.533\n-BS2\t2706\t2717\t0\n-BS2\t2717\t2718\t537.91\n-BS2\t2718\t2738\t563.525\n-BS2\t2738\t2739\t25.6148\n-BS2\t2739\t2784\t0\n-BS2\t2784\t2805\t25.6148\n-BS2\t2805\t2850\t0\n-BS2\t2850\t2859\t25.6148\n-BS2\t2859\t2871\t51.2295\n-BS2\t2871\t2872\t25.6148\n-BS2\t2872\t2880\t51.2295\n-BS2\t2880\t2884\t25.6148\n-BS2\t2884\t2893\t51.2295\n-BS2\t2893\t2905\t25.6148\n-BS2\t2905\t2916\t0\n-BS2\t2916\t2937\t25.6148\n-BS2\t2937\t2958\t0\n-BS2\t2958\t2963\t25.6148\n-BS2\t2963\t2979\t102.459\n-BS2\t2979\t2984\t76.8443\n-BS2\t2984\t3027\t0\n-BS2\t3027\t3048\t25.6148\n-BS2\t3048\t3058\t0\n-BS2\t3058\t3079\t25.6148\n-BS2\t3079\t3116\t0\n-BS2\t3116\t3137\t25.6148\n-BS2\t3137\t3164\t0\n-BS2\t3164\t3185\t51.2295\n-BS2\t3185\t3219\t0\n-BS2\t3219\t3224\t51.2295\n-BS2\t3224\t3226\t435.451\n-BS2\t3226\t3228\t486.68\n-BS2\t3228\t3230\t84'..b'sy2-LTR_DM\t280\t301\t25.6148\n-Gypsy2-LTR_DM\t301\t338\t0\n-I_DM\t0\t2989\t0\n-I_DM\t2989\t3010\t25.6148\n-I_DM\t3010\t3248\t0\n-I_DM\t3248\t3269\t25.6148\n-I_DM\t3269\t4914\t0\n-I_DM\t4914\t4919\t25.6148\n-I_DM\t4919\t4935\t51.2295\n-I_DM\t4935\t4940\t25.6148\n-I_DM\t4940\t5374\t0\n-MAX_I\t0\t29\t0\n-MAX_I\t29\t50\t25.6148\n-MAX_I\t50\t102\t0\n-MAX_I\t102\t122\t25.6148\n-MAX_I\t122\t123\t51.2295\n-MAX_I\t123\t128\t25.6148\n-MAX_I\t128\t131\t51.2295\n-MAX_I\t131\t143\t76.8443\n-MAX_I\t143\t149\t51.2295\n-MAX_I\t149\t152\t25.6148\n-MAX_I\t152\t237\t0\n-MAX_I\t237\t258\t51.2295\n-MAX_I\t258\t7914\t0\n-MAX_LTR\t0\t18\t0\n-MAX_LTR\t18\t39\t25.6148\n-MAX_LTR\t39\t80\t0\n-MAX_LTR\t80\t97\t76.8443\n-MAX_LTR\t97\t99\t102.459\n-MAX_LTR\t99\t101\t153.689\n-MAX_LTR\t101\t102\t76.8443\n-MAX_LTR\t102\t118\t102.459\n-MAX_LTR\t118\t120\t76.8443\n-MAX_LTR\t120\t123\t25.6148\n-MAX_LTR\t123\t154\t0\n-MAX_LTR\t154\t175\t25.6148\n-MAX_LTR\t175\t321\t0\n-PROTOP\t0\t2492\t0\n-PROTOP\t2492\t2493\t25.6148\n-PROTOP\t2493\t2513\t51.2295\n-PROTOP\t2513\t2514\t25.6148\n-PROTOP\t2514\t3223\t0\n-PROTOP\t3223\t3244\t25.6148\n-PROTOP\t3244\t3464\t0\n-PROTOP\t3464\t3478\t25.6148\n-PROTOP\t3478\t3485\t51.2295\n-PROTOP\t3485\t3487\t25.6148\n-PROTOP\t3487\t3499\t51.2295\n-PROTOP\t3499\t3508\t25.6148\n-PROTOP\t3508\t4480\t0\n+FW\t2195\t2216\t252.016\n+FW\t2216\t2266\t0\n+FW\t2266\t2287\t504.032\n+FW\t2287\t2288\t0\n+FW\t2288\t2309\t252.016\n+FW\t2309\t2376\t0\n+FW\t2376\t2377\t252.016\n+FW\t2377\t2379\t504.032\n+FW\t2379\t2380\t1008.06\n+FW\t2380\t2381\t2520.16\n+FW\t2381\t2384\t3024.19\n+FW\t2384\t2385\t3528.23\n+FW\t2385\t2397\t3780.24\n+FW\t2397\t2398\t3528.23\n+FW\t2398\t2400\t3276.21\n+FW\t2400\t2401\t2772.18\n+FW\t2401\t2402\t1260.08\n+FW\t2402\t2405\t756.048\n+FW\t2405\t2406\t252.016\n+FW\t2406\t2408\t0\n+FW\t2408\t2418\t252.016\n+FW\t2418\t2419\t504.032\n+FW\t2419\t2420\t756.048\n+FW\t2420\t2422\t1008.06\n+FW\t2422\t2425\t1260.08\n+FW\t2425\t2429\t1512.1\n+FW\t2429\t2439\t1260.08\n+FW\t2439\t2440\t1008.06\n+FW\t2440\t2441\t756.048\n+FW\t2441\t2443\t504.032\n+FW\t2443\t2446\t252.016\n+FW\t2446\t2480\t0\n+FW\t2480\t2501\t504.032\n+FW\t2501\t2556\t0\n+FW\t2556\t2577\t756.048\n+FW\t2577\t2623\t0\n+FW\t2623\t2644\t252.016\n+FW\t2644\t2672\t0\n+FW\t2672\t2686\t252.016\n+FW\t2686\t2693\t504.032\n+FW\t2693\t2701\t252.016\n+FW\t2701\t2702\t1260.08\n+FW\t2702\t2707\t1512.1\n+FW\t2707\t2722\t1260.08\n+FW\t2722\t2723\t252.016\n+FW\t2723\t2751\t0\n+FW\t2751\t2758\t252.016\n+FW\t2758\t2772\t504.032\n+FW\t2772\t2779\t252.016\n+FW\t2779\t2823\t0\n+FW\t2823\t2844\t252.016\n+FW\t2844\t2864\t0\n+FW\t2864\t2885\t252.016\n+FW\t2885\t2976\t0\n+FW\t2976\t2997\t252.016\n+FW\t2997\t3035\t0\n+FW\t3035\t3056\t252.016\n+FW\t3056\t3109\t0\n+FW\t3109\t3110\t252.016\n+FW\t3110\t3130\t1008.06\n+FW\t3130\t3131\t756.048\n+FW\t3131\t3150\t0\n+FW\t3150\t3151\t252.016\n+FW\t3151\t3171\t756.048\n+FW\t3171\t3172\t504.032\n+FW\t3172\t3194\t0\n+FW\t3194\t3199\t252.016\n+FW\t3199\t3215\t504.032\n+FW\t3215\t3218\t252.016\n+FW\t3218\t3220\t504.032\n+FW\t3220\t3239\t252.016\n+FW\t3239\t3373\t0\n+FW\t3373\