# HG changeset patch
# User iuc
# Date 1502361429 14400
# Node ID 418b961e0576050bf180ad0e79f4c8e812bed892

planemo upload commit 453bb3b44d9f27908cbe2677378da88b9f77b5cf

diff -r 000000000000 -r 418b961e0576 test-data/out_R1.fastq.gz
Binary file test-data/out_R1.fastq.gz has changed
diff -r 000000000000 -r 418b961e0576 test-data/out_R2.fastq.gz
Binary file test-data/out_R2.fastq.gz has changed
diff -r 000000000000 -r 418b961e0576 test-data/out_SE.fastq
--- /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
diff -r 000000000000 -r 418b961e0576 test-data/out_paired.log
--- /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
diff -r 000000000000 -r 418b961e0576 test-data/out_single.log
--- /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
diff -r 000000000000 -r 418b961e0576 test-data/t_R1.fastq
--- /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<
diff -r 000000000000 -r 418b961e0576 test-data/t_R1.fastq.gz
Binary file test-data/t_R1.fastq.gz has changed
diff -r 000000000000 -r 418b961e0576 test-data/t_R2.fastq.gz
Binary file test-data/t_R2.fastq.gz has changed
diff -r 000000000000 -r 418b961e0576 umi-tools_extract.xml
--- /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>