Mercurial > repos > iuc > umi_tools_extract
changeset 0:418b961e0576 draft
planemo upload commit 453bb3b44d9f27908cbe2677378da88b9f77b5cf
author | iuc |
---|---|
date | Thu, 10 Aug 2017 06:37:09 -0400 |
parents | |
children | 79436b3019e9 |
files | test-data/out_R1.fastq.gz test-data/out_R2.fastq.gz test-data/out_SE.fastq test-data/out_paired.log test-data/out_single.log test-data/t_R1.fastq test-data/t_R1.fastq.gz test-data/t_R2.fastq.gz umi-tools_extract.xml |
diffstat | 9 files changed, 1151 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_SE.fastq Thu Aug 10 06:37:09 2017 -0400 @@ -0,0 +1,288 @@ +@HISEQ:105:C2UE1ACXX:3:1101:11160:2245_TTA 1:N:0:CAGATC +AAAAGTAGTTAATATATTAGATTTGTTTGATAGTGGTAGTATATATTTTTTATTTTAGTATTTAGGAGGTAGAGGTAGATGAATTTTTGAGTTTAAAG ++ +BBBFFFFBFFFFFIIIIIIBIIIIBIFFBFIIBBFFFFFFFFIIIIIIIIIIIIIIIBFIIIIIB7BBBFBBFFFF77<F7BFFFFFF7B7BBFFFF7 +@HISEQ:105:C2UE1ACXX:3:1101:19467:2281_TTT 1:N:0:CATATC +TTGGTTAGGGTGAGATGTATAGTTTGGATTTTAGTGATTTTTGTAAAGGGGGAAAAGAATGGAGTTTTGGGTGTAGTGAGAGGTTATAGGAGTAGGGA ++ +<B<<FFFBBFFFFFFFFFIFIBFFI<<BFFFIIBBBFFIIIIBFFIIBBF7BBFFFBFFF77BBFBFF777BBBBBB<<<B<7<7BBF77<7<70000 +@HISEQ:105:C2UE1ACXX:3:1101:7009:2740_TAG 1:N:0:CAGATC +AAGTTTTGTTTTTTATTTGGAGGTTATGGAATGTTAAGTAAGGTTTTTTTGGGTTTTGTTATTTATTTGATAATTGTGATTGTAATGTTAATAAGGGA ++ +BBBFFFFFFFFFFIIIIIB<FFFFFFIBBFIIFFFIIFIIIFFIFFIIII<0<BBFFBFFFFFFFFFF<BBFFFF<BBBBF7BFFF<BBFFFFF<00< +@HISEQ:105:C2UE1ACXX:3:1101:19067:2707_TTT 1:N:0:CAGATC +GTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTAGAAAATTTTTTTTAGTAAGATAGATTTTAAAGGGTTTGTTTTTTTTTTTTTTTTTT ++ +BBBFFFFFFFFFBBFFFFIIIFIFFIFFIIIIIIIFFFFFB7'0<B0<BBFF'7<0'0<<''0<'0'0<BBB<<B'7'0'0'0<BFFFFFFFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:4999:3182_AGG 1:N:0:CAGATC +GTTTTATGAGGATTTTAGGGGAGTGATTGTTTAAAGTTTATAAGATTTATGATTTATATATAGTTAGAATAGTATGTGTTAAATAAATATAAAGGGAG ++ +<BBFFFFBFFFFFFIIFBBBFFFIIFFIBFFIFIIBFFIIIIIFFIIIIIBFFIIIIIIIIIBFFIBFIII<FFFBFBFFFFFFFFFFFFFFF<07<7 +@HISEQ:105:C2UE1ACXX:3:1101:2300:3263_GTT 1:N:0:TAGATC +TTATTTTTAATAAAATTTTTATTATTTAATTTATTAGTTAATATTTAGGAGTTTTATGTTGTGGTAAAATTTTGTTAGAGAGATAGAGAAAGTATTTA ++ +BBBFFFFFFFFBFFIIIIIIBIBBFFI0<FFFBFF70B00<'0<FFFBBBBFF''0B0BB000'7BBFFFFII'<BF0<'<''07'70BBF'7BBBFB +@HISEQ:105:C2UE1ACXX:3:1101:5605:3427_AGA 1:N:0:CAGATC +AGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAGATAAGAAGTGGTTCGGTTATAGGATTTGTTTTAGATTTTTAGATTTTTTTGTGT ++ +BBBFBFFFFFFFFFFBFFFFIIIIIIIBFFFBFFIBFFIIIIIFFIIIFFIBF7BFBFBBFFIFF<<FFFFBBFFBF0<BFFFFF7<BFFFFFF0B7B +@HISEQ:105:C2UE1ACXX:3:1101:8129:3589_GAT 1:N:0:CAGATC +TTTTAGTTTTTAGTTAGGATTATACGTTTATTGTGATAAAAGAGTTTTTTGATTTATCGGGTTATGTTAGGGTTTATTGATATTAGGGAATTTGAAGA ++ +BBBFFBFFFFFFBFFFBBFIIFIIFBFFFFII<BBFFFIIIBFFIFIIIIBBFFIIII<7<FBFF<FBF<7<BBFFFF7<BFFFF700<BBFF0<B'< +@HISEQ:105:C2UE1ACXX:3:1101:14304:3866_TAA 1:N:0:CAGATC +GTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAATGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAA ++ +<BBFFFFFFFFFFFFFFFFII<BBFFFBFFIFBFFBFFFII7FFFFFFFIF<BFIIII<F<BBFIFBFB7<BFFFBBBBBF777<B7BBF7B<BB7BB +@HISEQ:105:C2UE1ACXX:3:1101:12720:4398_AGT 1:N:0:CAGATC +GTATGTGTGTGTGTGTGTGTATTTAATTGAAGTTGGGTTTGGTGATATATATGTTTAATTTTAGTATTTTAGTGGTAGAGGTAGGTTAATTTTTGTTG ++ +<BBFBFFFFFFFFIFIFIFFFFFIIFII0BFBFFB7BFFF<BFFFFIIIIIIBFIIIIFIIII<FIFIIIFBFBBFB7B<<BB7<B<BFFFFFF0<B0 +@HISEQ:105:C2UE1ACXX:3:1101:14945:4439_ATT 1:N:0:CAGATC +AGTGTTGAGTGGAGTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTT ++ +BBBBFFBFFFFFFFFFFIIBIFFIFFBFFIIIIBFFIIIIIIBFFIIIBFFBFFFIIIFBFFBFBFFIIIIIFFFBBF77BBFFF7BBFF<BBF<<BF +@HISEQ:105:C2UE1ACXX:3:1101:8616:4508_AGG 1:N:0:CAGATC +AGAAATTTTGGGGGTGTAGGAGTGGTAGGATAGGAGTGTTGTTTTGTAATAGTTTTTTTTGAGGTTTAATAGGTAGGGTAGTTATTTTTAGTATTGTA ++ +BBBFFFFFFBBBFFFIIFFFIFFFIIFFIIFIFBFFFIIF<FBFI<FFIIIBFFFFFFFF077<B<BBBFF<<BBBBBB<7B<BFFFFFF0BBFF0<B +@HISEQ:105:C2UE1ACXX:3:1101:18975:4834_GAG 1:N:0:CAGATC +TATAAATGGTAATTTTGTAATTTAAAGATTTAAAAGTAATTATTGGTAATAGTTATTTGTGGGAGGTTGAGGTAGGGGGATTTTTGTAGAGATCGGAA ++ +BBBFFFFBBFFFFIIIBFIIIIIFIIFFFFIFIIIBFIIIIIIIB<FFIFIBFFFIIIBFFBFFFII<<BFBFFFFIFF<BBBFF0BB7<<<BF707B +@HISEQ:105:C2UE1ACXX:3:1101:4984:5374_TTG 1:N:0:CAGATC +TGTATCGAGGTTTGAATGAGAGTGGTATTTTTGTTATTTGTTAGTTAATGGTTTTGAGTATTAGTTTGGAAAATGATAATAAGTATTAGTTGAGGTGT ++ +B<BFFFBFFFFBF<FFFBFFFFFFFIFFFIII<BFFIIIBFFFFFFIIIBBFFFIBBBFFFIIBFFF<<BFFFFBBFFFFFF<BBFFF<BB7<7<BBB +@HISEQ:105:C2UE1ACXX:3:1101:12336:6058_TTT 1:N:0:CAGATC +ATTTAGATGATGGTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTTTAAAAAATTTTTTTTATAAAAATAAATTTTAAAGGGTTTTTTTT ++ +BBBFFBFFBFFBBFFFIIIIIIIIBFFIIIIIIIIBFFFFIIIIIFFFFFFFFF700<BF0BBFFF0<70''00'0'000'<<'<B<00'0'00007< +@HISEQ:105:C2UE1ACXX:3:1101:5999:6265_ATG 1:N:0:CAGATC +TATATTGTTATATATTTGTGTTTTTTTTGAATTTATTTTTTGTTTATTAGTTTTTGTGGTTGATAGGGTTTTTGGATATTGGGTTGTTTTTATATATA ++ +BBBFFFBFFFFFFIIIIBIFIFIIIIII<BFFIIFIIIIII7BFFFIIFBFFIII<B<BFB<BBF<BBBBBFF00<BFFF700B<7<BFFFFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:5836:6568_TTT 1:N:0:CAGATC +ATTTGGATGTTAAGGATTGGTTTTTTTTTTGATTTAGGGTATTGTTAGATAGTATAGATTTTACGGAGTTTTGTATTTGAAAGGTTGTTGGTATGTTT ++ +BBBFBBFFFFFFFFFFFFBFIFIIIIIIII'0<FFB<BBFFBF7BFF7BFF<BBFF<BFFFFFF<<BBFBBF7BBBFF'<BB0'<B0<B0'7<B<BFF +@HISEQ:105:C2UE1ACXX:3:1101:12432:6996_GAT 1:N:0:CAGATC +AAGTTATTTATGAGATTAGTTTATAGTAAATTAAAAAGGGTCTTAGTATTTTGATTATGAAATTAATTATTTTAGTAATATTTGAAGTTGTAATTTTA ++ +BBBFFFFFFFFBFBFFIIBIIIIIIBFIIIIIIIIIIFBFFFFFIFFIIIIIBFFIIIBFIIIIIIIIIIIIIIBFFIIIIII7BF<BF<BFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:2440:7931_TGA 1:N:0:CAGATC +ATTTGAAAAGTGTTATAGATATTAGAAAGGTATGGAGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAAGATCGGAAGAGCACACGTC ++ +BBBFBFFFFFFFFFIIIBFFIIIIBFFIBBFFIBBFFIFFFFFFFIFFIBBFFFFFFFIFIIBFFIBFFFBFFFFFFFF7BBF70<B0<7<BBBF0<B +@HISEQ:105:C2UE1ACXX:3:1101:6407:7896_ATC 1:N:0:CAGATC +TTTATAGGTTTGGGTTGAGGATATGTATTGGGAGTTATTAGAGGGTTATAGTTAGGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC ++ +BBBFFFBBFFF<BBFFBFFFFFIIBFFIIBBBFFFFFIFFBFFFFIBFFIBFFIBBFBFFFFI<BBF<F<BFFFFBFBF<BBFFFFB<BBFFFB0<BF +@HISEQ:105:C2UE1ACXX:3:1101:19497:7952_ACC 1:N:0:CAGATC +ATACGTAGATGTTTAAAAGTTTAAATAAATGTATTTAGAGGTTTATGAGGTTTATGGTTAAGTGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC ++ +BBBFBFFBFFBFFFIIIIBIIIIIIIIIII<BFFIIFBFBFFFFFIBFBBFFFIIB7FFFIBFBBBFFFFFBBBFB<0<BFFF7<BB7BBBFFFF<BB +@HISEQ:105:C2UE1ACXX:3:1101:3853:8232_TCC 1:N:0:CAGATC +GGTTAGGTTGTTGTTGTATTTAGAGGTTTTTAGGAGTTGTTTTTGAGTTGTTGTTTATTTAGTTTGTCGGTAGAGATCGGAAGAGCACACGTCTGAAC ++ +<<BBFBFFFBFFBFFBFFFIIF<FBFIFFIIFBBFFIFBFFFIIBFBFFBFFFFFIFIIII<FFIBFI<<BF<BB<BF70<B0<7BBFFF0BBB7BBF +@HISEQ:105:C2UE1ACXX:3:1101:7150:8384_TTA 1:N:0:CAGATC +GAGTAGTAGTTTTTGTGTAGGTTTTGGTTTGTGTGGTATTAGTAGGTAGTAGTGTGTTAGTTGGAGCGATAGTAGTAAGTTATGGTTATTGTTTATTA ++ +BBBFFFFFFFFFFIBFBFFFFFFFFB<FFF<BBFFFFFFIFBFIFFFIIIIFFFIFIFF<FF7<BFFFFFFBBFBBBF<BBFF77<BBFF7BBFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:11512:8610_TGT 1:N:0:CAGATC +TGTGTTTTGAAGTTGGCGGAGTTCGCGTTTTTAGGAATTTTGTTTTGGAACGGTTTGGTCGGGGTTTTCGTTTTTTTTTGTAGAAGTGTAGGAGATGT ++ +B<BFFFFF<FFBFFBBFFFFBFFFBFFFFFIII<7BFFIII7BFFI00<BFBBBBB77<B0<<<B7BBB7BFFFFFFFF'7<000'<'0B'0<<BB0< +@HISEQ:105:C2UE1ACXX:3:1101:18629:8512_TAT 1:N:0:CAGATC +TGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGTTTTTTTGTTTGTTTAGGTTTTGGTT ++ +B<BFFFFFFBFFFIIIIIIIIIIII<FFIBFFFBFF7FFFIIF<<BBF7BFFIIIF7B<BBFFFFFFFF0<7BBBFFFF'0BB'0<B<'0<<B'''7B +@HISEQ:105:C2UE1ACXX:3:1101:5146:8981_AGT 1:N:0:CAGATC +TTTAGGTTTTAGTTGTTGTTGTTTGTTTTGTATTAGTGTAGTTATAATTTTTTTGTTGATTTTGTTGTTTTTAGAAGGTTTGGGGTGAGTTTAGTATG ++ +BBBFBBFFFFFBFF<FF<BFBFFI0BFFI0BFFFF<BBFFFFFFIIIIIIIIII7BF7BFIII<BF7BFFFFF0<<7'<<B00'0<<77BBBF'<BB0 +@HISEQ:105:C2UE1ACXX:3:1101:3344:9104_ATT 1:N:0:CAGATC +TAGATGTTGAGTGTTTGTTTTGTGTTAGGTATTAGGTGGGATTAGGTGGTTATTATCGAGTTTTTAGGAGAGAGTATAGTTGTAAGCGGACGATAATA ++ +BB<FFFFFBFBFFFFFBFFIIBFBFFFBBFFFFFBBFFFIIFFFFBFFFIFFIIIII<FBFBFIIF<<BBFFFFFBBF<BB7<BF0<007B7<BFFFF +@HISEQ:105:C2UE1ACXX:3:1101:2097:9536_GTT 1:N:0:CAGATC +TTGGATTTTTTGGTTTGATAAGGAGTTTTGTAGGTTAAAGAATGTTTTTTAAGGGATTTTTGTTATGTGATTAGTTAATGGGATTTTATTTAAGTTTG ++ +BB<BFFFFFFFBBFFFBFFIIFBFFIFFIBFIFFFFFIIBFFIFFFIIIIII<<BFFFIFF<FFFFBFBFFFFBFBFFF700<BFFFFFFFFF<BBF< +@HISEQ:105:C2UE1ACXX:3:1101:16351:9944_TTG 1:N:0:CAGATC +TTGGACGGGATGGTTGTGGTAAAGTTTTAATAGTTTTATTGGGGGATGGTATAGAAGTAGTTTAGGTTGTATTGTGGGATTTATTTTTATTGTTTGTT ++ +<B<<FFFFFFFFFIFBFFFFFIIBFFIIIIIIBFFFIFFI70BFFFFFFFFFIBFFBFFBFFFFBBBB<BFFF<B<BBBBBBFFFFFFFFF0<BF0BB +@HISEQ:105:C2UE1ACXX:3:1101:17628:10309_GTC 1:N:0:CAGATC +TGTATGTTTAGATTTGTTTTGAATTTGCGTTTTTGGTTGTTGATTATTTTTTATTATTTTTTGTTTTTTCGTGTGTTCGGGAGATCGGAAGAGCACAC ++ +B<BFFBFFFFBFFIIBFFFI<BFFFI<F<FFFII<0BF<FF0BFFFIIIIIIIIIIIIIIIF7BFFFFFF7B7B<BBB7''707BF007B0<07<BBF +@HISEQ:105:C2UE1ACXX:3:1101:1440:10515_TGT 1:N:0:CAGATC +AGAGTGTTTTTAGTGTGAGGAGTTGGATGTTTTAGATATTTATTTTTATATTGTTTATTTAGGTTATGATTTATGTTTTATTTTAGTTTAATTTTTTG ++ +BBBFFFFFFFFFBFBFFFFIIIIFBBFFFFFFIF<BFFIIIFIIIIIFFFFIBFFIFIIIFBBFFFF<BFFIIIBFFFIIIIFFF7BFFFFFFFFFF7 +@HISEQ:105:C2UE1ACXX:3:1101:11787:10735_ATT 1:N:0:CAGATC +AGAATAGGGAAGTGTATAGAAGTGATATATAGTTTAGATTTGAGTTTTTATTTTGTTTTTTATATTTTTAGATATAAGTAGTTATTAGATTTTTTTGA ++ +B<BFFFBBBFFFFFIFFIBFIBFFIFIIIIIBFFIIBFFIIBFFFFFIIIIIIIBFFIIIIIIIIIIIII<FFIIIF<FF<BFFFFF0BFFFFFFF0< +@HISEQ:105:C2UE1ACXX:3:1101:10231:11124_TGT 1:N:0:CAGATC +TTGTTTTAGTTATTTTTTGGTTTTTTAGATTTTATGTTTTTAGTTTTTATAATTTTTATATTGTATTTGTTTATTAAGTGTGAAATGTTTTTGTAGGA ++ +BB<FFFFFBFFFFIIIIIBBFFFFIIF<FFFIIFF<FFIIIFBFFFIIIIFFIIIIIIIIII<FFFFF<FFFFFFFF<B<B<BFFF<BBFFF0<B70< +@HISEQ:105:C2UE1ACXX:3:1101:9833:11396_CAC 1:N:0:CAGATC +GTTTTTATTTTTGGGATTAAGGTAGTTGTTTTTTGATTTTTGTGTGTTATAGTAAGAATGATATAGGAGATCGGAAGAGCACACGTCTGAACTCCAGT ++ +<BBFFFFFFFFFBBBFFFIIFFFFFFIBFFIIII<BFFIII7FBFBFFIII<FFFBFIIBFFIIF<7BBBFF<7B<0<7<BFFF7BBF7BBFFFFF<B +@HISEQ:105:C2UE1ACXX:3:1101:13437:11566_TTT 1:N:0:CAGATC +TTATTATTGTGGATTTTTTTAATAGTTTGAGAATGAGTTGATTTAGGGTTTTTATTTTATTTTTAAAATTAGGAGTATAATGGGTTTAAGATATAGTT ++ +BBBFFFFFBFFFFFFIIIIIIIIIBFFF<BBFFF<FBFFBFFFIFB7BFBFFIIIIIIIIIIIIIFIFFFF<7BBBBBFFF700<<BFF<BBFFF<<B +@HISEQ:105:C2UE1ACXX:3:1101:10809:14594_AGT 1:N:0:CAGATC +GTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTAT ++ +<BBFFFBFBFFFFFFFIIIIBFFIIIIIIBFFFIIBFF0BBFFFIBBFFFFFFFIIIIIIBFB7BFBBFFFII<BBFF<BBF<BBFFFFFF7<B<BBF +@HISEQ:105:C2UE1ACXX:3:1101:7778:14963_TAT 1:N:0:CAGATC +AGTGGATGATAATAATTTAGGTGATTTATAGTGAGATAAGAGGTATATGAATTTTAGTATTTATTTGTTTTTTTATTTTGGGTTATTTGAGGGTGTTT ++ +BBBFBFFBFFFFFIIIIIIBBBFFFIFFIIBFBFBFFFIBFFFFFFIIBFIIIIIIBFIIIIIIIIBFIIIIIIFFFFF707<<BFFF7<''077<BB +@HISEQ:105:C2UE1ACXX:3:1101:2575:15554_AAA 1:N:0:CAGATC +TTTGGGTTGGTTTTTTTTTTTTTTAAAAAGGTTTTAGGGTTTTGGTTTTTTTTATAATTTTATTAAAATATTAAATATTTATAAAATTTTTATTTTAA ++ +BBBBBBFFBBFFFIIIIIIIIIIB7'0'00'7<'00<B0<<BB7'7BBFFFFB'0<'<BFB'<<BB'00'0<'0'00<'000'0B0<BFF<'<BF<BF +@HISEQ:105:C2UE1ACXX:3:1101:20234:16099_GGT 1:N:0:CATATC +TAAGAGGAAAGAATGGAGAAGAAGATTGGTTTTAGGTATATGATGGAATAGGGTAAAAATGATAGTTGAGGTTAATGGTTTAATTTTTGGGAATTATA ++ +BBBBFFFFFFFFFIBBFFFFFFIBFFFB<BBFFFBBFFFFIBFFBBFFFFBBBFFFIIII<BFIBFF<BBFFFFFB77BBFFFFFFFF000<BBFFFF +@HISEQ:105:C2UE1ACXX:3:1101:20842:16102_TTA 1:N:0:CAGATC +TTGGGATTGTTTTTGTTTGAATTATTTTTTTGTATTATATTTTAATGTGTTGTTTATTTTTAGAATATGGAATTTGTAGGAAATTTTTAAAATTTATT ++ +<B<BBFFFFFFFFIBFFIBFFIIIIIIIIII7BFFIIIIIIIIIIIFFFFFBFFIIIIIIII<BFFFF<7BBFFF<BB00<BBBFFFFFFFFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:21194:16434_TTT 1:N:0:CAAATC +TATAGGTTTTTATTTATGTAGTTTTTTGTATTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +BBBF<<BBFFFFFIIFI<BFBFFFIII7BFFBF0BFFFI7BFFFIIFIFFFFFBFBBFFFBBBFFFBFFFFFFFFFFFFFFBFFB<<7BBFFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:7164:16848_ATA 1:N:0:CAGATC +TTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAACGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAATAAATTTTTATGTTGT ++ +BBBFFBBBFFFBFFIBBFIBFFFII<BFBFFFIIFBFFFFIIBFB0BFFIBFF<<FFFI77BFFI<<<FF<BBF<B<<B7BBFFFFFFFFFFF'<B7B +@HISEQ:105:C2UE1ACXX:3:1101:12454:17532_TTT 1:N:0:CAGATC +TTGGTGTAGAGGTTTGTTAAGTGTGGTATGGTTGAGAATATTCGTGTTTTATTGGTTAAATGTGATTTTTGTATTAAGTTGAGAGTTAGGGGTTTTGT ++ +<B<<BFFFBFFFFFF<FFFFBFFIFFIFFBBFF<BBFFFFIIIFFFFFFIFIIB7FFFFII<FBFFIIII<FFFFFF<BB7B7B<B<B7''7<<BF<B +@HISEQ:105:C2UE1ACXX:3:1101:2584:17964_TTT 1:N:0:CAGATC +TAGAGGGTTTTGTAGAGTATTTGAGTATTTGTTATTATTGTTGTATTTATAGTATTAATTTTTTTAGGAGTAAAGTAATTTTATTAAGTTTTAATAGA ++ +<B<FFFFFFFFBFFBFFFFFFIBFBFFFIIBFFFFIIIIBFFBFIIIIIIIBFIIIIIIIIIIIII<7BBFFFFFFBFFFFFFFFFF<BBFFFFFF7< +@HISEQ:105:C2UE1ACXX:3:1101:9624:17911_AAT 1:N:0:CAGATC +ATTTTGATGTTATTATTTATTTATAAAGTAAGAATAAGGTTATTGGTTTTGTTGTTTTTTAGAGTTGTAAGGAGGATTTTATATAGTAAAAGATGTAG ++ +BBBFFBFFBFFFFIIIIIIIIIIIIIIFFFFFFIIII<BFFFFIBBFFFIBFIBFFIIIIFBFBFB<FFIBBB<<BBFFFFFFFF7<BFFF<BB7BB7 +@HISEQ:105:C2UE1ACXX:3:1101:19795:18124_GGA 1:N:0:CAGATC +TTTATATTAATTTTTGGGTATTATTTTAGTGTGTTTAAGATGATATTTTAAGAGAAATTTGAATTGAAGAGATTAGTTTTTTATAAATGGCGTATGAA ++ +BBBFFFFFFFFFFII<<<FFFFIIIIII<FBFFFFFIIBFFBBFIIIIIIIBFBFFIIIIBFFFI<BFBFBFFFIFFIIIFFFFFFFF7'70<BB7<B +@HISEQ:105:C2UE1ACXX:3:1101:2293:18893_TGA 1:N:0:CAGATC +TGGATGCATGAAAAGTGTATTTAATTGGTGAGTTATATTTTTTGTCTTTTGGTTTTCGTTTTTAGATATTTATTTATTAGTTTTTATTGTTTTTAGTT ++ +<<<BFBFFFBFFFIBFBFFFIIFIIIB<BBFBFFFFFIIIIIIBFFIIII70BFFII7BFIIII7BFFFFFFFFFFFFF7BBFFFFFF<BBFFFF7BB +@HISEQ:105:C2UE1ACXX:3:1101:12741:20220_TGT 1:N:0:CAGATC +ATTTTTTTGGAAGAGAAGGAATTTATTTAGGGGAAATATATGTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTT ++ +BBBFFFFFB<FFBFFFFFFFFIIIIIIIIBBFFFFFIIIIIBFFFFIIIIII<77BBBFFFF7BBFBF<BBF<<B<<BBFFF7BF7B<'0<<0<BFFF +@HISEQ:105:C2UE1ACXX:3:1101:18680:20134_TTT 1:N:0:CAGATC +TGTTTGGAAGTATGGTGTTTTTTAAGAGGTTTTTGGTTATTTAGTTTGAAATGATTTAGATTATTTTGTTTTTTTGGTTGGGGTAGGTTTTGGAAATT ++ +B<BFFBBFFFFFFFFFFIFFIIIIIBFFFIBFFIB7BFFIIIIFFFI<BFIIBFFIIIBFFIIIIIIBFFFFFFF<7BB70077777BBBF7'<BBFF +@HISEQ:105:C2UE1ACXX:3:1101:19451:20037_TAT 1:N:0:CATATC +GTTGGTATATTGAGTTTACGTTGCGTTTGTATTATGGAATTTTTTTTGGTGTAGTTTTTGAAGGTGTATTGAGGTTTGAATGAGAGAGGTATTTTTGT ++ +0BB<BBFFBFF0BBFFIIIBFF<B0BFF0BFFFIIB<BFFFIIIIII<7B<BBBFFFFF7<B<BBBBBBF0<70<7<'<BB'<7<'707<<BBFFB07 +@HISEQ:105:C2UE1ACXX:3:1101:14848:20360_GAT 1:N:0:CAGATC +TCTTTATTAATATATAAAAAAAGATATTAGGGAGGATCGAGGGTGTTTTTGTTATGTTTGTTTTATAGAGGAGTATATAGATTGAGGTATAGATACAG ++ +BBBFFFFFFFFFFIIIIIIIIIBFFIIIIBBBFFFFFFBFFFFIIIFFII<BFFFBFFFBFFFFFFF<B<<BBBBBFFF7<BF7<00<<BF0<BFFF0 +@HISEQ:105:C2UE1ACXX:3:1101:12295:20565_TTT 1:N:0:CAGATC +ATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATATAGTA ++ +BBBFFFFFFFFFFFFIIIIFII<FBFFIFBBFFFIFFFIIFIIIFFF7BFBBFFFIIBFFIIFFFIFIFFIIIFI<<B7<BFF07<BFFFFFFFF77< +@HISEQ:105:C2UE1ACXX:3:1101:11915:21129_GTA 1:N:0:CAGATC +TTTGTTAGTTTTATATTTTTAAGTTTTTTTTTAGGTTCGTTTTAGAAATAGTATGTGTTAAATAGTGAAGTAATTTTTGGTTTTATAATGAGGAGTGG ++ +BBBBFFFFFFFFFIIIIIIIIIFIIIIIIIIIIB7FFF<FFFII<FFIIIBFIFBFFFFFFFFF<BBBFBBFFFFFFF00<BBFFFFFF7<00<0<<< +@HISEQ:105:C2UE1ACXX:3:1101:12442:21376_GTT 1:N:0:CAGATC +GTGTATATATTAATTATATTTTGATATGTTTGTATAGGACGGTTATTGGAATAAAATATAAAAAAGTAAGTAAGTAAATAAAAAAATATAAGGTGAAA ++ +BBBFFFFFFFFFFIIIIIIIIIBFIII<FFI<FFII<BFFBBFFFII77FFFFIIIIIIIIIIIIBFFFBFFFBFBBFFFFFFFFFFFFFF7077<BB +@HISEQ:105:C2UE1ACXX:3:1101:10225:21919_GTG 1:N:0:CAGATC +AGTGAAGAGGGAATGAAAAGTTTTTGATTTAATTTATATAATTAAAAAAGTTGGTAGTTATAGTAGTTTAATTTTTTATTATTAAGTTTGTGTGTGGT ++ +BBBFFFFFFFFFFFBFFIIFIFFII<BFFFIFFIIFIIIIIIIIIIIIIFFB77BFBFFFII<FFBFFFIFIFFFFFFFFFFFFF7<BF7B<B<B<7< +@HISEQ:105:C2UE1ACXX:3:1101:12240:21986_ATC 1:N:0:CAGATC +ATTGTTATTAATATAGGGGGTAGTTTTGGTTTGGGATTGAGGGAGGAATTATAGGAGAATTATTTTTTGTGTAGGAGGGAGAGTTTGAAATTAGGAAG ++ +BBBBFFFFFFFFFIIFBFFIIFFIFIIBBFFF77BFFF7B<BFFBFFFFIIFF<<B<BFFFFFFFFFF7BBBFB<<<<<<<BBBBB0BBFFFF00<B7 +@HISEQ:105:C2UE1ACXX:3:1101:2199:22213_GTT 1:N:0:CAGATC +TTAAAGTTATTATTGGAATTTTAAGTTAGGTTATATGTAGGTTATGTATAGGTTTTTATTGTGGGATGAATGGTATTTGGAGCTTGTTTAAAAGTTAG ++ +BBBFFFFFFFFFFIBBFFIIIIFIBFFIBBFFFIFIFIIFFIFFIBFIIIFBFFFIIIIIBFBBFFFBFFF<<FFFFI70<7BFF<BFFFFFFBBBF7 +@HISEQ:105:C2UE1ACXX:3:1101:13060:22287_TGT 1:N:0:CAGATC +TAGTGAAGAATAAATTTTTATGTTGTATATTATTTTTTTTTAGTTCGTATATATCGGTATACGTGTTAGGATTTATAAAGATAGTTATTATTTTTTGT ++ +BBBFFFFFFFFFFIIIIIIIIBFIFFIIIIIIIIIIIIIIII<FFIBFFIIIIIIB<BFFFFBBBBBF<<BBFFFBFFF<BBF7<BFFFFFFFFFF7B +@HISEQ:105:C2UE1ACXX:3:1101:7272:22581_TTA 1:N:0:CAGATC +TTAATGATATTAAGAATTTTTTAAAGAATTTTATTTTTTTTAGGAATAGAAGGAGGAGGAGTATTTTGATCGATTTTTTAGGTTTTTTATAGGTGGAG ++ +BBBFFBFFFFFFF<BFIIIIIIFIIBFFFFIIFIIIIIIIII<<FFFIBFIBBFFBFFFFFFBBFFF<BBF<BBFFFFFF00<BBFFFFFF000<777 +@HISEQ:105:C2UE1ACXX:3:1101:10060:23020_TTT 1:N:0:CAGATC +TTTTAGATTATTTAAGAAGGTATTAGGTTTTTAAGAGGAAAGGGTAGTCTTATAGTTTTGAGTATTTTTTTTAAAAGGAAGTAAGGATGGTGTTTTTA ++ +BBBFFBFFFFFFFIIBFIFFFFFIBBBFFFFIIIBFFFIFIBFFIFFFFIIFFFBFFII7B<FFFIIIIIFFFFBB77<B<BBF<7BB<<BBBBBFFF +@HISEQ:105:C2UE1ACXX:3:1101:14440:23104_TTT 1:N:0:CAGATC +TTTAAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAATTTTTGGTGT ++ +BBBFFFFFFFFFFFIIBBIFIBBBFFFFFBFFIIIIBFFIIBFBFFFFFFIIIIFFF7BB<<BBFB<BBBBFFB7<00B<BBFF00<BBFFFF''77B +@HISEQ:105:C2UE1ACXX:3:1101:6941:23338_GTT 1:N:0:CAGATC +AGAAAGGTTTTAAGTTGGTTGGGAATATAGGGGTTTTTTAGAGTTTTTATTAGGAGTTATAGTGTGTTGAATTTGGTTTTGGGTGTTGATTATAGGTT ++ +BBBFFFFFFFFFFBFFBBFFBBBFFFFIIBFFFIFFIIIIBFFFFFIIIIIIB<FFFFFFFBFBFFFF<BBFFF<<BBBB700<BBB0BBFFFF00<B +@HISEQ:105:C2UE1ACXX:3:1101:10069:23622_TTT 1:N:0:CAGATC +TTTTGTTTTAGGGTTTTATTTTTGTGTTTTATTTTTATTTTCGTATTATTAGTTTTTTTTATACGTTATTTGTAGAAGGTTAGTTTTTTTAATTTAGG ++ +BBBFBFFFFFBBBFFFIFIIIIIBFBFFIIBFIIIIIIIIIIBFFFIIIIIFFIIIIIIFFFFF<BFFFFF<BF<<B77BBB7BBFFFFFFFFFFF00 +@HISEQ:105:C2UE1ACXX:3:1101:14079:24078_AGT 1:N:0:CAGATC +TTTAAAGTTTTTAGTTTTGAGTGGAATTTTAAGAATATTAGTGCGTTTTAAGCTTAGGTAGTTTTGGTAGTTTGAAAGTAATAGGGTGTATTTTGTAA ++ +BBBFFFFFFFFFFBFFFI<BBFFFFFFIIIIIBFFFIIIIBFFFFFFIIIIBFFIIBBFFFFFFI<7BFBFFF<BBF<BBFFF<07BBBBBFFF<BFF +@HISEQ:105:C2UE1ACXX:3:1101:12064:24631_TTT 1:N:0:CCGATC +TTATAGTGTATTTATATATATGAAATGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGT ++ +BBBFFBFFFFFFFIIIIIIIIBFIFF0BFIIIIIBFFIIIIIIIIIIIIIBFIIFFFIBFFBFFFFFFB<BFF7BBFFFFF<B<BBBFFFFFFF'70< +@HISEQ:105:C2UE1ACXX:3:1101:11630:24964_GAT 1:N:0:TAGATC +TTAGTTTTTTTAGTGTTTTTTATTTATTTCGTTTTATTATTGGAGTTTGTTAAGAAAATTAGGGTTTGATTTGGATGTTAAGGATTGGTTTTTTTTTT ++ +BBBBFFFFFFFFBFFFFIIIIIIIIIIIIIBFFFIFIIIIIB7BFFFFBFFIIBFIIIIIFB<BFBFBFFFF<7BB<BBFF<7<BB77BBFFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:12594:24878_AAT 1:N:0:CCGATC +TTTAATAGGATATGATATTATTTAATTTATAGATTATGGAAATTTTTTATATTTAATGAAGAAAGTTGGAATGTTTTGGGAGGTGTTTAGAATAAATA ++ +BBBFFFFB0BFFF<FFIIIFIIFIIIFIFIF<BFFFF<<BFFFIIIIIIIIIIIIIIBFFBFFIBFB7'<FF<<BBF0''77<BFB<BB0<BBBBBFF +@HISEQ:105:C2UE1ACXX:3:1101:4483:25030_ATT 1:N:0:CAGATC +AGGATGGTGTTTTTATTTTTAGATTTATATTATTTTGTTATATTTGTATTTGAGTAAGTTTATGGGTTTTTTAAAGAGGTAGGAGGAAGTTTTTTGTT ++ +B<BFFFFFFFFFFIIIIIIIIBBFIIFIIIIFIIII<BFFIFFIIBFIIII<BBFFIFIFIIIB7<FFFIIIFBF<<77BB00<70<B7BBBFFF0BB +@HISEQ:105:C2UE1ACXX:3:1101:12198:25235_TTA 1:N:0:CAGATC +ATATATGTAGTTTGTATTATTTTTGTTATAGTATATAAAGGTTAAAGAGTAGTTGTTTTAATTTTAGAGGTGGAGATTGGGTTGTATAGTTTTGGTTT ++ +BBBFFFBFFFFFFBFFIIFIIIII0BF<FF0BFFFIFFIBBFBFII<FBFBBFF7FFFIIIIIIII<F7<B'<BB7<B''0<<0<BBB77<BB'0<<B +@HISEQ:105:C2UE1ACXX:3:1101:20477:25084_TGT 1:N:0:CATATC +AGAGTTTATTGAGAAGTAAAGTATTAATTTTATGGGAGAAATGGGATAGAGGTAGTAGAAGTTGTTATGGAATGGGATTAATTAGGAAGTTAATTAAG ++ +BBBFFFFFFF0BBFFBFFIIFFIIIIIIIIIFIBB7FFFFIIFFBFFIFIBFFFFIIFIIFFFBFFFF77BFF<<B<FFFFFFF70<B7BBFFFFFF7 +@HISEQ:105:C2UE1ACXX:3:1101:5725:25359_TAG 1:N:0:CAGATC +GAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATA ++ +BBBFFFFFFBFFFIIIIIIIIIIIBIFBFFFFIIBBFFFFFFFIIIIIIFFFBFFBBFFFIIBFFIIBFIIFIFIFFFFF<BF<BBFF7<<FFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:5502:25591_AGA 1:N:0:CAGATC +ATATGATTTTATTTTTAGGGATAATATTTTTTAAGTGAATTTTGATTTTTTGGTTAGTTATTTTGATGATGTGTAGAGGGTGTATAGTTTTTGGATAT ++ +BBBFBFFFFFFFFIIIIBBBFFFIIIIIIIIIIIBFFFIIIIIBFFIIIII<7BFFBFFFIIII<FF<FFBFFFFFB<<<BFBBBF<<BFFF00<BFB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_paired.log Thu Aug 10 06:37:09 2017 -0400 @@ -0,0 +1,116 @@ +# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat +# job started at Tue Aug 8 15:14:12 2017 on packer-test -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e +# pid: 32709, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 +# log2stderr : False +# loglevel : 1 +# pattern : NNNXXX +# pattern2 : None +# prime3 : False +# quality_encoding : None +# quality_filter_threshold : None +# random_seed : None +# read2_in : input_read2.gz +# read2_out : out2.gz +# short_help : None +# split : False +# stats : True +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'> +# stdlog : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +Barcode UMI Sample Count +AAAAGT AAA AGT 1 +TTTTTT TTT TTT 1 +TTGGTT TTG GTT 1 +AAGTTT AAG TTT 1 +ATATAA ATA TAA 1 +GTTTTT GTT TTT 4 +GTTTTA GTT TTA 1 +TATAGA TAT AGA 1 +AAGTAT AAG TAT 1 +TTATTT TTA TTT 1 +AGATGA AGA TGA 1 +TTTTAG TTT TAG 2 +GTGTTT GTG TTT 1 +GTATGT GTA TGT 1 +AGTGTT AGT GTT 1 +AGAAAT AGA AAT 1 +TATAAA TAT AAA 1 +TGTATC TGT ATC 1 +TAAAAT TAA AAT 1 +ATTATT ATT ATT 1 +ATTTAG ATT TAG 1 +TATATT TAT ATT 1 +ATTTGG ATT TGG 1 +AAAATA AAA ATA 1 +AAGTTA AAG TTA 1 +GTTGTA GTT GTA 1 +TTTGAA TTT GAA 1 +ATTTGA ATT TGA 1 +TTTATA TTT ATA 2 +ATACGT ATA CGT 1 +GGTTAG GGT TAG 1 +GGTGTT GGT GTT 1 +TGGTTG TGG TTG 1 +AGTTAT AGT TAT 1 +GAGTAG GAG TAG 1 +TGTGTT TGT GTT 1 +TGAATT TGA ATT 1 +TTTAGG TTT AGG 2 +TAGATG TAG ATG 1 +TTGGAT TTG GAT 1 +TTGGAC TTG GAC 1 +TGTATG TGT ATG 1 +AGAGTG AGA GTG 1 +AGAATA AGA ATA 1 +TTGTTT TTG TTT 1 +AATATA AAT ATA 1 +TTATTA TTA TTA 1 +TTAAAG TTA AAG 2 +AGGAGT AGG AGT 1 +ATAAGT ATA AGT 1 +TTGTGG TTG TGG 1 +GTATTA GTA TTA 1 +AGTGGA AGT GGA 1 +TTTGGG TTT GGG 1 +TAAGAG TAA GAG 1 +TTGGGA TTG GGA 1 +TATAGG TAT AGG 1 +TTTTTG TTT TTG 1 +AAGAGG AAG AGG 1 +GAGAGA GAG AGA 1 +TTGGTG TTG GTG 1 +TAGAGG TAG AGG 1 +ATTTTG ATT TTG 1 +TGGATG TGG ATG 1 +ATTTTT ATT TTT 1 +TTATAT TTA TAT 1 +TGTTTG TGT TTG 1 +GTTGGT GTT GGT 1 +TCTTTA TCT TTA 1 +ATTGTT ATT GTT 2 +ATAAGA ATA AGA 1 +TATCGA TAT CGA 1 +TTTGTT TTT GTT 1 +GTGTAT GTG TAT 1 +AGTGAA AGT GAA 1 +GTTGTG GTT GTG 1 +TAGTGA TAG TGA 1 +TATTGA TAT TGA 1 +TTAATG TTA ATG 1 +TTTAAA TTT AAA 2 +AGAAAG AGA AAG 1 +TTTTGT TTT TGT 1 +TTATAG TTA TAG 1 +AGGTGT AGG TGT 1 +TTAGTT TTA GTT 1 +TTTAAT TTT AAT 1 +AGGATG AGG ATG 1 +ATATAT ATA TAT 1 +AGAGTT AGA GTT 1 +GAGAAA GAG AAA 1 +ATATGA ATA TGA 1 +# job finished in 0 seconds at Tue Aug 8 15:14:12 2017 -- 0.41 0.02 0.00 0.00 -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_single.log Thu Aug 10 06:37:09 2017 -0400 @@ -0,0 +1,92 @@ +# output generated by extract --bc-pattern=XXXNNN --stdin=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat --stdout /home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat +# job started at Wed Aug 9 09:51:05 2017 on packer-test -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b +# pid: 7652, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 +# log2stderr : False +# loglevel : 1 +# pattern : XXXNNN +# pattern2 : None +# prime3 : True +# quality_encoding : phred33 +# quality_filter_threshold : 10 +# random_seed : None +# read2_in : None +# read2_out : None +# short_help : None +# split : False +# stats : True +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat' mode='r' encoding='UTF-8'> +# stdlog : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat' mode='w' encoding='UTF-8'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +Barcode UMI Sample Count +AAGTTA TTA AAG 1 +GGATTT TTT GGA 1 +GGATAG TAG GGA 1 +TTTTTT TTT TTT 4 +GAGAGG AGG GAG 1 +TTAGTT GTT TTA 1 +TGTAGA AGA TGT 1 +AGAGAT GAT AGA 1 +GAATAA TAA GAA 1 +TTGAGT AGT TTG 1 +TTTATT ATT TTT 1 +GTAAGG AGG GTA 1 +GAAGAG GAG GAA 1 +TGTTTG TTG TGT 1 +ATAATG ATG ATA 1 +TTAGAT GAT TTA 1 +GTCTGA TGA GTC 1 +ATCATC ATC ATC 1 +GTCACC ACC GTC 1 +AACTCC TCC AAC 1 +TTATTA TTA TTA 1 +TGTTGT TGT TGT 2 +GTTTAT TAT GTT 1 +ATGAGT AGT ATG 1 +ATAATT ATT ATA 1 +TTGGTT GTT TTG 1 +GTTTTG TTG GTT 1 +CACGTC GTC CAC 1 +TTGTGT TGT TTG 1 +TGAATT ATT TGA 1 +GGATGT TGT GGA 1 +AGTCAC CAC AGT 1 +GTTTTT TTT GTT 1 +TATAGT AGT TAT 1 +TTTTAT TAT TTT 1 +TAAAAA AAA TAA 1 +ATAGGT GGT ATA 1 +ATTTTA TTA ATT 1 +TGTATA ATA TGT 1 +TGTTTT TTT TGT 2 +AGATTT TTT AGA 1 +TAGAAT AAT TAG 1 +GAAGGA GGA GAA 1 +GTTTGA TGA GTT 1 +TTTTGT TGT TTT 1 +ATTTTT TTT ATT 1 +TGTTAT TAT TGT 1 +CAGGAT GAT CAG 1 +GTATTT TTT GTA 1 +TGGGTA GTA TGG 1 +AAAGTT GTT AAA 1 +GGTGTG GTG GGT 1 +AAGATC ATC AAG 1 +TAGGTT GTT TAG 1 +GAGTTA TTA GAG 1 +TTATTT TTT TTA 1 +GTTGTT GTT GTT 1 +AGGTTT TTT AGG 1 +TAAAGT AGT TAA 1 +AGTTTT TTT AGT 1 +TTTGAT GAT TTT 1 +ATAAAT AAT ATA 1 +GTTATT ATT GTT 1 +TTTTTA TTA TTT 1 +AAGTGT TGT AAG 1 +ATATAG TAG ATA 1 +TATAGA AGA TAT 1 +# job finished in 0 seconds at Wed Aug 9 09:51:05 2017 -- 0.36 0.02 0.00 0.00 -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t_R1.fastq Thu Aug 10 06:37:09 2017 -0400 @@ -0,0 +1,400 @@ +@HISEQ:105:C2UE1ACXX:3:1101:11160:2245 1:N:0:CAGATC +AAAAGTAGTTAATATATTAGATTTGTTTGATAGTGGTAGTATATATTTTTTATTTTAGTATTTAGGAGGTAGAGGTAGATGAATTTTTGAGTTTAAAGTTA ++ +BBBFFFFBFFFFFIIIIIIBIIIIBIFFBFIIBBFFFFFFFFIIIIIIIIIIIIIIIBFIIIIIB7BBBFBBFFFF77<F7BFFFFFF7B7BBFFFF7<BF +@HISEQ:105:C2UE1ACXX:3:1101:19338:2197 1:N:0:CAGATC +TTTTTTTTTAGAGGGATTAGTTTTTTTTATTGAGGTTTTTGAAAGTTGTTGTATGTTAATTGTTTTTAGAATGTTGGGTATAAGTAGGATTTAGGTCTATT ++ +BBBFFFFFFB0<BF7BBBF7BFFIIIII7BF'0<0BBFFF'<BB'<B7<B07<B7<BFBBF0<BBBBB0<<B0BB<<000<BF00<<'0<BBB0'00BBF# +@HISEQ:105:C2UE1ACXX:3:1101:19467:2281 1:N:0:CATATC +TTGGTTAGGGTGAGATGTATAGTTTGGATTTTAGTGATTTTTGTAAAGGGGGAAAAGAATGGAGTTTTGGGTGTAGTGAGAGGTTATAGGAGTAGGGATTT ++ +<B<<FFFBBFFFFFFFFFIFIBFFI<<BFFFIIBBBFFIIIIBFFIIBBF7BBFFFBFFF77BBFBFF777BBBBBB<<<B<7<7BBF77<7<700007BB +@HISEQ:105:C2UE1ACXX:3:1101:7009:2740 1:N:0:CAGATC +AAGTTTTGTTTTTTATTTGGAGGTTATGGAATGTTAAGTAAGGTTTTTTTGGGTTTTGTTATTTATTTGATAATTGTGATTGTAATGTTAATAAGGGATAG ++ +BBBFFFFFFFFFFIIIIIB<FFFFFFIBBFIIFFFIIFIIIFFIFFIIII<0<BBFFBFFFFFFFFFF<BBFFFF<BBBBF7BFFF<BBFFFFF<00<BB0 +@HISEQ:105:C2UE1ACXX:3:1101:13708:2613 1:N:0:CAGATC +ATATAATAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAAGATAATTAATTTTTAAAATTTTTTTTTTTTTAATAAAA ++ +BBBFFFFFBFFFFIIIIIIIIIIIFFFFFB7B007BB0''''''0077BFF7'077BF0''0''''''00''00''''00'<BBBFBBFFFFF######## +@HISEQ:105:C2UE1ACXX:3:1101:19067:2707 1:N:0:CAGATC +GTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTAGAAAATTTTTTTTAGTAAGATAGATTTTAAAGGGTTTGTTTTTTTTTTTTTTTTTTTTT ++ +BBBFFFFFFFFFBBFFFFIIIFIFFIFFIIIIIIIFFFFFB7'0<B0<BBFF'7<0'0<<''0<'0'0<BBB<<B'7'0'0'0<BFFFFFFFFFFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:4999:3182 1:N:0:CAGATC +GTTTTATGAGGATTTTAGGGGAGTGATTGTTTAAAGTTTATAAGATTTATGATTTATATATAGTTAGAATAGTATGTGTTAAATAAATATAAAGGGAGAGG ++ +<BBFFFFBFFFFFFIIFBBBFFFIIFFIBFFIFIIBFFIIIIIFFIIIIIBFFIIIIIIIIIBFFIBFIII<FFFBFBFFFFFFFFFFFFFFF<07<7<<7 +@HISEQ:105:C2UE1ACXX:3:1101:16790:3145 1:N:0:CAGATC +TATAGAGGTATTTTGTTATTTTGTTTTAGTTATTGCGGGTTAGAGTAGATGGTTATTTTTAGTAGAGTATTGTTTGTTGTTTTTTATATGTGGTATAGAGG ++ +BBBF<BBFFFFFFI<FFFIFIIBBFFIIBFFFFI<BBBFFFF<FFFF7FF70<BFFIFIIF7BFBB<FFBF'BBF'<<0<BFFBBBBBF'<70<<<B#### +@HISEQ:105:C2UE1ACXX:3:1101:18065:3106 1:N:0:CAGATC +AAGTATTTGTTATATATATTTTAAAGTTTTTTTTTTTTTTAGGAATTTTTTTTTATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTTT ++ +BBBFFFFFBFFFFIIIIFIIIIIIIFIFIIIIIIIIIIFF''00<<BB'<<'7''000<BFFF77<77BFF77BFBB07<7<BFFFFFFFF########## +@HISEQ:105:C2UE1ACXX:3:1101:2300:3263 1:N:0:TAGATC +TTATTTTTAATAAAATTTTTATTATTTAATTTATTAGTTAATATTTAGGAGTTTTATGTTGTGGTAAAATTTTGTTAGAGAGATAGAGAAAGTATTTAGTT ++ +BBBFFFFFFFFBFFIIIIIIBIBBFFI0<FFFBFF70B00<'0<FFFBBBBFF''0B0BB000'7BBFFFFII'<BF0<'<''07'70BBF'7BBBFB7<B +@HISEQ:105:C2UE1ACXX:3:1101:5605:3427 1:N:0:CAGATC +AGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAGATAAGAAGTGGTTCGGTTATAGGATTTGTTTTAGATTTTTAGATTTTTTTGTGTAGA ++ +BBBFBFFFFFFFFFFBFFFFIIIIIIIBFFFBFFIBFFIIIIIFFIIIFFIBF7BFBFBBFFIFF<<FFFFBBFFBF0<BFFFFF7<BFFFFFF0B7BF0< +@HISEQ:105:C2UE1ACXX:3:1101:8129:3589 1:N:0:CAGATC +TTTTAGTTTTTAGTTAGGATTATACGTTTATTGTGATAAAAGAGTTTTTTGATTTATCGGGTTATGTTAGGGTTTATTGATATTAGGGAATTTGAAGAGAT ++ +BBBFFBFFFFFFBFFFBBFIIFIIFBFFFFII<BBFFFIIIBFFIFIIIIBBFFIIII<7<FBFF<FBF<7<BBFFFF7<BFFFF700<BBFF0<B'<07B +@HISEQ:105:C2UE1ACXX:3:1101:14304:3866 1:N:0:CAGATC +GTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAATGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAATAA ++ +<BBFFFFFFFFFFFFFFFFII<BBFFFBFFIFBFFBFFFII7FFFFFFFIF<BFIIII<F<BBFIFBFB7<BFFFBBBBBF777<B7BBF7B<BB7BBFFF +@HISEQ:105:C2UE1ACXX:3:1101:12720:4398 1:N:0:CAGATC +GTATGTGTGTGTGTGTGTGTATTTAATTGAAGTTGGGTTTGGTGATATATATGTTTAATTTTAGTATTTTAGTGGTAGAGGTAGGTTAATTTTTGTTGAGT ++ +<BBFBFFFFFFFFIFIFIFFFFFIIFII0BFBFFB7BFFF<BFFFFIIIIIIBFIIIIFIIII<FIFIIIFBFBBFB7B<<BB7<B<BFFFFFF0<B0<7B +@HISEQ:105:C2UE1ACXX:3:1101:14945:4439 1:N:0:CAGATC +AGTGTTGAGTGGAGTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATT ++ +BBBBFFBFFFFFFFFFFIIBIFFIFFBFFIIIIBFFIIIIIIBFFIIIBFFBFFFIIIFBFFBFBFFIIIIIFFFBBF77BBFFF7BBFF<BBF<<BFFFB +@HISEQ:105:C2UE1ACXX:3:1101:8616:4508 1:N:0:CAGATC +AGAAATTTTGGGGGTGTAGGAGTGGTAGGATAGGAGTGTTGTTTTGTAATAGTTTTTTTTGAGGTTTAATAGGTAGGGTAGTTATTTTTAGTATTGTAAGG ++ +BBBFFFFFFBBBFFFIIFFFIFFFIIFFIIFIFBFFFIIF<FBFI<FFIIIBFFFFFFFF077<B<BBBFF<<BBBBBB<7B<BFFFFFF0BBFF0<BF00 +@HISEQ:105:C2UE1ACXX:3:1101:18975:4834 1:N:0:CAGATC +TATAAATGGTAATTTTGTAATTTAAAGATTTAAAAGTAATTATTGGTAATAGTTATTTGTGGGAGGTTGAGGTAGGGGGATTTTTGTAGAGATCGGAAGAG ++ +BBBFFFFBBFFFFIIIBFIIIIIFIIFFFFIFIIIBFIIIIIIIB<FFIFIBFFFIIIBFFBFFFII<<BFBFFFFIFF<BBBFF0BB7<<<BF707B0B0 +@HISEQ:105:C2UE1ACXX:3:1101:4984:5374 1:N:0:CAGATC +TGTATCGAGGTTTGAATGAGAGTGGTATTTTTGTTATTTGTTAGTTAATGGTTTTGAGTATTAGTTTGGAAAATGATAATAAGTATTAGTTGAGGTGTTTG ++ +B<BFFFBFFFFBF<FFFBFFFFFFFIFFFIII<BFFIIIBFFFFFFIIIBBFFFIBBBFFFIIBFFF<<BFFFFBBFFFFFF<BBFFF<BB7<7<BBBBF0 +@HISEQ:105:C2UE1ACXX:3:1101:14432:5660 1:N:0:CAGATC +TAAAATAAAAGATAGAGATAGAATAAAAGATAGAGATTTTAATTTTTCGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAA ++ +BBBFFFFFFFBFFIBFFFIIBIIIIIIIBFFIBFBFFFFIFFIIIIIFBFFIIIIIIFFFFFFFFFFFFFFFFFFFFF<BFBBBBBFFFB########### +@HISEQ:105:C2UE1ACXX:3:1101:17410:5545 