# HG changeset patch
# User iuc
# Date 1504042627 14400
# Node ID 79436b3019e9164f0e387134bab7646e6e770177
# Parent 418b961e0576050bf180ad0e79f4c8e812bed892
planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
diff -r 418b961e0576 -r 79436b3019e9 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Aug 29 17:37:07 2017 -0400
@@ -0,0 +1,23 @@
+
+
+
+
+ 10.1101/gr.209601.116
+
+ @misc{githubUMI-tools,
+ title = {UMI-tools},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/CGATOxford/UMI-tools},
+ }
+
+
+
+
+
+ umi_tools
+
+
+
+ 0.5.0
+
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_in1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group_in1.sam Tue Aug 29 17:37:07 2017 -0400
@@ -0,0 +1,666 @@
+@HD VN:1.0 SO:coordinate
+@PG ID:Bowtie VN:1.1.2 CL:"bowtie --wrapper basic-0 --threads 4 -v 2 -m 10 -a /ifs/mirror/genomes/bowtie/mm9 /dev/fd/63 --sam"
+@SQ SN:chr10 LN:129993255
+@SQ SN:chr11 LN:121843856
+@SQ SN:chr12 LN:121257530
+@SQ SN:chr13 LN:120284312
+@SQ SN:chr14 LN:125194864
+@SQ SN:chr15 LN:103494974
+@SQ SN:chr16 LN:98319150
+@SQ SN:chr17 LN:95272651
+@SQ SN:chr18 LN:90772031
+@SQ SN:chr19 LN:61342430
+@SQ SN:chr1 LN:197195432
+@SQ SN:chr2 LN:181748087
+@SQ SN:chr3 LN:159599783
+@SQ SN:chr4 LN:155630120
+@SQ SN:chr5 LN:152537259
+@SQ SN:chr6 LN:149517037
+@SQ SN:chr7 LN:152524553
+@SQ SN:chr8 LN:131738871
+@SQ SN:chr9 LN:124076172
+@SQ SN:chrM LN:16299
+@SQ SN:chrX LN:166650296
+@SQ SN:chrY LN:15902555
+SRR2057595.10000392_AAGTA 16 chr19 31326011 255 57M * 0 0 * * XA:i:1 MD:Z:23A33 NM:i:1 UG:i:512 BX:Z:AAGTA
+SRR2057595.10000468_GCTAT 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:706 BX:Z:GCTAT
+SRR2057595.10000704_TGATG 16 chr19 3544146 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:1 BX:Z:TGATG
+SRR2057595.10000838_TAGTA 0 chr19 10274608 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:324 BX:Z:TAGTA
+SRR2057595.10001118_TCTCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:1 MD:Z:43A6 NM:i:1 UG:i:36 BX:Z:TCTCA
+SRR2057595.10001329_CGGTC 16 chr19 28083193 255 60M * 0 0 * * XA:i:0 MD:Z:60 NM:i:0 UG:i:497 BX:Z:CGGTC
+SRR2057595.10001382_CTGCC 16 chr19 3957282 255 22M * 0 0 * * XA:i:2 MD:Z:17C1G2 NM:i:2 UG:i:9 BX:Z:CTGCC
+SRR2057595.10001382_CTGCC 16 chr19 3970897 255 22M * 0 0 * * XA:i:2 MD:Z:17C1G2 NM:i:2 UG:i:10 BX:Z:CTGCC
+SRR2057595.10002047_ATTAT 16 chr19 7546213 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:278 BX:Z:ATTAT
+SRR2057595.10002219_ATCAG 16 chr19 5796783 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:234 BX:Z:ATCAG
+SRR2057595.10002597_AATTA 16 chr19 50733887 255 64M * 0 0 * * XA:i:2 MD:Z:58C0C4 NM:i:2 UG:i:645 BX:Z:AATTA
+SRR2057595.10003084_GTCTA 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:124 BX:Z:GTCTA
+SRR2057595.10003230_ACATT 0 chr19 8799370 255 64M * 0 0 * * XA:i:0 MD:Z:64 NM:i:0 UG:i:297 BX:Z:ACATT
+SRR2057595.10003317_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:648 BX:Z:CGGCC
+SRR2057595.10003567_ATGTC 0 chr19 37052811 255 64M * 0 0 * * XA:i:1 MD:Z:11C52 NM:i:1 UG:i:542 BX:Z:ATGTC
+SRR2057595.10003576_AATCG 16 chr19 4078303 255 67M * 0 0 * * XA:i:2 MD:Z:38A21A6 NM:i:2 UG:i:88 BX:Z:AATCG
+SRR2057595.10003630_GTGTT 16 chr19 4078298 255 52M * 0 0 * * XA:i:2 MD:Z:42G0A8 NM:i:2 UG:i:45 BX:Z:GTGTT
+SRR2057595.10003869_TCTTG 16 chr19 4078423 255 67M * 0 0 * * XA:i:1 MD:Z:19A47 NM:i:1 UG:i:111 BX:Z:TCTTG
+SRR2057595.1000404_AACTT 16 chr19 4078420 255 64M * 0 0 * * XA:i:2 MD:Z:2T19A41 NM:i:2 UG:i:55 BX:Z:AACTT
+SRR2057595.10004161_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.1000475_TCTGG 0 chr19 13129234 255 28M * 0 0 * * XA:i:1 MD:Z:22T5 NM:i:1 UG:i:383 BX:Z:TCTGG
+SRR2057595.10004845_GGATA 0 chr19 24394180 255 29M * 0 0 * * XA:i:2 MD:Z:11C15T1 NM:i:2 UG:i:481 BX:Z:GGATA
+SRR2057595.10005100_TTAAA 16 chr19 4785463 255 21M * 0 0 * * XA:i:0 MD:Z:21 NM:i:0 UG:i:196 BX:Z:TTAAA
+SRR2057595.10005761_CTAGA 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:43 BX:Z:CTAGA