t3394\t756.048\n+FW\t3394\t3395\t0\n+FW\t3395\t3400\t252.016\n+FW\t3400\t3416\t504.032\n+FW\t3416\t3421\t252.016\n+FW\t3421\t3631\t0\n+FW\t3631\t3634\t252.016\n+FW\t3634\t3639\t504.032\n+FW\t3639\t3652\t756.048\n+FW\t3652\t3655\t504.032\n+FW\t3655\t3660\t252.016\n+FW\t3660\t3699\t0\n+FW\t3699\t3720\t252.016\n+FW\t3720\t3783\t0\n+FW\t3783\t3784\t252.016\n+FW\t3784\t3804\t504.032\n+FW\t3804\t3805\t252.016\n+FW\t3805\t3832\t0\n+FW\t3832\t3846\t252.016\n+FW\t3846\t3853\t504.032\n+FW\t3853\t3861\t252.016\n+FW\t3861\t3867\t504.032\n+FW\t3867\t3882\t252.016\n+FW\t3882\t4187\t0\n+FW\t4187\t4202\t252.016\n+FW\t4202\t4208\t1008.06\n+FW\t4208\t4223\t756.048\n+FW\t4223\t4287\t0\n+FW\t4287\t4308\t252.016\n+FW\t4308\t4391\t0\n+FW\t4391\t4392\t252.016\n+FW\t4392\t4408\t1008.06\n+FW\t4408\t4412\t1260.08\n+FW\t4412\t4413\t1008.06\n+FW\t4413\t4429\t252.016\n+FW\t4429\t4474\t0\n+FW\t4474\t4495\t504.032\n+FW\t4495\t4692\t0\n+G6_DM\t0\t1437\t0\n+G6_DM\t1437\t1438\t1260.08\n+G6_DM\t1438\t1458\t1512.1\n+G6_DM\t1458\t1459\t504.032\n+G6_DM\t1459\t1462\t252.016\n+G6_DM\t1462\t1479\t756.048\n+G6_DM\t1479\t1483\t504.032\n+G6_DM\t1483\t1690\t0\n+G6_DM\t1690\t1691\t252.016\n+G6_DM\t1691\t1711\t504.032\n+G6_DM\t1711\t1712\t252.016\n+G6_DM\t1712\t1887\t0\n+G6_DM\t1887\t1908\t252.016\n+G6_DM\t1908\t2042\t0\n+Gypsy2-LTR_DM\t0\t107\t0\n+Gypsy2-LTR_DM\t107\t108\t252.016\n+Gypsy2-LTR_DM\t108\t109\t504.032\n+Gypsy2-LTR_DM\t109\t128\t756.048\n+Gypsy2-LTR_DM\t128\t129\t504.032\n+Gypsy2-LTR_DM\t129\t130\t252.016\n+Gypsy2-LTR_DM\t130\t338\t0\n+MAX_LTR\t0\t80\t0\n+MAX_LTR\t80\t99\t504.032\n+MAX_LTR\t99\t101\t756.048\n+MAX_LTR\t101\t120\t252.016\n+MAX_LTR\t120\t321\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b'@@ -1,688 +1,93 @@\n-BATUMI_I\t0\t123\t0\n-BATUMI_I\t123\t144\t25.6148\n-BATUMI_I\t144\t7009\t0\n-BATUMI_I\t7009\t7010\t51.2295\n-BATUMI_I\t7010\t7017\t76.8443\n-BATUMI_I\t7017\t7030\t358.607\n-BATUMI_I\t7030\t7031\t307.377\n-BATUMI_I\t7031\t7036\t281.762\n-BATUMI_I\t7036\t7963\t0\n-BATUMI_LTR\t0\t192\t0\n-BATUMI_LTR\t192\t213\t25.6148\n-BATUMI_LTR\t213\t272\t0\n-BS2\t0\t187\t0\n-BS2\t187\t208\t25.6148\n-BS2\t208\t225\t0\n-BS2\t225\t246\t25.6148\n-BS2\t246\t276\t0\n-BS2\t276\t277\t51.2295\n-BS2\t277\t297\t76.8443\n-BS2\t297\t298\t25.6148\n-BS2\t298\t483\t0\n-BS2\t483\t504\t25.6148\n-BS2\t504\t587\t0\n-BS2\t587\t608\t51.2295\n-BS2\t608\t704\t0\n-BS2\t704\t725\t25.6148\n-BS2\t725\t726\t0\n-BS2\t726\t747\t25.6148\n-BS2\t747\t771\t0\n-BS2\t771\t792\t25.6148\n-BS2\t792\t797\t0\n-BS2\t797\t818\t25.6148\n-BS2\t818\t893\t0\n-BS2\t893\t914\t25.6148\n-BS2\t914\t1173\t0\n-BS2\t1173\t1183\t25.6148\n-BS2\t1183\t1194\t51.2295\n-BS2\t1194\t1204\t25.6148\n-BS2\t1204\t1325\t0\n-BS2\t1325\t1346\t25.6148\n-BS2\t1346\t1478\t0\n-BS2\t1478\t1499\t51.2295\n-BS2\t1499\t1578\t0\n-BS2\t1578\t1599\t51.2295\n-BS2\t1599\t1886\t0\n-BS2\t1886\t1907\t25.6148\n-BS2\t1907\t1943\t0\n-BS2\t1943\t1964\t25.6148\n-BS2\t1964\t2158\t0\n-BS2\t2158\t2159\t25.6148\n-BS2\t2159\t2179\t51.2295\n-BS2\t2179\t2180\t25.6148\n+BS2\t0\t797\t0\n+BS2\t797\t818\t252.016\n+BS2\t818\t1886\t0\n+BS2\t1886\t1907\t252.016\n+BS2\t1907\t2158\t0\n+BS2\t2158\t2159\t252.016\n+BS2\t2159\t2179\t504.032\n+BS2\t2179\t2180\t252.016\n BS2\t2180\t2248\t0\n-BS2\t2248\t2269\t25.6148\n-BS2\t2269\t2303\t0\n-BS2\t2303\t2309\t25.6148\n-BS2\t2309\t2324\t51.2295\n-BS2\t2324\t2329\t25.6148\n-BS2\t2329\t2330\t51.2295\n-BS2\t2330\t2346\t25.6148\n-BS2\t2346\t2350\t51.2295\n-BS2\t2350\t2354\t25.6148\n-BS2\t2354\t2362\t204.918\n-BS2\t2362\t2367\t230.533\n-BS2\t2367\t2375\t204.918\n-BS2\t2375\t2382\t25.6148\n-BS2\t2382\t2383\t76.8443\n-BS2\t2383\t2403\t51.2295\n-BS2\t2403\t2471\t0\n-BS2\t2471\t2492\t128.074\n-BS2\t2492\t2558\t0\n-BS2\t2558\t2579\t25.6148\n-BS2\t2579\t2673\t0\n-BS2\t2673\t2694\t25.6148\n-BS2\t2694\t2801\t0\n-BS2\t2801\t2802\t25.6148\n-BS2\t2802\t2815\t51.2295\n-BS2\t2815\t2819\t76.8443\n-BS2\t2819\t2822\t102.459\n-BS2\t2822\t2823\t76.8443\n-BS2\t2823