1:N:0:CAGATC +ATTATTTTTTTGAAGTTGTTAGGGTTATTTAGTGAAATTTGAGTATATTTAATTATTTTAGATGTTAGTTTTATTTAGGTTTTATTTTATTAGAGGTTTGG ++ +BBBFFFFFFFB<FFFIFBFFFBBBFFFFIII<FBFIIIII7FBFFFIIIIIIIIIIIIIF<FF<FFFBFFIFFFFFF77BBFFFFFFFFFFF'<70<BB## +@HISEQ:105:C2UE1ACXX:3:1101:12336:6058 1:N:0:CAGATC +ATTTAGATGATGGTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTTTAAAAAATTTTTTTTATAAAAATAAATTTTAAAGGGTTTTTTTTTTT ++ +BBBFFBFFBFFBBFFFIIIIIIIIBFFIIIIIIIIBFFFFIIIIIFFFFFFFFF700<BF0BBFFF0<70''00'0'000'<<'<B<00'0'00007<BFF +@HISEQ:105:C2UE1ACXX:3:1101:5999:6265 1:N:0:CAGATC +TATATTGTTATATATTTGTGTTTTTTTTGAATTTATTTTTTGTTTATTAGTTTTTGTGGTTGATAGGGTTTTTGGATATTGGGTTGTTTTTATATATAATG ++ +BBBFFFBFFFFFFIIIIBIFIFIIIIII<BFFIIFIIIIII7BFFFIIFBFFIII<B<BFB<BBF<BBBBBFF00<BFFF700B<7<BFFFFFFFFFFFF0 +@HISEQ:105:C2UE1ACXX:3:1101:5836:6568 1:N:0:CAGATC +ATTTGGATGTTAAGGATTGGTTTTTTTTTTGATTTAGGGTATTGTTAGATAGTATAGATTTTACGGAGTTTTGTATTTGAAAGGTTGTTGGTATGTTTTTT ++ +BBBFBBFFFFFFFFFFFFBFIFIIIIIIII'0<FFB<BBFFBF7BFF7BFF<BBFF<BFFFFFF<<BBFBBF7BBBFF'<BB0'<B0<B0'7<B<BFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:15437:6678 1:N:0:CAGATC +AAAATAAGAAATTAGTTAAGAGGAGGAGGTTGTAGTGGGGGTAAGGAAGGAGAGTTTTTGCAAGTTTGGAAATTTGAAAATTATTGTTTTTTATGTTTAGA ++ +BBBFFFFBFFFFFIFFFIIBFFFFFIIIIIB<FFFFFIIIIFBFBBFFFFFFFFFBFFF<BFFBFBF<7BBFFFF<BBFFFFFFF7BBFFFFFF0BBFF## +@HISEQ:105:C2UE1ACXX:3:1101:12432:6996 1:N:0:CAGATC +AAGTTATTTATGAGATTAGTTTATAGTAAATTAAAAAGGGTCTTAGTATTTTGATTATGAAATTAATTATTTTAGTAATATTTGAAGTTGTAATTTTAGAT ++ +BBBFFFFFFFFBFBFFIIBIIIIIIBFIIIIIIIIIIFBFFFFFIFFIIIIIBFFIIIBFIIIIIIIIIIIIIIBFFIIIIII7BF<BF<BFFFFFFF0BB +@HISEQ:105:C2UE1ACXX:3:1101:19878:7022 1:N:0:CATATC +GTTGTATTCGCGTTGTTTTTGTAGGGTTTATGTATTTTTTTTTTTGGTGGAGAGTTTCGTTGAGTGATTTTTTAGTTCGTTTTTCGTTTATTATTTTTCTT ++ +<BBBFFFFFBFBFFBFFIII<BFBFFFFFFF'BBFIIIIIIIIFF''00'7'<7<<B<'7B'0'<0<<BFFFF7'<B<'7'7BB7'0BB0BB<'0BB#### +@HISEQ:105:C2UE1ACXX:3:1101:6837:7574 1:N:0:CAGATC +TTTGAAGATTTTATCGTTAGTTTTTTAGTTTTTATTTGGAGTTGATTTTGAGGTGTTAGTTGTTGTTGTTTTTGTTAGAGGTTAGGTTGTTTTTTATTTGG ++ +BBBBFFFFFFFFFIIBFFIBFFIIIIF<FFIIIFFII<0BBFBBFFFIIBBBBFFFFFBFF<FF<FF<BFFFF7BBB7<77B<B<7<BBBFFFFFFFFF## +@HISEQ:105:C2UE1ACXX:3:1101:15853:7717 1:N:0:CAGATC +GTTTTTTTTTTATATTGTGGTGATAAGTGTTTAAGGTGGGTGAAGGTAGAATTAATCGTAGTTGTGGCTGTTAGTGTTTAGTATATTGTTTTTTGTTAAGG ++ +BBBFFFFFFFFFFFFI<BBFFFBBFFBB7BBFFFB<BFFIIFBFBBBF<BFFFFFFF7<B<BB7<BB'7<BBB<BB<BBB0<<BFFF'<BBFFF'<BBF## +@HISEQ:105:C2UE1ACXX:3:1101:2440:7931 1:N:0:CAGATC +ATTTGAAAAGTGTTATAGATATTAGAAAGGTATGGAGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAAGATCGGAAGAGCACACGTCTGA ++ +BBBFBFFFFFFFFFIIIBFFIIIIBFFIBBFFIBBFFIFFFFFFFIFFIBBFFFFFFFIFIIBFFIBFFFBFFFFFFFF7BBF70<B0<7<BBBF0<BF7< +@HISEQ:105:C2UE1ACXX:3:1101:6407:7896 1:N:0:CAGATC +TTTATAGGTTTGGGTTGAGGATATGTATTGGGAGTTATTAGAGGGTTATAGTTAGGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATC ++ +BBBFFFBBFFF<BBFFBFFFFFIIBFFIIBBBFFFFFIFFBFFFFIBFFIBFFIBBFBFFFFI<BBF<F<BFFFFBFBF<BBFFFFB<BBFFFB0<BFFBB +@HISEQ:105:C2UE1ACXX:3:1101:19497:7952 1:N:0:CAGATC +ATACGTAGATGTTTAAAAGTTTAAATAAATGTATTTAGAGGTTTATGAGGTTTATGGTTAAGTGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC ++ +BBBFBFFBFFBFFFIIIIBIIIIIIIIIII<BFFIIFBFBFFFFFIBFBBFFFIIB7FFFIBFBBBFFFFFBBBFB<0<BFFF7<BB7BBBFFFF<BBFFB +@HISEQ:105:C2UE1ACXX:3:1101:3853:8232 1:N:0:CAGATC +GGTTAGGTTGTTGTTGTATTTAGAGGTTTTTAGGAGTTGTTTTTGAGTTGTTGTTTATTTAGTTTGTCGGTAGAGATCGGAAGAGCACACGTCTGAACTCC ++ +<<BBFBFFFBFFBFFBFFFIIF<FBFIFFIIFBBFFIFBFFFIIBFBFFBFFFFFIFIIII<FFIBFI<<BF<BB<BF70<B0<7BBFFF0BBB7BBFFFF +@HISEQ:105:C2UE1ACXX:3:1101:7442:8079 1:N:0:CAGATC +GGTGTTTGATTTTTTTGAAATTATGTCGGGGTATATTGAGGGTTAGGTTTTATGGGTAGTATTTTATTATTTTTTTGTTGTTTGGAGTTTCGGTTTTGGAT ++ +BBBFFFFBFFFFFFIIBFFIIIII<FFBBFFFFFIFF7<<BFF<BBBFFFIFF7<BFFBFFFFFFFFFFFFFFFFF0<B0BBB'000<7BF00<<<B''0B +@HISEQ:105:C2UE1ACXX:3:1101:14324:8171 1:N:0:CAGATC +TGGTTGTAGTTTTTTATTGGTGTGTGTGTGTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGTGATAGTTTGTTGGGGATTGTTTTTTGTAGGACG ++ +B<<FFBFFFFFFFIIFII<<BFFFIFFFFFFF<FBFFFFIFIIFFIFIIIFIIIFIFFFFFFFFFBBB<BBB7BBB0<B70''7<<'<BBFF######### +@HISEQ:105:C2UE1ACXX:3:1101:3147:8365 1:N:0:CAGATC +AGTTATAATTGTTTTAAGAGTTATCGTGTGGGTATTGGGAGATTGGATGAATGAAAAGTGTATTTAATTGGTGAGTTATATTTTTTGTTCTTTGGTTTTCG ++ +B<BFFFFFFFBFFFIIIBFFFIFIIBFBFFFFIFFIB<BFFFFFB7BFBFFIBFFII<FBFFFIIIIII<7BBFFBBBFFFFFFFF0BBFFFF0'7BBFF# +@HISEQ:105:C2UE1ACXX:3:1101:7150:8384 1:N:0:CAGATC +GAGTAGTAGTTTTTGTGTAGGTTTTGGTTTGTGTGGTATTAGTAGGTAGTAGTGTGTTAGTTGGAGCGATAGTAGTAAGTTATGGTTATTGTTTATTATTA ++ +BBBFFFFFFFFFFIBFBFFFFFFFFB<FFF<BBFFFFFFIFBFIFFFIIIIFFFIFIFF<FF7<BFFFFFFBBFBBBF<BBFF77<BBFF7BBFFFFFFFB +@HISEQ:105:C2UE1ACXX:3:1101:11512:8610 1:N:0:CAGATC +TGTGTTTTGAAGTTGGCGGAGTTCGCGTTTTTAGGAATTTTGTTTTGGAACGGTTTGGTCGGGGTTTTCGTTTTTTTTTGTAGAAGTGTAGGAGATGTTGT ++ +B<BFFFFF<FFBFFBBFFFFBFFFBFFFFFIII<7BFFIII7BFFI00<BFBBBBB77<B0<<<B7BBB7BFFFFFFFF'7<000'<'0B'0<<BB0<B<B +@HISEQ:105:C2UE1ACXX:3:1101:18380:8734 1:N:0:CAGATC +GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTGTTTAAAATTTTTTTTTTTTTTTTTTTTCATTTTTTTTTTTAAAAAATTTTTTTTTTTAAATTT ++ +<BBFFFFFFFFFFIIIFFFFFFFFFFFF0''0''''''00'07B<'0<BFFBB77BFB########################################### +@HISEQ:105:C2UE1ACXX:3:1101:18629:8512 1:N:0:CAGATC +TGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGTTTTTTTGTTTGTTTAGGTTTTGGTTTAT ++ +B<BFFFFFFBFFFIIIIIIIIIIII<FFIBFFFBFF7FFFIIF<<BBF7BFFIIIF7B<BBFFFFFFFF0<7BBBFFFF'0BB'0<B<'0<<B'''7BBBB +@HISEQ:105:C2UE1ACXX:3:1101:5146:8981 1:N:0:CAGATC +TTTAGGTTTTAGTTGTTGTTGTTTGTTTTGTATTAGTGTAGTTATAATTTTTTTGTTGATTTTGTTGTTTTTAGAAGGTTTGGGGTGAGTTTAGTATGAGT ++ +BBBFBBFFFFFBFF<FF<BFBFFI0BFFI0BFFFF<BBFFFFFFIIIIIIIIII7BF7BFIII<BF7BFFFFF0<<7'<<B00'0<<77BBBF'<BB0<0B +@HISEQ:105:C2UE1ACXX:3:1101:3344:9104 1:N:0:CAGATC +TAGATGTTGAGTGTTTGTTTTGTGTTAGGTATTAGGTGGGATTAGGTGGTTATTATCGAGTTTTTAGGAGAGAGTATAGTTGTAAGCGGACGATAATAATT ++ +BB<FFFFFBFBFFFFFBFFIIBFBFFFBBFFFFFBBFFFIIFFFFBFFFIFFIIIII<FBFBFIIF<<BBFFFFFBBF<BB7<BF0<007B7<BFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:8326:9445 1:N:0:CAGATC +TTTAGGAATTATATATTTTTTATATATTATTAAAGTGATTGGTTAGGAAATTAAAGTTTATTTGGAAGGTATTGTTTTTGAAAATGAAGTTATGTTTTTGG ++ +BBBFB<FFFFFFFIIIIIIIIIIIIIIIIIIIIIBFFFFI<BFFFBBFFIFIIIIFIFIFIII<7BFBBFFFFBFFFIF7BFFFF7BB<BBFF<BBFFF## +@HISEQ:105:C2UE1ACXX:3:1101:2097:9536 1:N:0:CAGATC +TTGGATTTTTTGGTTTGATAAGGAGTTTTGTAGGTTAAAGAATGTTTTTTAAGGGATTTTTGTTATGTGATTAGTTAATGGGATTTTATTTAAGTTTGGTT ++ +BB<BFFFFFFFBBFFFBFFIIFBFFIFFIBFIFFFFFIIBFFIFFFIIIIII<<BFFFIFF<FFFFBFBFFFFBFBFFF700<BFFFFFFFFF<BBF<0BB +@HISEQ:105:C2UE1ACXX:3:1101:16351:9944 1:N:0:CAGATC +TTGGACGGGATGGTTGTGGTAAAGTTTTAATAGTTTTATTGGGGGATGGTATAGAAGTAGTTTAGGTTGTATTGTGGGATTTATTTTTATTGTTTGTTTTG ++ +<B<<FFFFFFFFFIFBFFFFFIIBFFIIIIIIBFFFIFFI70BFFFFFFFFFIBFFBFFBFFFFBBBB<BFFF<B<BBBBBBFFFFFFFFF0<BF0BBFF0 +@HISEQ:105:C2UE1ACXX:3:1101:17628:10309 1:N:0:CAGATC +TGTATGTTTAGATTTGTTTTGAATTTGCGTTTTTGGTTGTTGATTATTTTTTATTATTTTTTGTTTTTTCGTGTGTTCGGGAGATCGGAAGAGCACACGTC ++ +B<BFFBFFFFBFFIIBFFFI<BFFFI<F<FFFII<0BF<FF0BFFFIIIIIIIIIIIIIIIF7BFFFFFF7B7B<BBB7''707BF007B0<07<BBF0<B +@HISEQ:105:C2UE1ACXX:3:1101:1440:10515 1:N:0:CAGATC +AGAGTGTTTTTAGTGTGAGGAGTTGGATGTTTTAGATATTTATTTTTATATTGTTTATTTAGGTTATGATTTATGTTTTATTTTAGTTTAATTTTTTGTGT ++ +BBBFFFFFFFFFBFBFFFFIIIIFBBFFFFFFIF<BFFIIIFIIIIIFFFFIBFFIFIIIFBBFFFF<BFFIIIBFFFIIIIFFF7BFFFFFFFFFF7B<B +@HISEQ:105:C2UE1ACXX:3:1101:11787:10735 1:N:0:CAGATC +AGAATAGGGAAGTGTATAGAAGTGATATATAGTTTAGATTTGAGTTTTTATTTTGTTTTTTATATTTTTAGATATAAGTAGTTATTAGATTTTTTTGAATT ++ +B<BFFFBBBFFFFFIFFIBFIBFFIFIIIIIBFFIIBFFIIBFFFFFIIIIIIIBFFIIIIIIIIIIIII<FFIIIF<FF<BFFFFF0BFFFFFFF0<BFF +@HISEQ:105:C2UE1ACXX:3:1101:10231:11124 1:N:0:CAGATC +TTGTTTTAGTTATTTTTTGGTTTTTTAGATTTTATGTTTTTAGTTTTTATAATTTTTATATTGTATTTGTTTATTAAGTGTGAAATGTTTTTGTAGGATGT ++ +BB<FFFFFBFFFFIIIIIBBFFFFIIF<FFFIIFF<FFIIIFBFFFIIIIFFIIIIIIIIII<FFFFF<FFFFFFFF<B<B<BFFF<BBFFF0<B70<<7< +@HISEQ:105:C2UE1ACXX:3:1101:12958:11220 1:N:0:CAGATC +AATATAATTTAATAAGTAGTGTTTTTTTTTTTTTTTTTTTTTTAATAGTTTATTTTTTTTTAGGAAATTCAAAATTTAGTTTTTCTTTAATTTTATAATTA ++ +BBBFFFFFFFFFFIIFFFFIFIIFIIIIIIIIIIF'07<BFFB########################################################## +@HISEQ:105:C2UE1ACXX:3:1101:9833:11396 1:N:0:CAGATC +GTTTTTATTTTTGGGATTAAGGTAGTTGTTTTTTGATTTTTGTGTGTTATAGTAAGAATGATATAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC ++ +<BBFFFFFFFFFBBBFFFIIFFFFFFIBFFIIII<BFFIII7FBFBFFIII<FFFBFIIBFFIIF<7BBBFF<7B<0<7<BFFF7BBF7BBFFFFF<BBBB +@HISEQ:105:C2UE1ACXX:3:1101:13437:11566 1:N:0:CAGATC +TTATTATTGTGGATTTTTTTAATAGTTTGAGAATGAGTTGATTTAGGGTTTTTATTTTATTTTTAAAATTAGGAGTATAATGGGTTTAAGATATAGTTTTT ++ +BBBFFFFFBFFFFFFIIIIIIIIIBFFF<BBFFF<FBFFBFFFIFB7BFBFFIIIIIIIIIIIIIFIFFFF<7BBBBBFFF700<<BFF<BBFFF<<BFFF +@HISEQ:105:C2UE1ACXX:3:1101:12514:13081 1:N:0:CAGATC +TTAAAGTTTTGATTTTAAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAA ++ +BBBFFBFFFF<FFFIIFIIIIIFIBFIIIBBFFFB<BFFFIBBFFIIII7FFII7F<<BFFBFFFFFFFF0<B77<0B700<<BFFB'<00<BBFFB#### +@HISEQ:105:C2UE1ACXX:3:1101:18902:13084 1:N:0:CAGATC +AGGAGTCGGGTTTTGTGAAATATTATAGTAGAGATAGGTGTTGGTTTTGGAATGGAGATTTTTAGTTTTTTTTTATTTTGATAGTTTTGGTAGATCGGAAG ++ +BBBFFFFFFFFFFIBFBFIIIFFIIIIBFFBFFFFFFFIFFB7BFFFIB7<FB<BFFIFFFIIIBFFFFFFFFFBBFFF0<BF0<BFF0'<B0<BB##### +@HISEQ:105:C2UE1ACXX:3:1101:3574:13312 1:N:0:GAGATC +ATAAGTTTAGTAGTTAGGTAATCAGGTTTTTGTTTTATAATTTGAGTTGGTTAGAATGGAATGGGTATTGTAATGTTTGTTGGAATTTTTTGGTTTTATTT ++ +BBBFFFFFFFFF<FFFB<FIFIBFB<BBFFI<BFFIIIFIIFI<B<BF0<FFF7BBF0'BBF<77BFFF7BBFFBB<B0BB''7BBFFFFB0'7BBBBBB# +@HISEQ:105:C2UE1ACXX:3:1101:5163:13594 1:N:0:CAGATC +TTGTGGGTTAGAAATGGGTTATTTAGAGGAATATATAGTTAATATGGTAATGGTTATTTTTAGTTTATTAGTTTAAGTATTTATTTTTTTTTTATAGATCG ++ +BB<FFFFFFFBFFIIBBFFFFFIIIBFBBFFFIIIIIBFFFIIIIB7BFIIBBFFFIIIIII<FFIFIIIBFFIIIBFFFFFFFFFFFFFFFFFFF0<BB# +@HISEQ:105:C2UE1ACXX:3:1101:10809:14594 1:N:0:CAGATC +GTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGT ++ +<BBFFFBFBFFFFFFFIIIIBFFIIIIIIBFFFIIBFF0BBFFFIBBFFFFFFFIIIIIIBFB7BFBBFFFII<BBFF<BBF<BBFFFFFF7<B<BBFF77 +@HISEQ:105:C2UE1ACXX:3:1101:7778:14963 1:N:0:CAGATC +AGTGGATGATAATAATTTAGGTGATTTATAGTGAGATAAGAGGTATATGAATTTTAGTATTTATTTGTTTTTTTATTTTGGGTTATTTGAGGGTGTTTTAT ++ +BBBFBFFBFFFFFIIIIIIBBBFFFIFFIIBFBFBFFFIBFFFFFFIIBFIIIIIIBFIIIIIIIIBFIIIIIIFFFFF707<<BFFF7<''077<BBBFF +@HISEQ:105:C2UE1ACXX:3:1101:2575:15554 1:N:0:CAGATC +TTTGGGTTGGTTTTTTTTTTTTTTAAAAAGGTTTTAGGGTTTTGGTTTTTTTTATAATTTTATTAAAATATTAAATATTTATAAAATTTTTATTTTAAAAA ++ +BBBBBBFFBBFFFIIIIIIIIIIB7'0'00'7<'00<B0<<BB7'7BBFFFFB'0<'<BFB'<<BB'00'0<'0'00<'000'0B0<BFF<'<BF<BFB00 +@HISEQ:105:C2UE1ACXX:3:1101:20234:16099 1:N:0:CATATC +TAAGAGGAAAGAATGGAGAAGAAGATTGGTTTTAGGTATATGATGGAATAGGGTAAAAATGATAGTTGAGGTTAATGGTTTAATTTTTGGGAATTATAGGT ++ +BBBBFFFFFFFFFIBBFFFFFFIBFFFB<BBFFFBBFFFFIBFFBBFFFFBBBFFFIIII<BFIBFF<BBFFFFFB77BBFFFFFFFF000<BBFFFF77< +@HISEQ:105:C2UE1ACXX:3:1101:20842:16102 1:N:0:CAGATC +TTGGGATTGTTTTTGTTTGAATTATTTTTTTGTATTATATTTTAATGTGTTGTTTATTTTTAGAATATGGAATTTGTAGGAAATTTTTAAAATTTATTTTA ++ +<B<BBFFFFFFFFIBFFIBFFIIIIIIIIII7BFFIIIIIIIIIIIFFFFFBFFIIIIIIII<BFFFF<7BBFFF<BB00<BBBFFFFFFFFFFFFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:21194:16434 1:N:0:CAAATC +TATAGGTTTTTATTTATGTAGTTTTTTGTATTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +BBBF<<BBFFFFFIIFI<BFBFFFIII7BFFBF0BFFFI7BFFFIIFIFFFFFBFBBFFFBBBFFFBFFFFFFFFFFFFFFBFFB<<7BBFFFFFFFFBBB +@HISEQ:105:C2UE1ACXX:3:1101:7164:16848 1:N:0:CAGATC +TTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAACGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAATAAATTTTTATGTTGTATA ++ +BBBFFBBBFFFBFFIBBFIBFFFII<BFBFFFIIFBFFFFIIBFB0BFFIBFF<<FFFI77BFFI<<<FF<BBF<B<<B7BBFFFFFFFFFFF'<B7BBFF +@HISEQ:105:C2UE1ACXX:3:1101:2125:17112 1:N:0:CAGATC +AAGAGGAGGAGGTTGTAGTGGGGTAAGGAAGGAGAGTTTTTGTAAGTTTGGAAATTTGAAAATTATTGTTTTTTATGTTTAGATTTTTTTATGACATTTGA ++ +BBBFFFFFFFFFFIBFFBFFIIFBBFF<FFF7B770BBFFI'7BF7BBF<'<F<FFF'<BFBFB<BF7BBFBBB<B'<BBB'7<BBBBBBBB'00<BBF## +@HISEQ:105:C2UE1ACXX:3:1101:6615:17184 1:N:0:CAGATC +GAGAGAGTTATATGTAATAGTTAGTTTTATTTAGAATATTAGAAGAATTATATGAGTAAGGTGTTTAATTATAAGGATAAGTTATAAGTTATAAAAATACG ++ +BBBFFFFFFFFFFBFFIIIFIIIBFFIIIIIII<FFIIIIIBFFFFIIIIIIIBFBFFIFFFFFFIIIIIIIIIBBBFFF<BFFIII<BFFFFFFFFFFF# +@HISEQ:105:C2UE1ACXX:3:1101:12454:17532 1:N:0:CAGATC +TTGGTGTAGAGGTTTGTTAAGTGTGGTATGGTTGAGAATATTCGTGTTTTATTGGTTAAATGTGATTTTTGTATTAAGTTGAGAGTTAGGGGTTTTGTTTT ++ +<B<<BFFFBFFFFFF<FFFFBFFIFFIFFBBFF<BBFFFFIIIFFFFFFIFIIB7FFFFII<FBFFIIII<FFFFFF<BB7B7B<B<B7''7<<BF<BBFF +@HISEQ:105:C2UE1ACXX:3:1101:2584:17964 1:N:0:CAGATC +TAGAGGGTTTTGTAGAGTATTTGAGTATTTGTTATTATTGTTGTATTTATAGTATTAATTTTTTTAGGAGTAAAGTAATTTTATTAAGTTTTAATAGATTT ++ +<B<FFFFFFFFBFFBFFFFFFIBFBFFFIIBFFFFIIIIBFFBFIIIIIIIBFIIIIIIIIIIIII<7BBFFFFFFBFFFFFFFFFF<BBFFFFFF7<BFF +@HISEQ:105:C2UE1ACXX:3:1101:9624:17911 1:N:0:CAGATC +ATTTTGATGTTATTATTTATTTATAAAGTAAGAATAAGGTTATTGGTTTTGTTGTTTTTTAGAGTTGTAAGGAGGATTTTATATAGTAAAAGATGTAGAAT ++ +BBBFFBFFBFFFFIIIIIIIIIIIIIIFFFFFFIIII<BFFFFIBBFFFIBFIBFFIIIIFBFBFB<FFIBBB<<BBFFFFFFFF7<BFFF<BB7BB7BBB +@HISEQ:105:C2UE1ACXX:3:1101:19795:18124 1:N:0:CAGATC +TTTATATTAATTTTTGGGTATTATTTTAGTGTGTTTAAGATGATATTTTAAGAGAAATTTGAATTGAAGAGATTAGTTTTTTATAAATGGCGTATGAAGGA ++ +BBBFFFFFFFFFFII<<<FFFFIIIIII<FBFFFFFIIBFFBBFIIIIIIIBFBFFIIIIBFFFI<BFBFBFFFIFFIIIFFFFFFFF7'70<BB7<B707 +@HISEQ:105:C2UE1ACXX:3:1101:2293:18893 1:N:0:CAGATC +TGGATGCATGAAAAGTGTATTTAATTGGTGAGTTATATTTTTTGTCTTTTGGTTTTCGTTTTTAGATATTTATTTATTAGTTTTTATTGTTTTTAGTTTGA ++ +<<<BFBFFFBFFFIBFBFFFIIFIIIB<BBFBFFFFFIIIIIIBFFIIII70BFFII7BFIIII7BFFFFFFFFFFFFF7BBFFFFFF<BBFFFF7BBF0< +@HISEQ:105:C2UE1ACXX:3:1101:12741:20220 1:N:0:CAGATC +ATTTTTTTGGAAGAGAAGGAATTTATTTAGGGGAAATATATGTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGT ++ +BBBFFFFFB<FFBFFFFFFFFIIIIIIIIBBFFFFFIIIIIBFFFFIIIIII<77BBBFFFF7BBFBF<BBF<<B<<BBFFF7BF7B<'0<<0<BFFFF0< +@HISEQ:105:C2UE1ACXX:3:1101:18080:20193 1:N:0:CAGATC +TTATATATTGTTGGATGTGTTGTTTAGGGTTTTGTTAGTGTTTTTTGAAGATAATGATTAATGATGTATGTAGATTTTTGTAGGTTTTAAGAAGTTGGTTG ++ +BBBFFFFFFBFF<BFFBFFIFBFFFFBBBFBFF<BFFBFFFFFIII7BFBFFIII<FFIIII7BFBFIF<FFBFFFFFF0BB07<<BBFF7<B######## +@HISEQ:105:C2UE1ACXX:3:1101:18680:20134 1:N:0:CAGATC +TGTTTGGAAGTATGGTGTTTTTTAAGAGGTTTTTGGTTATTTAGTTTGAAATGATTTAGATTATTTTGTTTTTTTGGTTGGGGTAGGTTTTGGAAATTTTT ++ +B<BFFBBFFFFFFFFFFIFFIIIIIBFFFIBFFIB7BFFIIIIFFFI<BFIIBFFIIIBFFIIIIIIBFFFFFFF<7BB70077777BBBF7'<BBFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:19451:20037 1:N:0:CATATC +GTTGGTATATTGAGTTTACGTTGCGTTTGTATTATGGAATTTTTTTTGGTGTAGTTTTTGAAGGTGTATTGAGGTTTGAATGAGAGAGGTATTTTTGTTAT ++ +0BB<BBFFBFF0BBFFIIIBFF<B0BFF0BFFFIIB<BFFFIIIIII<7B<BBBFFFFF7<B<BBBBBBF0<70<7<'<BB'<7<'707<<BBFFB07BBF +@HISEQ:105:C2UE1ACXX:3:1101:14848:20360 1:N:0:CAGATC +TCTTTATTAATATATAAAAAAAGATATTAGGGAGGATCGAGGGTGTTTTTGTTATGTTTGTTTTATAGAGGAGTATATAGATTGAGGTATAGATACAGGAT ++ +BBBFFFFFFFFFFIIIIIIIIIBFFIIIIBBBFFFFFFBFFFFIIIFFII<BFFFBFFFBFFFFFFF<B<<BBBBBFFF7<BF7<00<<BF0<BFFF007B +@HISEQ:105:C2UE1ACXX:3:1101:20622:20397 1:N:0:CAAATC +ATTGTTGTAGTAAAATTTTGAGTTTATAAGTTTTAAAGATTTTAGTAAATTGAGTTTTGTATAGTTTAATATGTATTAAGAATATTTTGGGGATTTTTTTT ++ +BBB<FF<BFBFFFFIIIII0B0BBFFFBFBFFFFFIIBFFFIIF7BFBFFI'00BBFFBBFFF'BFFBBFII0BBB<BB0BBFIIIIF7'''07BB<BBB# +@HISEQ:105:C2UE1ACXX:3:1101:12295:20565 1:N:0:CAGATC +ATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATATAGTATTT ++ +BBBFFFFFFFFFFFFIIIIFII<FBFFIFBBFFFIFFFIIFIIIFFF7BFBBFFFIIBFFIIFFFIFIFFIIIFI<<B7<BFF07<BFFFFFFFF77<BFF +@HISEQ:105:C2UE1ACXX:3:1101:8987:20904 1:N:0:CAGATC +TATCGATTTTTTCGGTTATGTGGATTTTTTTTTAGAGGTGATAGTTGTTTTGCGTGTTATCGATGGAGTTTTGGTGGTGGTGGATTGTGTGTTTGGCGTGT ++ +BBBF<BFFFFFFFB<BFFI0<B0BFFIIIIIIIB'<7<F'7BB<BB7BFFF'B0<7<BBFB7BB7'<BBBBB0'7<B<0'7<77BB0<000<<B####### +@HISEQ:105:C2UE1ACXX:3:1101:11915:21129 1:N:0:CAGATC +TTTGTTAGTTTTATATTTTTAAGTTTTTTTTTAGGTTCGTTTTAGAAATAGTATGTGTTAAATAGTGAAGTAATTTTTGGTTTTATAATGAGGAGTGGGTA ++ +BBBBFFFFFFFFFIIIIIIIIIFIIIIIIIIIIB7FFF<FFFII<FFIIIBFIFBFFFFFFFFF<BBBFBBFFFFFFF00<BBFFFFFF7<00<0<<<B<B +@HISEQ:105:C2UE1ACXX:3:1101:12442:21376 1:N:0:CAGATC +GTGTATATATTAATTATATTTTGATATGTTTGTATAGGACGGTTATTGGAATAAAATATAAAAAAGTAAGTAAGTAAATAAAAAAATATAAGGTGAAAGTT ++ +BBBFFFFFFFFFFIIIIIIIIIBFIII<FFI<FFII<BFFBBFFFII77FFFFIIIIIIIIIIIIBFFFBFFFBFBBFFFFFFFFFFFFFF7077<BB<BB +@HISEQ:105:C2UE1ACXX:3:1101:10225:21919 1:N:0:CAGATC +AGTGAAGAGGGAATGAAAAGTTTTTGATTTAATTTATATAATTAAAAAAGTTGGTAGTTATAGTAGTTTAATTTTTTATTATTAAGTTTGTGTGTGGTGTG ++ +BBBFFFFFFFFFFFBFFIIFIFFII<BFFFIFFIIFIIIIIIIIIIIIIFFB77BFBFFFII<FFBFFFIFIFFFFFFFFFFFFF7<BF7B<B<B<7<BB7 +@HISEQ:105:C2UE1ACXX:3:1101:12240:21986 1:N:0:CAGATC +ATTGTTATTAATATAGGGGGTAGTTTTGGTTTGGGATTGAGGGAGGAATTATAGGAGAATTATTTTTTGTGTAGGAGGGAGAGTTTGAAATTAGGAAGATC ++ +BBBBFFFFFFFFFIIFBFFIIFFIFIIBBFFF77BFFF7B<BFFBFFFFIIFF<<B<BFFFFFFFFFF7BBBFB<<<<<<<BBBBB0BBFFFF00<B7<BB +@HISEQ:105:C2UE1ACXX:3:1101:2199:22213 1:N:0:CAGATC +TTAAAGTTATTATTGGAATTTTAAGTTAGGTTATATGTAGGTTATGTATAGGTTTTTATTGTGGGATGAATGGTATTTGGAGCTTGTTTAAAAGTTAGGTT ++ +BBBFFFFFFFFFFIBBFFIIIIFIBFFIBBFFFIFIFIIFFIFFIBFIIIFBFFFIIIIIBFBBFFFBFFF<<FFFFI70<7BFF<BFFFFFFBBBF77<B +@HISEQ:105:C2UE1ACXX:3:1101:9023:22492 1:N:0:CAGATC +GTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGATAGATTGTTTGTTATTGATTTTTTTTGGTAGGACTTTTTATGTTATTTATAGTGAGGAAGAAAGATAT ++ +<BBBFBFFFFFFF<FFFFFFFBFBFFFBBBFFF'''0B0'BBF77B'''''0B0BBFF########################################### +@HISEQ:105:C2UE1ACXX:3:1101:13060:22287 1:N:0:CAGATC +TAGTGAAGAATAAATTTTTATGTTGTATATTATTTTTTTTTAGTTCGTATATATCGGTATACGTGTTAGGATTTATAAAGATAGTTATTATTTTTTGTTGT ++ +BBBFFFFFFFFFFIIIIIIIIBFIFFIIIIIIIIIIIIIIII<FFIBFFIIIIIIB<BFFFFBBBBBF<<BBFFFBFFF<BBF7<BFFFFFFFFFF7BB07 +@HISEQ:105:C2UE1ACXX:3:1101:16084:22385 1:N:0:CAGATC +TATTGAGTTATTGTTTTAGTTTTATGGAAGATTTTTTAAATTGGATTGTTTGTGTTTTTATAGTTTTGAGAGTTTTGTTTGATTTTGTTTTTTTTGTGTTG ++ +BBBF<<BFFFFF0BFFIF<IIIIFFB<FF<FFFFIIIFFFF'0<BFFBFFFBF7FBFIIFIF7BFFI7<7B<BBFB'<BF'7BBFF7BBBBBBB####### +@HISEQ:105:C2UE1ACXX:3:1101:7272:22581 1:N:0:CAGATC +TTAATGATATTAAGAATTTTTTAAAGAATTTTATTTTTTTTAGGAATAGAAGGAGGAGGAGTATTTTGATCGATTTTTTAGGTTTTTTATAGGTGGAGTTA ++ +BBBFFBFFFFFFF<BFIIIIIIFIIBFFFFIIFIIIIIIIII<<FFFIBFIBBFFBFFFFFFBBFFF<BBF<BBFFFFFF00<BBFFFFFF000<777B<B +@HISEQ:105:C2UE1ACXX:3:1101:10060:23020 1:N:0:CAGATC +TTTTAGATTATTTAAGAAGGTATTAGGTTTTTAAGAGGAAAGGGTAGTCTTATAGTTTTGAGTATTTTTTTTAAAAGGAAGTAAGGATGGTGTTTTTATTT ++ +BBBFFBFFFFFFFIIBFIFFFFFIBBBFFFFIIIBFFFIFIBFFIFFFFIIFFFBFFII7B<FFFIIIIIFFFFBB77<B<BBF<7BB<<BBBBBFFFFFF +@HISEQ:105:C2UE1ACXX:3:1101:14440:23104 1:N:0:CAGATC +TTTAAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAATTTTTGGTGTTTT ++ +BBBFFFFFFFFFFFIIBBIFIBBBFFFFFBFFIIIIBFFIIBFBFFFFFFIIIIFFF7BB<<BBFB<BBBBFFB7<00B<BBFF00<BBFFFF''77BBBF +@HISEQ:105:C2UE1ACXX:3:1101:6941:23338 1:N:0:CAGATC +AGAAAGGTTTTAAGTTGGTTGGGAATATAGGGGTTTTTTAGAGTTTTTATTAGGAGTTATAGTGTGTTGAATTTGGTTTTGGGTGTTGATTATAGGTTGTT ++ +BBBFFFFFFFFFFBFFBBFFBBBFFFFIIBFFFIFFIIIIBFFFFFIIIIIIB<FFFFFFFBFBFFFF<BBFFF<<BBBB700<BBB0BBFFFF00<B7<B +@HISEQ:105:C2UE1ACXX:3:1101:10069:23622 1:N:0:CAGATC +TTTTGTTTTAGGGTTTTATTTTTGTGTTTTATTTTTATTTTCGTATTATTAGTTTTTTTTATACGTTATTTGTAGAAGGTTAGTTTTTTTAATTTAGGTTT ++ +BBBFBFFFFFBBBFFFIFIIIIIBFBFFIIBFIIIIIIIIIIBFFFIIIIIFFIIIIIIFFFFF<BFFFFF<BF<<B77BBB7BBFFFFFFFFFFF00<BB +@HISEQ:105:C2UE1ACXX:3:1101:14079:24078 1:N:0:CAGATC +TTTAAAGTTTTTAGTTTTGAGTGGAATTTTAAGAATATTAGTGCGTTTTAAGCTTAGGTAGTTTTGGTAGTTTGAAAGTAATAGGGTGTATTTTGTAAAGT ++ +BBBFFFFFFFFFFBFFFI<BBFFFFFFIIIIIBFFFIIIIBFFFFFFIIIIBFFIIBBFFFFFFI<7BFBFFF<BBF<BBFFF<07BBBBBFFF<BFFF<B +@HISEQ:105:C2UE1ACXX:3:1101:12064:24631 1:N:0:CCGATC +TTATAGTGTATTTATATATATGAAATGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGTTTT ++ +BBBFFBFFFFFFFIIIIIIIIBFIFF0BFIIIIIBFFIIIIIIIIIIIIIBFIIFFFIBFFBFFFFFFB<BFF7BBFFFFF<B<BBBFFFFFFF'70<<BF +@HISEQ:105:C2UE1ACXX:3:1101:6662:24968 1:N:0:CAGATC +AGGTGTCGTTTAATTGTTTAGGTTTATGGTATTGTGTTTCGTTTTTTTGGTATTTGTGAGGGTAGAATTGTTTTTGGGTTTTAATTTTTTTAAGTATGGGA ++ +BBBFFFFFFFFFFIIBFFIFBBFFFFIB<FFFI<FBFFFFBFFIIIII77BFFIIBFBFBBBFBBFFFF<BBFFF'07BBBBFFFFFFFFFFB0<BF#### +@HISEQ:105:C2UE1ACXX:3:1101:11630:24964 1:N:0:TAGATC +TTAGTTTTTTTAGTGTTTTTTATTTATTTCGTTTTATTATTGGAGTTTGTTAAGAAAATTAGGGTTTGATTTGGATGTTAAGGATTGGTTTTTTTTTTGAT ++ +BBBBFFFFFFFFBFFFFIIIIIIIIIIIIIBFFFIFIIIIIB7BFFFFBFFIIBFIIIIIFB<BFBFBFFFF<7BB<BBFF<7<BB77BBFFFFFFFF0<B +@HISEQ:105:C2UE1ACXX:3:1101:12594:24878 1:N:0:CCGATC +TTTAATAGGATATGATATTATTTAATTTATAGATTATGGAAATTTTTTATATTTAATGAAGAAAGTTGGAATGTTTTGGGAGGTGTTTAGAATAAATAAAT ++ +BBBFFFFB0BFFF<FFIIIFIIFIIIFIFIF<BFFFF<<BFFFIIIIIIIIIIIIIIBFFBFFIBFB7'<FF<<BBF0''77<BFB<BB0<BBBBBFFBBF +@HISEQ:105:C2UE1ACXX:3:1101:4483:25030 1:N:0:CAGATC +AGGATGGTGTTTTTATTTTTAGATTTATATTATTTTGTTATATTTGTATTTGAGTAAGTTTATGGGTTTTTTAAAGAGGTAGGAGGAAGTTTTTTGTTATT ++ +B<BFFFFFFFFFFIIIIIIIIBBFIIFIIIIFIIII<BFFIFFIIBFIIII<BBFFIFIFIIIB7<FFFIIIFBF<<77BB00<70<B7BBBFFF0BBFFF +@HISEQ:105:C2UE1ACXX:3:1101:12198:25235 1:N:0:CAGATC +ATATATGTAGTTTGTATTATTTTTGTTATAGTATATAAAGGTTAAAGAGTAGTTGTTTTAATTTTAGAGGTGGAGATTGGGTTGTATAGTTTTGGTTTTTA ++ +BBBFFFBFFFFFFBFFIIFIIIII0BF<FF0BFFFIFFIBBFBFII<FBFBBFF7FFFIIIIIIII<F7<B'<BB7<B''0<<0<BBB77<BB'0<<BBFB +@HISEQ:105:C2UE1ACXX:3:1101:20477:25084 1:N:0:CATATC +AGAGTTTATTGAGAAGTAAAGTATTAATTTTATGGGAGAAATGGGATAGAGGTAGTAGAAGTTGTTATGGAATGGGATTAATTAGGAAGTTAATTAAGTGT ++ +BBBFFFFFFF0BBFFBFFIIFFIIIIIIIIIFIBB7FFFFIIFFBFFIFIBFFFFIIFIIFFFBFFFF77BFF<<B<FFFFFFF70<B7BBFFFFFF7B<B +@HISEQ:105:C2UE1ACXX:3:1101:5725:25359 1:N:0:CAGATC +GAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATATAG ++ +BBBFFFFFFBFFFIIIIIIIIIIIBIFBFFFFIIBBFFFFFFFIIIIIIFFFBFFBBFFFIIBFFIIBFIIFIFIFFFFF<BF<BBFF7<<FFFFFFFFF0 +@HISEQ:105:C2UE1ACXX:3:1101:5502:25591 1:N:0:CAGATC +ATATGATTTTATTTTTAGGGATAATATTTTTTAAGTGAATTTTGATTTTTTGGTTAGTTATTTTGATGATGTGTAGAGGGTGTATAGTTTTTGGATATAGA ++ +BBBFBFFFFFFFFIIIIBBBFFFIIIIIIIIIIIBFFFIIIIIBFFIIIII<7BFFBFFFIIII<FF<FFBFFFFFB<<<BFBBBF<<BFFF00<BFBF7<