+SRR2057595.10005808_CAGTA 16 chr19 7545872 255 24M * 0 0 * * XA:i:0 MD:Z:24 NM:i:0 UG:i:276 BX:Z:CAGTA
+SRR2057595.10005955_GACAT 16 chr19 4078302 255 67M * 0 0 * * XA:i:2 MD:Z:39A21A5 NM:i:2 UG:i:82 BX:Z:GACAT
+SRR2057595.10006011_TCTCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:1 MD:Z:43A6 NM:i:1 UG:i:36 BX:Z:TCTCA
+SRR2057595.10006546_GCTAC 16 chr19 4078446 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:97 BX:Z:GCTAC
+SRR2057595.1000663_ACGCA 16 chr19 51217013 255 67M * 0 0 * * XA:i:2 MD:Z:3A46A16 NM:i:2 UG:i:647 BX:Z:ACGCA
+SRR2057595.10006870_GTCCA 16 chr19 4078431 255 67M * 0 0 * * XA:i:1 MD:Z:11A55 NM:i:1 UG:i:107 BX:Z:GTCCA
+SRR2057595.10006926_GGATA 0 chr19 24394180 255 29M * 0 0 * * XA:i:2 MD:Z:11C15T1 NM:i:2 UG:i:481 BX:Z:GGATA
+SRR2057595.10006986_GCGGA 16 chr19 4078298 255 48M * 0 0 * * XA:i:1 MD:Z:43A4 NM:i:1 UG:i:19 BX:Z:GCGGA
+SRR2057595.10007554_TATTG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:404 BX:Z:TATTG
+SRR2057595.10008217_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10008433_AGAGT 16 chr19 24180225 255 55M * 0 0 * * XA:i:1 MD:Z:41C13 NM:i:1 UG:i:474 BX:Z:AGAGT
+SRR2057595.10008484_GGATC 16 chr19 4078298 255 61M * 0 0 * * XA:i:2 MD:Z:42G0A17 NM:i:2 UG:i:61 BX:Z:GGATC
+SRR2057595.10008523_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:405 BX:Z:TATGG
+SRR2057595.10008761_AGCTG 16 chr19 4806926 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:201 BX:Z:AGCTG
+SRR2057595.10009130_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:648 BX:Z:CGGCC
+SRR2057595.10009213_CCCCG 16 chr19 4078298 255 38M * 0 0 * * XA:i:1 MD:Z:35C2 NM:i:1 UG:i:184 BX:Z:CCCCG
+SRR2057595.10009394_TAGAT 16 chr19 5797239 255 48M * 0 0 * * XA:i:0 MD:Z:48 NM:i:0 UG:i:229 BX:Z:TAGAT
+SRR2057595.10009607_TTGCA 0 chr19 41640185 255 61M * 0 0 * * XA:i:0 MD:Z:61 NM:i:0 UG:i:581 BX:Z:TTGCA
+SRR2057595.1001008_TATCA 16 chr19 60837460 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:691 BX:Z:TATCA
+SRR2057595.10010444_AGTGC 0 chr19 8798525 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:296 BX:Z:AGTGC
+SRR2057595.10011106_CGGTC 16 chr19 28083193 255 60M * 0 0 * * XA:i:0 MD:Z:60 NM:i:0 UG:i:497 BX:Z:CGGTC
+SRR2057595.10011603_ATGAA 0 chr19 56177103 255 20M * 0 0 * * XA:i:2 MD:Z:12G0T6 NM:i:2 UG:i:667 BX:Z:ATGAA
+SRR2057595.10011612_GTTTC 0 chr19 58015463 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:683 BX:Z:GTTTC
+SRR2057595.10011924_CCCCG 16 chr19 4078298 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:184 BX:Z:CCCCG
+SRR2057595.10012143_ATGAA 0 chr19 56007800 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:666 BX:Z:ATGAA
+SRR2057595.10012487_TGGGT 16 chr19 4917801 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:202 BX:Z:TGGGT
+SRR2057595.1001256_TGATG 16 chr19 3544146 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:1 BX:Z:TGATG
+SRR2057595.10013018_GGGGC 16 chr19 4078446 255 67M * 0 0 * * XA:i:1 MD:Z:66T0 NM:i:1 UG:i:98 BX:Z:GGGGC
+SRR2057595.10013156_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:52 BX:Z:GTCAA
+SRR2057595.10013642_AATTC 0 chr19 13129322 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:403 BX:Z:AATTC
+SRR2057595.10013703_ATGTA 0 chr19 39042685 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:558 BX:Z:ATGTA
+SRR2057595.10014121_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.1001419_CAGTA 16 chr19 7545872 255 24M * 0 0 * * XA:i:0 MD:Z:24 NM:i:0 UG:i:276 BX:Z:CAGTA
+SRR2057595.10014588_AAGGT 0 chr19 8798514 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:294 BX:Z:AAGGT
+SRR2057595.10014904_GCGAC 0 chr19 13129553 255 26M * 0 0 * * XA:i:2 MD:Z:3A0T21 NM:i:2 UG:i:399 BX:Z:GCGAC
+SRR2057595.10015153_ATTAT 16 chr19 7546213 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:278 BX:Z:ATTAT
+SRR2057595.10015867_ATCCG 16 chr19 37369602 255 35M * 0 0 * * XA:i:0 MD:Z:35 NM:i:0 UG:i:544 BX:Z:ATCCG
+SRR2057595.10015949_CTTTC 16 chr19 4078298 255 53M * 0 0 * * XA:i:2 MD:Z:42G0A9 NM:i:2 UG:i:47 BX:Z:CTTTC