\t2836\t51.2295\n-BS2\t2836\t2840\t25.6148\n-BS2\t2840\t2858\t0\n-BS2\t2858\t2879\t25.6148\n-BS2\t2879\t2974\t0\n-BS2\t2974\t2979\t25.6148\n-BS2\t2979\t2995\t51.2295\n-BS2\t2995\t3000\t25.6148\n-BS2\t3000\t3078\t0\n-BS2\t3078\t3099\t76.8443\n-BS2\t3099\t3123\t0\n-BS2\t3123\t3131\t25.6148\n-BS2\t3131\t3132\t51.2295\n-BS2\t3132\t3144\t76.8443\n-BS2\t3144\t3152\t51.2295\n-BS2\t3152\t3153\t25.6148\n-BS2\t3153\t3362\t0\n-BS2\t3362\t3383\t51.2295\n-BS2\t3383\t3893\t0\n-BS2\t3893\t3894\t25.6148\n-BS2\t3894\t3908\t51.2295\n-BS2\t3908\t3914\t102.459\n-BS2\t3914\t3915\t76.8443\n-BS2\t3915\t3929\t51.2295\n-BS2\t3929\t3968\t0\n-BS2\t3968\t3989\t25.6148\n-BS2\t3989\t4138\t0\n-BS2\t4138\t4159\t25.6148\n-BS2\t4159\t4187\t0\n-BS2\t4187\t4206\t25.6148\n-BS2\t4206\t4208\t51.2295\n-BS2\t4208\t4227\t25.6148\n-BS2\t4227\t4244\t0\n-BS2\t4244\t4265\t25.6148\n-BS2\t4265\t4313\t0\n-BS2\t4313\t4334\t25.6148\n-BS2\t4334\t4415\t0\n-BS2\t4415\t4433\t102.459\n-BS2\t4433\t4436\t128.074\n-BS2\t4436\t4454\t25.6148\n-BS2\t4454\t4463\t0\n-BS2\t4463\t4464\t76.8443\n-BS2\t4464\t4484\t102.459\n-BS2\t4484\t4485\t25.6148\n-BS2\t4485\t4533\t0\n-BS2\t4533\t4554\t51.2295\n-BS2\t4554\t4668\t0\n-BS2\t4668\t4689\t25.6148\n-BS2\t4689\t4721\t0\n-DMCR1A\t0\t87\t0\n-DMCR1A\t87\t108\t25.6148\n-DMCR1A\t108\t979\t0\n-DMCR1A\t979\t1000\t76.8443\n-DMCR1A\t1000\t1161\t0\n-DMCR1A\t1161\t1182\t25.6148\n-DMCR1A\t1182\t1859\t0\n-DMCR1A\t1859\t1880\t25.6148\n+BS2\t2248\t2269\t252.016\n+BS2\t2269\t2329\t0\n+BS2\t2329\t2350\t252.016\n+BS2\t2350\t2558\t0\n+BS2\t2558\t2579\t252.016\n+BS2\t2579\t4244\t0\n+BS2\t4244\t4265\t252.016\n+BS2\t4265\t4533\t0\n+BS2\t4533\t4554\t252.016\n+BS2\t4554\t4721\t0\n+DMCR1A\t0\t1859\t0\n+DMCR1A\t1859\t1880\t252.016\n DMCR1A\t1880\t4470\t0\n-DMRT1B\t0\t424\t0\n-DMRT1B\t424\t445\t25.6148\n-DMRT1B\t445\t564\t0\n-DMRT1B\t564\t585\t25.6148\n-DMRT1B\t585\t798\t0\n-DMRT1B\t798\t819\t25.6148\n-DMRT1B\t819\t1226\t0\n-DMRT1B\t1226\t1247\t25.6148\n-DMRT1B\t1247\t1280\t0\n-DMRT1B\t1280\t1301\t25.6148\n-DMRT1B\t1301\t1316\t0\n-DMRT1B\t1316\t1337\t25.6148\n-DMRT1B\t1337\t1346\t0\n-DMRT1B\t1346\t1361\t25.6148\n-DMRT1B\t1361\t1363\t51.2295\n-DMRT1B\t1363\t1367\t76.8443\n-DMRT1B\t1367\t1370\t51.2295\n-DMRT1B\t1370\t1373\t76.8443\n-DMRT1B\t1373\t1382\t102.459\n-DMRT1B\t1382\t1384\t76.8443\n-DMRT1B\t1384\t1391\t51.2295\n-DMRT1B\t1391\t1394\t25.6148\n-DMRT1B\t1394\t5183\t0\n-FW\t0\t337\t0\n-FW\t337\t358\t25.6148\n-FW\t358\t400\t0\n-FW\t400\t411\t25.6148\n-FW\t411\t421\t51.2295\n-FW\t421\t432\t25.6148\n-FW\t432\t438\t0\n-FW\t438\t450\t25.6148\n-FW'..b'2295\n-FW\t3737\t3745\t0\n-FW\t3745\t3750\t25.6148\n-FW\t3750\t3756\t51.2295\n-FW\t3756\t3759\t76.8443\n-FW\t3759\t3766\t102.459\n-FW\t3766\t3771\t76.8443\n-FW\t3771\t3777\t51.2295\n-FW\t3777\t3780\t25.6148\n-FW\t3780\t3916\t0\n-FW\t3916\t3937\t25.6148\n-FW\t3937\t3950\t0\n-FW\t3950\t3971\t25.6148\n-FW\t3971\t3994\t0\n-FW\t3994\t4008\t25.6148\n-FW\t4008\t4010\t51.2295\n-FW\t4010\t4013\t307.377\n-FW\t4013\t4014\t332.992\n-FW\t4014\t4015\t358.607\n-FW\t4015\t4029\t332.992\n-FW\t4029\t4030\t307.377\n-FW\t4030\t4031\t384.221\n-FW\t4031\t4034\t128.074\n-FW\t4034\t4035\t102.459\n-FW\t4035\t4044\t76.8443\n-FW\t4044\t4051\t102.459\n-FW\t4051\t4065\t25.6148\n-FW\t4065\t4089\t0\n-FW\t4089\t4098\t25.6148\n-FW\t4098\t4100\t51.2295\n-FW\t4100\t4110\t76.8443\n-FW\t4110\t4119\t51.2295\n-FW\t4119\t4121\t25.6148\n-FW\t4121\t4169\t0\n-FW\t4169\t4171\t25.6148\n-FW\t4171\t4174\t51.2295\n-FW\t4174\t4179\t76.8443\n-FW\t4179\t4186\t102.459\n-FW\t4186\t4190\t128.074\n-FW\t4190\t4192\t102.459\n-FW\t4192\t4195\t76.8443\n-FW\t4195\t4200\t51.2295\n-FW\t4200\t4207\t25.6148\n-FW\t4207\t4235\t0\n-FW\t4235\t4236\t51.2295\n-FW\t4236\t4238\t76.8443\n-FW\t4238\t4242\t102.459\n-FW\t4242\t4248\t128.074\n-FW\t4248\t4256\t153.689\n-FW\t4256\t4257\t128.074\n-FW\t4257\t4259\t102.459\n-FW\t4259\t4263\t76.8443\n-FW\t4263\t4269\t51.2295\n-FW\t4269\t4277\t25.6148\n-FW\t4277\t4322\t0\n-FW\t4322\t4343\