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/umi-tools_extract.xml Thu Aug 10 06:37:09 2017 -0400 @@ -0,0 +1,255 @@ +<tool id="umi_tools_extract" name="UMI-tools extract" version="0.4.4.0"> + <description>Extract UMI from fastq files</description> + <requirements> + <requirement type="package" version="0.4.4">umi_tools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #set $gz = False + #if $input_type.type == 'single': + #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"): + ln -s '$input_type.input_single' input_single.gz && + #set $gz = True + #end if + #else + #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): + ln -s '$input_type.input_read1' input_read1.gz && + ln -s '$input_type.input_read2' input_read2.gz && + #set $gz = True + #end if + #end if + umi_tools extract + --bc-pattern='$bc_pattern' + #if $input_type.type == 'single': + #if $gz: + --stdin=input_single.gz + --stdout out.gz + #else + --stdin='$input_type.input_single' + --stdout '$out' + #end if + #else: + #if $gz: + --stdin=input_read1.gz + --read2-in=input_read2.gz + --stdout out1.gz + --read2-out=out2.gz + #else: + --stdin='$input_type.input_read1' + --read2-in='$input_type.input_read2' + --stdout '$out1' + --read2-out='$out2' + #end if + #if $input_type.barcode.split == "1": + --split-barcode + --bc-pattern2='$input_type.barcode.bc_pattern2' + #end if + #end if + #if not $prime3: + --3prime + #end if + #if $quality.quality_selector =='true': + --quality-filter-threshold '$quality.quality_filter_threshold' + --quality-encoding '$quality.quality_encoding' + #end if + #if $print_log == "1": + --log='$out_log' + #else + --supress-stats + #end if + #if $gz: + #if $input_type.type == 'single': + && mv out.gz '$out' + #else + && mv out1.gz '$out1' + && mv out2.gz '$out2' + #end if + #end if + ]]></command> + <inputs> + <conditional name="input_type"> + <param name="type" type="select" label="Library type"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> + </when> + <when value="paired"> + <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> + <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> + <conditional name="barcode"> + <param name="split" argument="--split-barcode" type="select" label="Barcode on both reads?"> + <option value="0">Barcode on first read only</option> + <option value="1">Barcode on both reads</option> + </param> + <when value="0"> + </when> + <when value="1"> + <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read" + help="Use this option to specify the format of the UMI/barcode for + the second read pair if required."> + </param> + </when> + </conditional> + </when> + </conditional> + <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" + help="Use this option to specify the format of the UMI/barcode. Use Ns to + represent the random positions and Xs to indicate the bc positions. + Bases with Ns will be extracted and added to the read name. Remaining + bases, marked with an X will be reattached to the read."> + </param> + <param name="prime3" argument="--3prime" type="boolean" label="Is the barcode at the 5' end?" + truevalue="1" falsevalue="0" checked="true" + help="By default the barcode is assumed to be on the 5' end of the read, but + use this option to sepecify that it is on the 3' end instead." /> + <param name="print_log" argument="-L" type="boolean" label="Output log?" + truevalue="1" falsevalue="0" checked="true" + help="Choose if you want to generate a text file containing logging information." /> + <conditional name="quality"> + <param name="quality_selector" type="select" label="Enable quality filter?" > + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false"> + </when> + <when value="true"> + <param name="quality_filter_threshold" label="Phred score threshold" + type="integer" value="20" argument="--quality-filter-threshold" + help="Remove reads where any UMI base quality score falls below this threshold." /> + <param name="quality_encoding" argument="--quality-encoding" type="select" label="Library type" + help="Quality score encoding. Choose from phred33 [33-77], phred64 [64-106] or solexa [59-106]."> + <option value="phred33">phred33 [33-77]</option> + <option value="phred64">phred64 [64-106]</option> + <option value="solexa">solexa [59-106]</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="out" format_source="input_single"> + <filter>input_type['type'] == "single"</filter> + </data> + <data name="out1" format_source="input_read1"> + <filter>input_type['type'] == "paired"</filter> + </data> + <data name="out2" format_source="input_read2"> + <filter>input_type['type'] == "paired"</filter> + </data> + <data name="out_log" format="txt"> + <filter>print_log == True</filter> + </data> + </outputs> + <tests> + <test> + <param name="type" value="single" /> + <param name="input_single" value="t_R1.fastq" ftype="fastq" /> + <param name="bc_pattern" value="XXXNNN" /> + <param name="prime3" value="0" /> + <param name="quality_selector" value="true" /> + <param name="quality_filter_threshold" value="10" /> + <param name="quality_encoding" value="phred33" /> + <output name="out" file="out_SE.fastq" /> + <output name="out_log" file="out_single.log" lines_diff="15"/> + </test> + <test> + <param name="type" value="paired" /> + <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" /> + <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" /> + <param name="bc_pattern" value="NNNXXX" /> + <output name="out1" file="out_R1.fastq.gz" decompress="true" /> + <output name="out2" file="out_R2.fastq.gz" decompress="true" /> + <output name="out_log" file="out_paired.log" lines_diff="10"/> + </test> + </tests> + <help><![CDATA[ + + +UMI-tools extract.py - Extract UMI from fastq +============================================= + +Purpose +------- + +Extract UMI barcode from a read and add it to the read name, leaving +any sample barcode in place. Can deal with paired end reads and UMIs +split across the paired ends + +Options +------- + +--split-barcode + By default the UMI is assumed to be on the first read. Use this + option if the UMI is contained on both reads and specify the + pattern of the barcode/UMI on the second read using the option + ``--bc-pattern2`` + +--bc-pattern + Use this option to specify the format of the UMI/barcode. Use Ns to + represent the random positions and Xs to indicate the bc positions. + Bases with Ns will be extracted and added to the read name. Remaining + bases, marked with an X will be reattached to the read. + + E.g. If the pattern is NNXXNN, + Then the read: + + @HISEQ:87:00000000 read1 + AAGGTTGCTGATTGGATGGGCTAG + DA1AEBFGGCG01DFH00B1FF0B + + + + will become: + @HISEQ:87:00000000_AATT read1 + GGGCTGATTGGATGGGCTAG + 1AFGGCG01DFH00B1FF0B + + + +--bc-pattern2 + Use this option to specify the format of the UMI/barcode for + the second read pair if required. If --bc-pattern2 is not + supplied, this defaults to the same pattern as --bc-pattern + +--3prime + By default the barcode is assumed to be on the 5' end of the read, but + use this option to sepecify that it is on the 3' end instead + +-L + Specify a log file to retain logging information and final statistics + +--split-barcode + barcode is split across read pair + +--quality-filter-threshold=QUALITY_FILTER_THRESHOLD + Remove reads where any UMI base quality score falls + below this threshold +--quality-encoding=QUALITY_ENCODING + Quality score encoding. Choose from phred33[33-77] + phred64 [64-106] or solexa [59-106] + +Usage: +------ + +For single ended reads: + umi_tools extract --bc-pattern=[PATTERN] -L extract.log [OPTIONS] + +reads from stdin and outputs to stdout. + +For paired end reads: + umi_tools extract --bc-pattern=[PATTERN] --read2-in=[FASTQIN] --read2-out=[FASTQOUT] -L extract.log [OPTIONS] + +reads end one from stdin and end two from FASTQIN and outputs end one to stdin +and end two to FASTQOUT. + + ]]></help> + <citations> + <citation type="doi">10.1101/gr.209601.116</citation> + <citation type="bibtex"> + @misc{githubUMI-tools, + title = {UMI-tools}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/CGATOxford/UMI-tools}, + } + </citation> + </citations> +</tool>