+SRR2057595.10016080_TATCA 16 chr19 60837460 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:691 BX:Z:TATCA
+SRR2057595.10016534_ACGCA 16 chr19 51217013 255 67M * 0 0 * * XA:i:2 MD:Z:3A46A16 NM:i:2 UG:i:647 BX:Z:ACGCA
+SRR2057595.10016692_TGGAC 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:127 BX:Z:TGGAC
+SRR2057595.10016737_GTTGT 16 chr19 12564367 255 21M * 0 0 * * XA:i:2 MD:Z:0A12A7 NM:i:2 UG:i:380 BX:Z:GTTGT
+SRR2057595.10016874_TTGCA 0 chr19 44434953 255 43M * 0 0 * * XA:i:0 MD:Z:43 NM:i:0 UG:i:602 BX:Z:TTGCA
+SRR2057595.10017358_AGATC 16 chr19 24352786 255 67M * 0 0 * * XA:i:1 MD:Z:25C41 NM:i:1 UG:i:479 BX:Z:AGATC
+SRR2057595.10017433_GGCAG 0 chr19 13129322 255 22M * 0 0 * * XA:i:0 MD:Z:22 NM:i:0 UG:i:409 BX:Z:GGCAG
+SRR2057595.10017742_TAGCG 0 chr19 25429456 255 20M * 0 0 * * XA:i:2 MD:Z:5A9A4 NM:i:2 UG:i:485 BX:Z:TAGCG
+SRR2057595.10018091_TAACA 0 chr19 8799023 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:299 BX:Z:TAACA
+SRR2057595.10018143_CCATC 0 chr19 5008676 255 30M * 0 0 * * XA:i:2 MD:Z:1A23G4 NM:i:2 UG:i:203 BX:Z:CCATC
+SRR2057595.10018237_GCTTG 16 chr19 5797471 255 50M * 0 0 * * XA:i:0 MD:Z:50 NM:i:0 UG:i:226 BX:Z:GCTTG
+SRR2057595.10018343_AATTC 0 chr19 13129322 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:403 BX:Z:AATTC
+SRR2057595.10018510_TTCGT 0 chr19 47167097 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:623 BX:Z:TTCGT
+SRR2057595.10018668_GAGAG 16 chr19 4078298 255 50M * 0 0 * * XA:i:1 MD:Z:43A6 NM:i:1 UG:i:35 BX:Z:GAGAG
+SRR2057595.10018780_CTAGA 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:43 BX:Z:CTAGA
+SRR2057595.10018930_TGATT 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:41 BX:Z:TGATT
+SRR2057595.10019300_TTATA 16 chr19 4078298 255 49M * 0 0 * * XA:i:2 MD:Z:42G0A5 NM:i:2 UG:i:22 BX:Z:TTATA
+SRR2057595.10019327_TTATA 16 chr19 4078298 255 49M * 0 0 * * XA:i:2 MD:Z:42G0A5 NM:i:2 UG:i:22 BX:Z:TTATA
+SRR2057595.10019367_AGTAT 0 chr19 10600420 255 29M * 0 0 * * XA:i:0 MD:Z:29 NM:i:0 UG:i:328 BX:Z:AGTAT
+SRR2057595.10019428_CTAAT 0 chr19 40194243 255 44M * 0 0 * * XA:i:2 MD:Z:5T20A17 NM:i:2 UG:i:562 BX:Z:CTAAT
+SRR2057595.10019544_CCCCG 16 chr19 4078298 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:184 BX:Z:CCCCG
+SRR2057595.100195_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.10019604_TCCAG 0 chr19 29662201 255 26M * 0 0 * * XA:i:1 MD:Z:0C25 NM:i:1 UG:i:509 BX:Z:TCCAG
+SRR2057595.10019935_ACCGT 16 chr19 15980484 255 29M * 0 0 * * XA:i:1 MD:Z:12C16 NM:i:1 UG:i:431 BX:Z:ACCGT
+SRR2057595.10020101_CTAGA 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:43 BX:Z:CTAGA
+SRR2057595.10020134_CTTTC 16 chr19 4078298 255 45M * 0 0 * * XA:i:1 MD:Z:43A1 NM:i:1 UG:i:15 BX:Z:CTTTC
+SRR2057595.10020463_GTCCT 16 chr19 59694502 255 21M * 0 0 * * XA:i:2 MD:Z:8T0A11 NM:i:2 UG:i:688 BX:Z:GTCCT
+SRR2057595.10020843_TTAAA 16 chr19 4785463 255 21M * 0 0 * * XA:i:0 MD:Z:21 NM:i:0 UG:i:196 BX:Z:TTAAA
+SRR2057595.10020890_AGTAT 0 chr19 10600420 255 29M * 0 0 * * XA:i:0 MD:Z:29 NM:i:0 UG:i:328 BX:Z:AGTAT
+SRR2057595.10021356_CAGTA 16 chr19 61240266 255 26M * 0 0 * * XA:i:1 MD:Z:12C13 NM:i:1 UG:i:697 BX:Z:CAGTA
+SRR2057595.10021429_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:249 BX:Z:CACTG
+SRR2057595.10021850_AGTCT 0 chr19 13129558 255 37M * 0 0 * * XA:i:1 MD:Z:21A15 NM:i:1 UG:i:398 BX:Z:AGTCT
+SRR2057595.10022647_TTGTT 16 chr19 61240268 255 24M * 0 0 * * XA:i:1 MD:Z:10C13 NM:i:1 UG:i:696 BX:Z:TTGTT
+SRR2057595.10022675_GTGGA 16 chr19 35902240 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:535 BX:Z:GTGGA
+SRR2057595.10023366_AGCTT 16 chr19 5799262 255 20M * 0 0 * * XA:i:0 MD:Z:20 NM:i:0 UG:i:245 BX:Z:AGCTT
+SRR2057595.10023594_ATGAA 0 chr19 56007800 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:666 BX:Z:ATGAA
+SRR2057595.10023941_TACGG 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:1T43A21 NM:i:2 UG:i:71 BX:Z:TACGG
+SRR2057595.10023975_TCGTC 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:704 BX:Z:TCGTC