t204.918\n-FW\t4343\t4346\t0\n-FW\t4346\t4347\t51.2295\n-FW\t4347\t4349\t76.8443\n-FW\t4349\t4355\t153.689\n-FW\t4355\t4366\t179.303\n-FW\t4366\t4367\t204.918\n-FW\t4367\t4368\t153.689\n-FW\t4368\t4370\t128.074\n-FW\t4370\t4376\t51.2295\n-FW\t4376\t4387\t25.6148\n-FW\t4387\t4499\t0\n-FW\t4499\t4520\t25.6148\n-FW\t4520\t4529\t0\n-FW\t4529\t4530\t153.689\n-FW\t4530\t4531\t179.303\n-FW\t4531\t4550\t204.918\n-FW\t4550\t4551\t51.2295\n-FW\t4551\t4552\t25.6148\n-FW\t4552\t4692\t0\n-G6_DM\t0\t1190\t0\n-G6_DM\t1190\t1211\t25.6148\n-G6_DM\t1211\t1225\t0\n-G6_DM\t1225\t1232\t25.6148\n-G6_DM\t1232\t1246\t51.2295\n-G6_DM\t1246\t1253\t25.6148\n-G6_DM\t1253\t1258\t0\n-G6_DM\t1258\t1279\t25.6148\n-G6_DM\t1279\t1310\t0\n-G6_DM\t1310\t1331\t25.6148\n-G6_DM\t1331\t1334\t0\n-G6_DM\t1334\t1350\t102.459\n-G6_DM\t1350\t1355\t128.074\n-G6_DM\t1355\t1371\t25.6148\n-G6_DM\t1371\t1413\t0\n-G6_DM\t1413\t1434\t25.6148\n-G6_DM\t1434\t1489\t0\n-G6_DM\t1489\t1510\t25.6148\n-G6_DM\t1510\t1533\t0\n-G6_DM\t1533\t1554\t204.918\n-G6_DM\t1554\t1620\t0\n-G6_DM\t1620\t1629\t25.6148\n-G6_DM\t1629\t1641\t51.2295\n-G6_DM\t1641\t1650\t25.6148\n-G6_DM\t1650\t1665\t0\n-G6_DM\t1665\t1667\t25.6148\n-G6_DM\t1667\t1673\t51.2295\n-G6_DM\t1673\t1686\t76.8443\n-G6_DM\t1686\t1688\t51.2295\n-G6_DM\t1688\t1694\t25.6148\n-G6_DM\t1694\t1702\t0\n-G6_DM\t1702\t1723\t51.2295\n+FW\t3547\t3568\t252.016\n+FW\t3568\t3994\t0\n+FW\t3994\t4010\t252.016\n+FW\t4010\t4015\t504.032\n+FW\t4015\t4031\t252.016\n+FW\t4031\t4242\t0\n+FW\t4242\t4263\t252.016\n+FW\t4263\t4322\t0\n+FW\t4322\t4343\t252.016\n+FW\t4343\t4355\t0\n+FW\t4355\t4376\t252.016\n+FW\t4376\t4529\t0\n+FW\t4529\t4550\t252.016\n+FW\t4550\t4692\t0\n+G6_DM\t0\t1533\t0\n+G6_DM\t1533\t1554\t504.032\n+G6_DM\t1554\t1665\t0\n+G6_DM\t1665\t1686\t252.016\n+G6_DM\t1686\t1702\t0\n+G6_DM\t1702\t1723\t252.016\n G6_DM\t1723\t2042\t0\n-Gypsy2-LTR_DM\t0\t90\t0\n-Gypsy2-LTR_DM\t90\t111\t25.6148\n-Gypsy2-LTR_DM\t111\t122\t0\n-Gypsy2-LTR_DM\t122\t134\t25.6148\n-Gypsy2-LTR_DM\t134\t136\t51.2295\n-Gypsy2-LTR_DM\t136\t143\t76.8443\n-Gypsy2-LTR_DM\t143\t146\t51.2295\n-Gypsy2-LTR_DM\t146\t155\t76.8443\n-Gypsy2-LTR_DM\t155\t157\t51.2295\n-Gypsy2-LTR_DM\t157\t164\t102.459\n-Gypsy2-LTR_DM\t164\t167\t128.074\n-Gypsy2-LTR_DM\t167\t178\t102.459\n-Gypsy2-LTR_DM\t178\t185\t25.6148\n-Gypsy2-LTR_DM\t185\t201\t0\n-Gypsy2-LTR_DM\t201\t207\t25.6148\n-Gypsy2-LTR_DM\t207\t222\t76.8443\n-Gypsy2-LTR_DM\t222\t228\t51.2295\n-Gypsy2-LTR_DM\t228\t258\t0\n-Gypsy2-LTR_DM\t258\t268\t25.6148\n-Gypsy2-LTR_DM\t268\t279\t51.2295\n-Gypsy2-LTR_DM\t279\t289\t25.6148\n-Gypsy2-LTR_DM\t289\t338\t0\n-I_DM\t0\t4908\t0\n-I_DM\t4908\t4929\t25.6148\n-I_DM\t4929\t5374\t0\n-MAX_I\t0\t119\t0\n-MAX_I\t119\t140\t25.6148\n-MAX_I\t140\t7914\t0\n+Gypsy2-LTR_DM\t0\t258\t0\n+Gypsy2-LTR_DM\t258\t279\t252.016\n+Gypsy2-LTR_DM\t279\t338\t0\n MAX_LTR\t0\t84\t0\n-MAX_LTR\t84\t105\t51.2295\n-MAX_LTR\t105\t138\t0\n-MAX_LTR\t138\t159\t25.6148\n-MAX_LTR\t159\t321\t0\n-PROTOP\t0\t449\t0\n-PROTOP\t449\t470\t25.6148\n-PROTOP\t470\t2499\t0\n-PROTOP\t2499\t2520\t25.6148\n-PROTOP\t2520\t2745\t0\n-PROTOP\t2745\t2746\t51.2295\n-PROTOP\t2746\t2752\t128.074\n-PROTOP\t2752\t2766\t153.689\n-PROTOP\t2766\t2767\t102.459\n-PROTOP\t2767\t2773\t25.6148\n-PROTOP\t2773\t3258\t0\n-PROTOP\t3258\t3279\t51.2295\n-PROTOP\t3279\t4480\t0\n+MAX_LTR\t84\t105\t252.016\n+MAX_LTR\t105\t321\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 21 67.55 910.83 333333.33 687.85 15 6 86.6666666666667 0 50 50 -BATUMI_LTR 5 470.86 216.86 79365.08 163.77 1 4 0 0 0 25 -BS2 423 2295.07 18346.63 6714285.71 13855.22 83 340 38.5542168674699 40.9638554216867 3.82352941176471 22.6470588235294 +BATUMI_I 3 94.95 1284.25 333333.33 974.03 0 3 0 0 66.6666666666667 66.6666666666667 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 39 2081.90 16695.21 4333333.33 12662.34 9 30 22.2222222222222 11.1111111111111 0 40 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 14 80.23 607.22 