+SRR2057595.10024016_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10024824_ACCGG 16 chr19 10924297 255 49M * 0 0 * * XA:i:0 MD:Z:49 NM:i:0 UG:i:336 BX:Z:ACCGG
+SRR2057595.10025477_AGTAT 0 chr19 10600420 255 29M * 0 0 * * XA:i:0 MD:Z:29 NM:i:0 UG:i:328 BX:Z:AGTAT
+SRR2057595.10025641_CGAAC 0 chr19 13129273 255 36M * 0 0 * * XA:i:2 MD:Z:25C1T8 NM:i:2 UG:i:386 BX:Z:CGAAC
+SRR2057595.10025783_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:53 BX:Z:GCATA
+SRR2057595.10025842_GATCT 16 chr19 4078433 255 67M * 0 0 * * XA:i:1 MD:Z:9A57 NM:i:1 UG:i:90 BX:Z:GATCT
+SRR2057595.10026676_GGATC 16 chr19 4078298 255 61M * 0 0 * * XA:i:2 MD:Z:42G0A17 NM:i:2 UG:i:61 BX:Z:GGATC
+SRR2057595.1002669_TATTC 16 chr19 5038295 255 24M * 0 0 * * XA:i:0 MD:Z:24 NM:i:0 UG:i:206 BX:Z:TATTC
+SRR2057595.10027010_TGTTT 16 chr19 50526830 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:643 BX:Z:TGTTT
+SRR2057595.10027016_GACGT 0 chr19 40194275 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:565 BX:Z:GACGT
+SRR2057595.10027043_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:405 BX:Z:TATGG
+SRR2057595.10027109_GGGGC 16 chr19 4078446 255 67M * 0 0 * * XA:i:1 MD:Z:66T0 NM:i:1 UG:i:98 BX:Z:GGGGC
+SRR2057595.10027286_ATGAA 0 chr19 56177103 255 20M * 0 0 * * XA:i:2 MD:Z:12G0T6 NM:i:2 UG:i:667 BX:Z:ATGAA
+SRR2057595.10027736_CCGAT 16 chr19 4078300 255 49M * 0 0 * * XA:i:2 MD:Z:40G0A7 NM:i:2 UG:i:44 BX:Z:CCGAT
+SRR2057595.10027811_AAAGG 16 chr19 23347776 255 34M * 0 0 * * XA:i:1 MD:Z:9T24 NM:i:1 UG:i:467 BX:Z:AAAGG
+SRR2057595.10028205_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10028311_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10029121_AGCCG 0 chr19 8799400 255 33M * 0 0 * * XA:i:0 MD:Z:33 NM:i:0 UG:i:302 BX:Z:AGCCG
+SRR2057595.10029169_GGTTC 16 chr19 56896659 255 23M * 0 0 * * XA:i:2 MD:Z:0C0A21 NM:i:2 UG:i:674 BX:Z:GGTTC
+SRR2057595.10029364_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10029373_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10029475_ACAAA 16 chr19 5688438 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:222 BX:Z:ACAAA
+SRR2057595.10029622_TCAGG 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:407 BX:Z:TCAGG
+SRR2057595.10029643_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:405 BX:Z:TATGG
+SRR2057595.10030278_TATTG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:404 BX:Z:TATTG
+SRR2057595.10030560_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.10030639_GCGAC 0 chr19 13129553 255 26M * 0 0 * * XA:i:2 MD:Z:3A0T21 NM:i:2 UG:i:399 BX:Z:GCGAC
+SRR2057595.10031002_AAGGT 0 chr19 8798514 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:294 BX:Z:AAGGT
+SRR2057595.10031358_TAGTA 16 chr19 61240268 255 27M * 0 0 * * XA:i:1 MD:Z:10C16 NM:i:1 UG:i:702 BX:Z:TAGTA
+SRR2057595.10031368_TAACA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:32 BX:Z:TAACA
+SRR2057595.10032378_CAGCA 16 chr19 5801892 255 47M * 0 0 * * XA:i:0 MD:Z:47 NM:i:0 UG:i:258 BX:Z:CAGCA
+SRR2057595.10032451_ACCGT 16 chr19 15980484 255 29M * 0 0 * * XA:i:1 MD:Z:12C16 NM:i:1 UG:i:431 BX:Z:ACCGT
+SRR2057595.10032626_CATAA 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:401 BX:Z:CATAA
+SRR2057595.10033730_AACTG 16 chr19 40362914 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:571 BX:Z:AACTG
+SRR2057595.10034125_CTCTT 16 chr19 10761035 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:332 BX:Z:CTCTT
+SRR2057595.1003424_GGATA 0 chr19 24394180 255 29M * 0 0 * * XA:i:2 MD:Z:11C15T1 NM:i:2 UG:i:481 BX:Z:GGATA
+SRR2057595.10034498_ATGAA 0 chr19 56177103 255 20M * 0 0 * * XA:i:2 MD:Z:12G0T6 NM:i:2 UG:i:667 BX:Z:ATGAA
+SRR2057595.10034756_ATGAA 0 chr19 56007800 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:666 BX:Z:ATGAA
+SRR2057595.10034981_TTCGT 0 chr19 47167097 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:623 BX:Z:TTCGT
+SRR2057595.10035130_GGATG 0 chr19 13129322 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:402 BX:Z:GGATG
+SRR2057595.10035284_TACGT 0 chr19 40194308 255 34M * 0 0 * * XA:i:1 MD:Z:3A30 NM:i:1 UG:i:563 BX:Z:TACGT
+SRR2057595.1003559_CCATA 0 chr19 13129322 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:408 BX:Z:CCATA
+SRR2057595.10035727_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.1003581_TAACA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:32 BX:Z:TAACA
+SRR2057595.10036346_AGTCG 0 chr19 17767763 255 67M * 0 0 * * XA:i:2 MD:Z:10A4A51 NM:i:2 UG:i:440 BX:Z:AGTCG
+SRR2057595.10036388_CCAAG 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:37 BX:Z:CCAAG
+SRR2057595.10037180_GGTAG 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:177 BX:Z:GGTAG
+SRR2057595.10037421_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10037481_CATAA 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:401 BX:Z:CATAA
+SRR2057595.10037635_TTCGT 0 chr19 47167097 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:623 BX:Z:TTCGT
+SRR2057595.10037650_GATGA 0 chr19 48194137 255 59M * 0 0 * * XA:i:0 MD:Z:59 NM:i:0 UG:i:635 BX:Z:GATGA
+SRR2057595.10037690_TCCCG 16 chr19 56004832 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:663 BX:Z:TCCCG
+SRR2057595.10038156_AAACA 16 chr19 4078299 255 49M * 0 0 * * XA:i:1 MD:Z:42A6 NM:i:1 UG:i:33 BX:Z:AAACA
+SRR2057595.10038276_TAGTA 0 chr19 10274608 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:324 BX:Z:TAGTA
+SRR2057595.10038572_TGTTT 0 chr19 41595518 255 38M * 0 0 * * XA:i:1 MD:Z:25G12 NM:i:1 UG:i:579 BX:Z:TGTTT
+SRR2057595.10038660_CAGAT 0 chr19 13129299 255 32M * 0 0 * * XA:i:2 MD:Z:1T18G11 NM:i:2 UG:i:396 BX:Z:CAGAT
+SRR2057595.1003901_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:173 BX:Z:AGCCG
+SRR2057595.1003905_CCTCA 0 chr19 8798505 255 48M * 0 0 * * XA:i:0 MD:Z:48 NM:i:0 UG:i:292 BX:Z:CCTCA
+SRR2057595.10039161_CTTAC 16 chr19 4078298 255 54M * 0 0 * * XA:i:2 MD:Z:42G0A10 NM:i:2 UG:i:49 BX:Z:CTTAC
+SRR2057595.10039249_TCTGT 16 chr19 45885126 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:608 BX:Z:TCTGT
+SRR2057595.10039623_CGCCG 16 chr19 4078299 255 59M * 0 0 * * XA:i:1 MD:Z:42A16 NM:i:1 UG:i:58 BX:Z:CGCCG
+SRR2057595.1004011_GTCGC 0 chr19 12080548 255 51M * 0 0 * * XA:i:2 MD:Z:28C20G1 NM:i:2 UG:i:345 BX:Z:GTCGC
+SRR2057595.1004011_GTCGC 16 chr19 12084189 255 51M * 0 0 * * XA:i:2 MD:Z:1C20G28 NM:i:2 UG:i:352 BX:Z:GTCGC
+SRR2057595.10040530_CCTTG 16 chr19 4078298 255 49M * 0 0 * * XA:i:1 MD:Z:43A5 NM:i:1 UG:i:24 BX:Z:CCTTG
+SRR2057595.10041125_GACGC 16 chr19 32419974 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:514 BX:Z:GACGC
+SRR2057595.10041133_ACAGA 16 chr19 4078299 255 22M * 0 0 * * XA:i:2 MD:Z:0C0C20 NM:i:2 UG:i:136 BX:Z:ACAGA
+SRR2057595.10041495_TGTTT 0 chr19 41595518 255 38M * 0 0 * * XA:i:1 MD:Z:25G12 NM:i:1 UG:i:579 BX:Z:TGTTT
+SRR2057595.10041520_TGACA 16 chr19 51217013 255 43M * 0 0 * * XA:i:2 MD:Z:3A1C37 NM:i:2 UG:i:646 BX:Z:TGACA
+SRR2057595.10041577_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:52 BX:Z:GTCAA
+SRR2057595.10041629_GATGA 0 chr19 48194137 255 59M * 0 0 * * XA:i:0 MD:Z:59 NM:i:0 UG:i:635 BX:Z:GATGA
+SRR2057595.10041662_GGGGC 16 chr19 4078446 255 67M * 0 0 * * XA:i:1 MD:Z:66T0 NM:i:1 UG:i:98 BX:Z:GGGGC
+SRR2057595.10042115_GACAT 16 chr19 4078302 255 67M * 0 0 * * XA:i:2 MD:Z:39A21A5 NM:i:2 UG:i:82 BX:Z:GACAT
+SRR2057595.10042422_TCTGG 0 chr19 13129234 255 28M * 0 0 * * XA:i:1 MD:Z:22T5 NM:i:1 UG:i:383 BX:Z:TCTGG
+SRR2057595.1004285_CCAAC 0 chr19 8820047 255 33M * 0 0 * * XA:i:0 MD:Z:33 NM:i:0 UG:i:315 BX:Z:CCAAC
+SRR2057595.10042887_AAAGG 16 chr19 23347776 255 34M * 0 0 * * XA:i:1 MD:Z:9T24 NM:i:1 UG:i:467 BX:Z:AAAGG
+SRR2057595.10043446_CAGAC 0 chr19 5493782 255 41M * 0 0 * * XA:i:0 MD:Z:41 NM:i:0 UG:i:218 BX:Z:CAGAC
+SRR2057595.10043768_GGCGT 16 chr19 5797126 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:233 BX:Z:GGCGT
+SRR2057595.10043877_TGTTC 16 chr19 44470840 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:605 BX:Z:TGTTC