222222.22 458.57 6 8 50 16.6666666666667 0 0 -DMRT1B 27 133.44 1171.06 428571.43 884.38 11 16 36.3636363636364 18.1818181818182 18.75 18.75 -FW 1588 8669.27 68875.78 25206349.21 52014.41 407 1181 28.992628992629 40.2948402948403 12.0237087214225 20.9991532599492 -G6_DM 118 1480.19 5117.97 1873015.87 3865.05 27 91 22.2222222222222 66.6666666666667 5.49450549450549 17.5824175824176 +DMCR1A 1 56.38 428.08 111111.11 324.68 1 0 0 0 0 0 +DMRT1B 2 97.25 856.16 222222.22 649.35 1 1 0 100 0 0 +FW 161 8647.61 68921.23 17888888.89 52272.73 31 130 25.8064516129032 54.8387096774194 10.7692307692308 16.1538461538462 +G6_DM 16 1974.66 6849.32 1777777.78 5194.81 4 12 25 100 0 16.6666666666667 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 30 2273.50 1301.18 476190.48 982.64 14 16 35.7142857142857 14.2857142857143 0 25 -I_DM 5 23.83 216.86 79365.08 163.77 1 4 0 0 0 25 -MAX_I 8 25.89 346.98 126984.13 262.04 1 7 100 0 28.5714285714286 0 -MAX_LTR 12 957.56 520.47 190476.19 393.06 3 9 33.3333333333333 0 22.2222222222222 0 -PROTOP 16 91.48 693.96 253968.25 524.07 10 6 80 50 0 16.6666666666667 +Gypsy2-LTR_DM 4 2982.44 1712.33 444444.44 1298.70 1 3 100 100 0 33.3333333333333 +I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_LTR 4 3140.39 1712.33 444444.44 1298.70 1 3 0 0 33.3333333333333 0 +PROTOP 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_mismatches.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_mismatches.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_mismatches.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 15 48.25 650.59 238095.24 491.32 12 3 91.6666666666667 0 66.6666666666667 33.3333333333333 -BATUMI_LTR 4 376.69 173.49 63492.06 131.02 1 3 0 0 0 33.3333333333333 -BS2 8 43.41 346.98 126984.13 262.04 4 4 25 25 0 50 +BATUMI_I 2 63.30 856.16 222222.22 649.35 0 2 0 0 50 50 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 4 22.92 173.49 63492.06 131.02 1 3 0 0 0 0 -DMRT1B 16 79.07 693.96 253968.25 524.07 6 10 33.3333333333333 16.6666666666667 30 20 -FW 12 65.51 520.47 190476.19 393.06 3 9 33.3333333333333 33.3333333333333 0 22.2222222222222 +DMCR1A 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMRT1B 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FW 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 Gypsy2-LTR_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -I_DM 3 14.30 130.12 47619.05 98.26 0 3 0 0 0 33.3333333333333 -MAX_I 3 9.71 130.12 47619.05 98.26 0 3 0 0 33.3333333333333 0 -MAX_LTR 5 398.98 216.86 79365.08 163.77 0 5 0 0 40 0 -PROTOP 7 40.02 303.61 111111.11 229.28 4 3 50 75 0 33.3333333333333 +I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_LTR 1 785.10 428.08 111111.11 324.68 0 1 0 0 100 0 +PROTOP 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_nomismatches.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_nomismatches.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_nomismatches.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,18 +1,18 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -BATUMI_I 6 19.30 260.24 95238.10 196.53 3 3 66.6666666666667 0 33.3333333333333 66.6666666666667 -BATUMI_LTR 1 94.17 43.37 15873.02 32.75 0 1 0 0 0 0 -BS2 415 2251.67 17999.65 6587301.59 13593.19 79 336 39.2405063291139 41.7721518987342 3.86904761904762 22.3214285714286 +BATUMI_I 1 31.65 428.08 111111.11 324.68 0 1 0 0 100 100 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 39 2081.90 16695.21 4333333.33 12662.34 9 30 22.2222222222222 11.1111111111111 0 40 COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -DMCR1A 10 57.30 433.73 158730.16 327.55 5 5 60 20 0 0 -DMRT1B 11 54.36 477.10 174603.17 360.30 5 6 40 20 0 16.6666666666667 -FW 1576 8603.76 68355.31 25015873.02 51621.36 404 1172 28.960396039604 40.3465346534653 12.1160409556314 20.9897610921502 -G6_DM 118 1480.19 5117.97 1873015.87 3865.05 27 91 22.2222222222222 66.6666666666667 5.49450549450549 17.5824175824176 +DMCR1A 