+SRR2057595.10043959_GACGT 0 chr19 40194275 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:565 BX:Z:GACGT
+SRR2057595.10044281_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10044428_TCTAC 0 chr19 8798544 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:288 BX:Z:TCTAC
+SRR2057595.10044882_TTAAA 16 chr19 4785463 255 21M * 0 0 * * XA:i:0 MD:Z:21 NM:i:0 UG:i:196 BX:Z:TTAAA
+SRR2057595.10044970_GTGGA 16 chr19 35902240 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:535 BX:Z:GTGGA
+SRR2057595.10045235_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:648 BX:Z:CGGCC
+SRR2057595.10045410_TGGTC 16 chr19 4078419 255 67M * 0 0 * * XA:i:2 MD:Z:3T19A43 NM:i:2 UG:i:119 BX:Z:TGGTC
+SRR2057595.10045875_TTGGC 16 chr19 36085526 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:536 BX:Z:TTGGC
+SRR2057595.10045996_TAACA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:32 BX:Z:TAACA
+SRR2057595.10046273_TCCAG 0 chr19 29662201 255 26M * 0 0 * * XA:i:1 MD:Z:0C25 NM:i:1 UG:i:509 BX:Z:TCCAG
+SRR2057595.10047157_GTGGA 16 chr19 35902240 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:535 BX:Z:GTGGA
+SRR2057595.10047180_CCTCA 0 chr19 8798505 255 48M * 0 0 * * XA:i:0 MD:Z:48 NM:i:0 UG:i:292 BX:Z:CCTCA
+SRR2057595.10047439_AATTA 16 chr19 50733890 255 61M * 0 0 * * XA:i:2 MD:Z:55C0C4 NM:i:2 UG:i:645 BX:Z:AATTA
+SRR2057595.10047481_ACGCA 16 chr19 5796074 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:230 BX:Z:ACGCA
+SRR2057595.10047803_TTCGT 16 chr19 40658723 255 67M * 0 0 * * XA:i:1 MD:Z:53T13 NM:i:1 UG:i:576 BX:Z:TTCGT
+SRR2057595.10047915_TCACA 0 chr19 13129273 255 45M * 0 0 * * XA:i:2 MD:Z:25C1T17 NM:i:2 UG:i:388 BX:Z:TCACA
+SRR2057595.10048372_GTCCC 0 chr19 12347657 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:372 BX:Z:GTCCC
+SRR2057595.10048372_GTCCC 0 chr19 12348043 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:374 BX:Z:GTCCC
+SRR2057595.10048372_GTCCC 16 chr19 15035071 255 32M * 0 0 * * XA:i:1 MD:Z:29T2 NM:i:1 UG:i:428 BX:Z:GTCCC
+SRR2057595.10048721_CTAAT 0 chr19 40194243 255 44M * 0 0 * * XA:i:2 MD:Z:5T20A17 NM:i:2 UG:i:562 BX:Z:CTAAT
+SRR2057595.10048861_CTAGA 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:43 BX:Z:CTAGA
+SRR2057595.10048933_GTCGC 0 chr19 12080548 255 51M * 0 0 * * XA:i:2 MD:Z:28C20G1 NM:i:2 UG:i:345 BX:Z:GTCGC
+SRR2057595.10048933_GTCGC 16 chr19 12084189 255 51M * 0 0 * * XA:i:2 MD:Z:1C20G28 NM:i:2 UG:i:352 BX:Z:GTCGC
+SRR2057595.10049852_AAAGG 16 chr19 23347776 255 34M * 0 0 * * XA:i:1 MD:Z:9T24 NM:i:1 UG:i:467 BX:Z:AAAGG
+SRR2057595.10049896_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.10050290_AAAGA 0 chr19 42921257 255 44M * 0 0 * * XA:i:2 MD:Z:4G9G29 NM:i:2 UG:i:590 BX:Z:AAAGA
+SRR2057595.10050342_TGAAC 16 chr19 5798677 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:250 BX:Z:TGAAC
+SRR2057595.10050663_GACGT 0 chr19 40194275 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:565 BX:Z:GACGT
+SRR2057595.10051008_TTCGT 16 chr19 40658723 255 67M * 0 0 * * XA:i:1 MD:Z:53T13 NM:i:1 UG:i:576 BX:Z:TTCGT
+SRR2057595.10051043_GCCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:66 BX:Z:GCCGA
+SRR2057595.1005223_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.10052510_ATACG 0 chr19 13129421 255 31M * 0 0 * * XA:i:1 MD:Z:11A19 NM:i:1 UG:i:393 BX:Z:ATACG
+SRR2057595.10052666_ATCCG 16 chr19 37369602 255 35M * 0 0 * * XA:i:0 MD:Z:35 NM:i:0 UG:i:544 BX:Z:ATCCG
+SRR2057595.10053188_CTTTC 16 chr19 4078298 255 45M * 0 0 * * XA:i:1 MD:Z:43A1 NM:i:1 UG:i:15 BX:Z:CTTTC
+SRR2057595.10053341_TTGCA 0 chr19 41640185 255 61M * 0 0 * * XA:i:0 MD:Z:61 NM:i:0 UG:i:581 BX:Z:TTGCA
+SRR2057595.10053375_ATGAA 0 chr19 56007800 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:666 BX:Z:ATGAA
+SRR2057595.10053481_CTCCG 0 chr19 11195966 255 44M * 0 0 * * XA:i:1 MD:Z:0T43 NM:i:1 UG:i:338 BX:Z:CTCCG
+SRR2057595.10053518_AATCG 16 chr19 4078303 255 67M * 0 0 * * XA:i:2 MD:Z:38A21A6 NM:i:2 UG:i:88 BX:Z:AATCG
+SRR2057595.1005354_GAGAG 16 chr19 4078298 255 50M * 0 0 * * XA:i:1 MD:Z:43A6 NM:i:1 UG:i:35 BX:Z:GAGAG
+SRR2057595.1005379_CCAAC 0 chr19 8820047 255 33M * 0 0 * * XA:i:0 MD:Z:33 NM:i:0 UG:i:315 BX:Z:CCAAC
+SRR2057595.10053918_AGTAT 0 chr19 10600420 255 29M * 0 0 * * XA:i:0 MD:Z:29 NM:i:0 UG:i:328 BX:Z:AGTAT
+SRR2057595.10053970_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:405 BX:Z:TATGG
+SRR2057595.10054046_ATAAA 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:175 BX:Z:ATAAA
+SRR2057595.10054497_AAAGA 0 chr19 42921257 255 44M * 0 0 * * XA:i:2 MD:Z:4G9G29 NM:i:2 UG:i:590 BX:Z:AAAGA
+SRR2057595.10055409_TAGAC 0 chr19 23806079 255 67M * 0 0 * * XA:i:1 MD:Z:41T25 NM:i:1 UG:i:468 BX:Z:TAGAC
+SRR2057595.10055838_CAGAC 0 chr19 5493782 255 41M * 0 0 * * XA:i:0 MD:Z:41 NM:i:0 UG:i:218 BX:Z:CAGAC
+SRR2057595.10055912_TCTCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:1 MD:Z:43A6 NM:i:1 UG:i:36 BX:Z:TCTCA
+SRR2057595.10055955_AGGAT 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:70 BX:Z:AGGAT
+SRR2057595.10056203_TGCAA 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:703 BX:Z:TGCAA
+SRR2057595.10056249_TCAGG 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:407 BX:Z:TCAGG
+SRR2057595.10057756_CGAAC 0 chr19 13129273 255 36M * 0 0 * * XA:i:2 MD:Z:25C1T8 NM:i:2 UG:i:386 BX:Z:CGAAC
+SRR2057595.10058241_TTAAA 16 chr19 4785463 255 21M * 0 0 * * XA:i:0 MD:Z:21 NM:i:0 UG:i:196 BX:Z:TTAAA
+SRR2057595.10058572_TCTTA 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:705 BX:Z:TCTTA
+SRR2057595.10058802_TAGTA 0 chr19 10274608 255 34M * 0 0 * * XA:i:1 MD:Z:9C24 NM:i:1 UG:i:324 BX:Z:TAGTA
+SRR2057595.10058946_AGCCA 0 chr19 43786861 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:594 BX:Z:AGCCA
+SRR2057595.10059254_GGTTC 16 chr19 56896659 255 23M * 0 0 * * XA:i:2 MD:Z:0C0A21 NM:i:2 UG:i:674 BX:Z:GGTTC
+SRR2057595.10059642_CTAGC 16 chr19 4078298 255 62M * 0 0 * * XA:i:1 MD:Z:43A18 NM:i:1 UG:i:63 BX:Z:CTAGC
+SRR2057595.10060193_ATAGA 0 chr19 38795805 255 62M * 0 0 * * XA:i:2 MD:Z:44C1A15 NM:i:2 UG:i:553 BX:Z:ATAGA
+SRR2057595.10060270_ATGGT 16 chr19 12086074 255 45M * 0 0 * * XA:i:1 MD:Z:19T25 NM:i:1 UG:i:361 BX:Z:ATGGT
+SRR2057595.10060437_TATAT 0 chr19 40194298 255 25M * 0 0 * * XA:i:1 MD:Z:13A11 NM:i:1 UG:i:567 BX:Z:TATAT
+SRR2057595.10060447_CTTAC 16 chr19 4078298 255 54M * 0 0 * * XA:i:2 MD:Z:42G0A10 NM:i:2 UG:i:49 BX:Z:CTTAC
+SRR2057595.10060568_GACGC 16 chr19 32419974 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:514 BX:Z:GACGC
+SRR2057595.10060757_AGCCG 16 chr19 4078299 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:11 BX:Z:AGCCG
+SRR2057595.10060776_TCTTG 16 chr19 4078423 255 67M * 0 0 * * XA:i:1 MD:Z:19A47 NM:i:1 UG:i:111 BX:Z:TCTTG
+SRR2057595.10061005_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:173 BX:Z:AGCCG
+SRR2057595.10061018_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:249 BX:Z:CACTG
+SRR2057595.10061192_ATCCG 16 chr19 37369602 255 35M * 0 0 * * XA:i:0 MD:Z:35 NM:i:0 UG:i:544 BX:Z:ATCCG
+SRR2057595.10061371_GCCTG 16 chr19 4078301 255 67M * 0 0 * * XA:i:2 MD:Z:40A21A4 NM:i:2 UG:i:75 BX:Z:GCCTG
+SRR2057595.10061403_AAGTA 16 chr19 31326011 255 57M * 0 0 * * XA:i:1 MD:Z:23A33 NM:i:1 UG:i:512 BX:Z:AAGTA
+SRR2057595.10061424_GCTAC 16 chr19 4078446 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:97 BX:Z:GCTAC
+SRR2057595.10061535_ATCAA 0 chr19 20547357 255 23M * 0 0 * * XA:i:0 MD:Z:23 NM:i:0 UG:i:452 BX:Z:ATCAA
+SRR2057595.10061661_ACAAA 16 chr19 5688438 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:222 BX:Z:ACAAA
+SRR2057595.10061745_ATATA 0 chr19 13129330 255 22M * 0 0 * * XA:i:1 MD:Z:0T21 NM:i:1 UG:i:422 BX:Z:ATATA
+SRR2057595.10062673_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.10062948_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10063079_GTCTA 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:124 BX:Z:GTCTA
+SRR2057595.10063521_AGATG 16 chr19 61240273 255 22M * 0 0 * * XA:i:1 MD:Z:5C16 NM:i:1 UG:i:707 BX:Z:AGATG