1 56.38 428.08 111111.11 324.68 1 0 0 0 0 0 +DMRT1B 2 97.25 856.16 222222.22 649.35 1 1 0 100 0 0 +FW 161 8647.61 68921.23 17888888.89 52272.73 31 130 25.8064516129032 54.8387096774194 10.7692307692308 16.1538461538462 +G6_DM 16 1974.66 6849.32 1777777.78 5194.81 4 12 25 100 0 16.6666666666667 Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 -Gypsy2-LTR_DM 30 2273.50 1301.18 476190.48 982.64 14 16 35.7142857142857 14.2857142857143 0 25 -I_DM 2 9.53 86.75 31746.03 65.51 1 1 0 0 0 0 -MAX_I 5 16.18 216.86 79365.08 163.77 1 4 100 0 25 0 -MAX_LTR 7 558.58 303.61 111111.11 229.28 3 4 33.3333333333333 0 0 0 -PROTOP 9 51.46 390.35 142857.14 294.79 6 3 100 33.3333333333333 0 0 +Gypsy2-LTR_DM 4 2982.44 1712.33 444444.44 1298.70 1 3 100 100 0 33.3333333333333 +I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_LTR 3 2355.29 1284.25 333333.33 974.03 1 2 0 0 0 0 +PROTOP 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_sorted.bam |
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| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_sorted.bam has changed |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_unique_sorted.bam |
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| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_unique_sorted.bam has changed |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
| b |
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chrom_1\t84969\t85094\t0\n-chrom_1\t85094\t85115\t51.2295\n-chrom_1\t85115\t85355\t0\n-chrom_1\t85355\t85376\t25.6148\n-chrom_1\t85376\t85407\t0\n-chrom_1\t85407\t85428\t25.6148\n-chrom_1\t85428\t85513\t0\n-chrom_1\t85513\t85534\t25.6148\n-chrom_1\t85534\t86344\t0\n-chrom_1\t86344\t86362\t51.2295\n-chrom_1\t86362\t86365\t76.8443\n-chrom_1\t86365\t86383\t25.6148\n-chrom_1\t86383\t86432\t0\n-chrom_1\t86432\t86453\t25.6148\n-chrom_1\t86453\t86950\t0\n-chrom_1\t86950\t86971\t25.6148\n-chrom_1\t86971\t87113\t0\n-chrom_1\t87113\t87134\t25.6148\n-chrom_1\t87134\t88633\t0\n-chrom_1\t88633\t88654\t25.6148\n-chrom_1\t88654\t89597\t0\n-chrom_1\t89597\t89618\t25.6148\n-chrom_1\t89618\t89999\t0\n-chrom_4\t0\t1151\t0\n-chrom_4\t1151\t1172\t25.6148\n-chrom_4\t1172\t1733\t0\n-chrom_4\t1733\t1754\t25.6148\n-chrom_4\t1754\t2000\t0\n-chrom_5\t0\t1648\t0\n-chrom_5\t1648\t1669\t25.6148\n-chrom_5\t1669\t1782\t0\n-chrom_5\t1782\t1803\t25.6148\n+chrom_1\t85094\t85115\t252.016\n+chrom_1\t85115\t86344\t0\n+chrom_1\t86344\t86365\t252.016\n+chrom_1\t86365\t89999\t0\n+chrom_5\t0\t1782\t0\n+chrom_5\t1782\t1803\t252.016\n chrom_5\t1803\t1999\t0\n-chrom_6\t0\t885\t0\n-chrom_6\t885\t906\t25.6148\n-chrom_6\t906\t1109\t0\n-chrom_6\t1109\t1115\t25.6148\n-chrom_6\t1115\t1130\t51.2295\n-chrom_6\t1130\t1136\t25.6148\n-chrom_6\t1136\t3999\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_minus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_minus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_minus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_plus.bedgraph --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_plus.bedgraph Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_plus.bedgraph Thu Jan 24 13:09:46 2019 -0500 |
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chrom_1\t84969\t85094\t0\n-chrom_1\t85094\t85115\t51.2295\n-chrom_1\t85115\t85355\t0\n-chrom_1\t85355\t85376\t25.6148\n-chrom_1\t85376\t85407\t0\n-chrom_1\t85407\t85428\t25.6148\n-chrom_1\t85428\t85513\t0\n-chrom_1\t85513\t85534\t25.6148\n-chrom_1\t85534\t86344\t0\n-chrom_1\t86344\t86362\t51.2295\n-chrom_1\t86362\t86365\t76.8443\n-chrom_1\t86365\t86383\t25.6148\n-chrom_1\t86383\t86432\t0\n-chrom_1\t86432\t86453\t25.6148\n-chrom_1\t86453\t86950\t0\n-chrom_1\t86950\t86971\t25.6148\n-chrom_1\t86971\t87113\t0\n-chrom_1\t87113\t87134\t25.6148\n-chrom_1\t87134\t88633\t0\n-chrom_1\t88633\t88654\t25.6148\n-chrom_1\t88654\t89597\t0\n-chrom_1\t89597\t89618\t25.6148\n-chrom_1\t89618\t89999\t0\n-chrom_4\t0\t1151\t0\n-chrom_4\t1151\t1172\t25.6148\n-chrom_4\t1172\t2000\t0\n-chrom_5\t0\t1648\t0\n-chrom_5\t1648\t1669\t25.6148\n-chrom_5\t1669\t1782\t0\n-chrom_5\t1782\t1803\t25.6148\n+chrom_1\t85094\t85115\t252.016\n+chrom_1\t85115\t86344\t0\n+chrom_1\t86344\t86365\t252.016\n+chrom_1\t86365\t89999\t0\n+chrom_5\t0\t1782\t0\n+chrom_5\t1782\t1803\t252.016\n chrom_5\t1803\t1999\t0\n-chrom_6\t0\t885\t0\n-chrom_6\t885\t906\t25.6148\n-chrom_6\t906\t1109\t0\n-chrom_6\t1109\t1115\t25.6148\n-chrom_6\t1115\t1130\t51.2295\n-chrom_6\t1130\t1136\t25.6148\n-chrom_6\t1136\t3999\t0\n' |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_reads_counts.txt --- a/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_reads_counts.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_reads_counts.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| @@ -1,14 +1,14 @@ ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A -FBtr0073689 5 33.75 216.86 79365.08 163.77 2 3 50 100 0 33.3333333333333 -FBtr0078666 22 232.29 954.20 349206.35 720.60 11 11 81.8181818181818 18.1818181818182 18.1818181818182 0 -FBtr0086080 12 77.64 520.47 190476.19 393.06 4 8 75 75 0 75 -FBtr0089125 6 21.25 260.24 95238.10 196.53 0 6 0 0 16.6666666666667 66.6666666666667 -FBtr0089196 17 99.51 737.34 269841.27 556.83 11 6 81.8181818181818 18.1818181818182 16.6666666666667 33.3333333333333 -FBtr0113825 2 17.53 86.75 31746.03 65.51 1 1 0 0 0 0 -FBtr0114365 16 64.07 693.96 253968.25 524.07 8 8 37.5 12.5 0 12.5 -FBtr0310270 36 300.47 1561.42 571428.57 1179.17 0 36 0 0 0 16.6666666666667 -FBtr0332656 1 7.35 43.37 15873.02 32.75 1 0 100 0 0 0 -FBtr0345361 10 198.72 433.73 158730.16 327.55 10 0 100 0 0 0 -FBtr0345575 16 138.50 693.96 253968.25 524.07 4 12 75 50 16.6666666666667 33.3333333333333 -FBtr0345650 11 34.06 477.10 174603.17 360.30 9 2 44.4444444444444 0 0 50 -FBtr0346343 3 12.31 130.12 47619.05 98.26 3 0 66.6666666666667 33.3333333333333 0 0 +FBtr0073689 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0078666 3 311.64 1284.25 333333.33 974.03 1 2 100 0 0 0 +FBtr0086080 2 127.31 856.16 222222.22 649.35 1 1 100 100 0 100 +FBtr0089125 3 104.56 1284.25 333333.33 974.03 0 3 0 0 33.3333333333333 66.6666666666667 +FBtr0089196 3 172.77 1284.25 333333.33 974.03 2 1 100 50 0 0 +FBtr0113825 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0114365 2 78.79 856.16 222222.22 649.35 1 1 0 100 0 0 +FBtr0310270 6 492.70 2568.49 666666.67 1948.05 0 6 0 0 0 16.6666666666667 +FBtr0332656 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0345361 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0345575 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0345650 1 30.47 428.08 111111.11 324.68 1 0 0 0 0 0 +FBtr0346343 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_unique_sorted.bam has changed |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err --- a/test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err Thu Jan 24 13:09:46 2019 -0500 |
| [ |
| @@ -1,6 +1,6 @@ -[bwa_aln_core] calculate SA coordinate... 0.26 sec +[bwa_aln_core] calculate SA coordinate... 0.07 sec [bwa_aln_core] write to the disk... 0.00 sec -[bwa_aln_core] 30530 sequences have been processed. +[bwa_aln_core] 3080 sequences have been processed. [main] Version: 0.7.12-r1039 -[main] CMD: bwa aln -t 8 -n 0 /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq -[main] Real time: 0.120 sec; CPU: 0.308 sec +[main] CMD: bwa aln -t 8 -n 0 /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq +[main] Real time: 0.019 sec; CPU: 0.076 sec |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err --- a/test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err Thu Jan 24 13:09:46 2019 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -[bwa_aln_core] convert to sequence coordinate... 0.01 sec +[bwa_aln_core] convert to sequence coordinate... 0.00 sec [bwa_aln_core] refine gapped alignments... 0.00 sec -[bwa_aln_core] print alignments... 0.02 sec -[bwa_aln_core] 30530 sequences have been processed. +[bwa_aln_core] print alignments... 0.00 sec +[bwa_aln_core] 3080 sequences have been processed. [main] Version: 0.7.12-r1039 -[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa /dev/stdin /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq -[main] Real time: 0.225 sec; CPU: 0.080 sec +[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa /dev/stdin /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq +[main] Real time: 0.034 sec; CPU: 0.016 sec |
| b |
| diff -r e6c4f3e96e47 -r 11708af40030 test-data/res_files/report.txt --- a/test-data/res_files/report.txt Thu Jan 17 09:56:52 2019 -0500 +++ b/test-data/res_files/report.txt Thu Jan 24 13:09:46 2019 -0500 |
| b |
| b"@@ -1,74 +1,74 @@\n-Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa\n-Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35114.dat_symlink.fa\n-Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa\n-Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35113.dat_symlink.fa\n-Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa\n-Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa\n-Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35114.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35112.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35113.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35116.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa\n -----------------------------\n-bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/dataset_35117_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/dataset_35117_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam'\n-Parsing /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam file\n-\treads: 45570\n-\tmappers: 39040\n-\tunique mappers: 38991\n+bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/dataset_35773_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/dataset_35773_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_dire"..b"xy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq just finished with PID 14243 and exit code: 0\n-** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/piRNAs.fastq started, pid: 14463\n-** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/siRNAs.fastq just finished with PID 14405 and exit code: 0\n-** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/piRNAs.fastq just finished with PID 14463 and exit code: 0\n-ping_pong_partners /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups//piRNAs/TEs.sam /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/PPPartners/\n-Fastq fork : /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat started, pid: 14070\n-Fastq fork /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat just finished with PID 14070 and exit code: 0\n+bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam'\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq started, pid: 22279\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq just finished with PID 22279 and exit code: 0\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/siRNAs.fastq started, pid: 22405\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq just finished with PID 22278 and exit code: 0\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/piRNAs.fastq started, pid: 22464\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/siRNAs.fastq just finished with PID 22405 and exit code: 0\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/piRNAs.fastq just finished with PID 22464 and exit code: 0\n+ping_pong_partners /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups//piRNAs/TEs.sam /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/PPPartners/\n+Fastq fork : /data/galaxy/galaxy-server/database/files/035/dataset_35773.dat started, pid: 22106\n+Fastq fork /data/galaxy/galaxy-server/database/files/035/dataset_35773.dat just finished with PID 22106 and exit code: 0\n Job done!\n" |