+SRR2057595.10064036_CAGCA 16 chr19 5801892 255 47M * 0 0 * * XA:i:0 MD:Z:47 NM:i:0 UG:i:258 BX:Z:CAGCA
+SRR2057595.1006417_GATCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:34 BX:Z:GATCA
+SRR2057595.10065256_AGGGG 0 chr19 13129331 255 37M * 0 0 * * XA:i:2 MD:Z:24C5A6 NM:i:2 UG:i:423 BX:Z:AGGGG
+SRR2057595.10065460_ATGGT 0 chr19 8798504 255 50M * 0 0 * * XA:i:0 MD:Z:50 NM:i:0 UG:i:291 BX:Z:ATGGT
+SRR2057595.10065656_GATGA 0 chr19 48194137 255 59M * 0 0 * * XA:i:0 MD:Z:59 NM:i:0 UG:i:635 BX:Z:GATGA
+SRR2057595.10065671_ATGAT 16 chr19 61240306 255 36M * 0 0 * * XA:i:2 MD:Z:16A4T14 NM:i:2 UG:i:716 BX:Z:ATGAT
+SRR2057595.10065713_ATGTC 0 chr19 37052811 255 64M * 0 0 * * XA:i:1 MD:Z:11C52 NM:i:1 UG:i:542 BX:Z:ATGTC
+SRR2057595.10065896_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10066051_AACTT 16 chr19 4078420 255 64M * 0 0 * * XA:i:2 MD:Z:2T19A41 NM:i:2 UG:i:55 BX:Z:AACTT
+SRR2057595.10066334_AGCCA 0 chr19 47324044 255 46M * 0 0 * * XA:i:0 MD:Z:46 NM:i:0 UG:i:627 BX:Z:AGCCA
+SRR2057595.10066646_GGTTC 16 chr19 56896659 255 23M * 0 0 * * XA:i:2 MD:Z:0C0A21 NM:i:2 UG:i:674 BX:Z:GGTTC
+SRR2057595.10066775_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:52 BX:Z:GTCAA
+SRR2057595.10066849_GGTCG 0 chr19 53686815 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:651 BX:Z:GGTCG
+SRR2057595.10066970_TAACA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:32 BX:Z:TAACA
+SRR2057595.10067118_TGATT 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:41 BX:Z:TGATT
+SRR2057595.10067277_TAGAC 0 chr19 23806079 255 67M * 0 0 * * XA:i:1 MD:Z:41T25 NM:i:1 UG:i:468 BX:Z:TAGAC
+SRR2057595.10067458_TACGG 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:1T43A21 NM:i:2 UG:i:71 BX:Z:TACGG
+SRR2057595.10067669_GCTTG 16 chr19 5797471 255 50M * 0 0 * * XA:i:0 MD:Z:50 NM:i:0 UG:i:226 BX:Z:GCTTG
+SRR2057595.10067834_GACGT 0 chr19 40194275 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:565 BX:Z:GACGT
+SRR2057595.1006784_GTCCA 16 chr19 4078431 255 67M * 0 0 * * XA:i:1 MD:Z:11A55 NM:i:1 UG:i:107 BX:Z:GTCCA
+SRR2057595.10067875_GCCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:66 BX:Z:GCCGA
+SRR2057595.1006816_GATCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:34 BX:Z:GATCA
+SRR2057595.10068282_TAACA 0 chr19 8799023 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:299 BX:Z:TAACA
+SRR2057595.1006840_TTAAA 16 chr19 4785463 255 21M * 0 0 * * XA:i:0 MD:Z:21 NM:i:0 UG:i:196 BX:Z:TTAAA
+SRR2057595.10068743_TTGGC 16 chr19 36085526 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:536 BX:Z:TTGGC
+SRR2057595.10068873_CTTTT 0 chr19 56656380 255 54M * 0 0 * * XA:i:0 MD:Z:54 NM:i:0 UG:i:669 BX:Z:CTTTT
+SRR2057595.10068999_AAGTA 16 chr19 31326011 255 57M * 0 0 * * XA:i:1 MD:Z:23A33 NM:i:1 UG:i:512 BX:Z:AAGTA
+SRR2057595.10069428_AACGC 16 chr19 4078298 255 51M * 0 0 * * XA:i:1 MD:Z:43A7 NM:i:1 UG:i:42 BX:Z:AACGC
+SRR2057595.10070094_TCTTA 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:705 BX:Z:TCTTA
+SRR2057595.10070448_GGATC 16 chr19 4078298 255 61M * 0 0 * * XA:i:2 MD:Z:42G0A17 NM:i:2 UG:i:61 BX:Z:GGATC
+SRR2057595.1007050_TATAC 0 chr19 8799026 255 60M * 0 0 * * XA:i:0 MD:Z:60 NM:i:0 UG:i:301 BX:Z:TATAC
+SRR2057595.10070871_GAAGT 16 chr19 27988575 255 52M * 0 0 * * XA:i:0 MD:Z:52 NM:i:0 UG:i:494 BX:Z:GAAGT
+SRR2057595.10071095_TGCAA 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:703 BX:Z:TGCAA
+SRR2057595.10071228_CTAGC 16 chr19 4078298 255 62M * 0 0 * * XA:i:1 MD:Z:43A18 NM:i:1 UG:i:63 BX:Z:CTAGC
+SRR2057595.10071424_CATTT 0 chr19 49059158 255 49M * 0 0 * * XA:i:2 MD:Z:30A7A10 NM:i:2 UG:i:639 BX:Z:CATTT
+SRR2057595.10071487_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:249 BX:Z:CACTG
+SRR2057595.10072063_CAGCA 16 chr19 5801892 255 47M * 0 0 * * XA:i:0 MD:Z:47 NM:i:0 UG:i:258 BX:Z:CAGCA
+SRR2057595.10072068_GCCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:66 BX:Z:GCCGA
+SRR2057595.10072172_TCTGC 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:178 BX:Z:TCTGC
+SRR2057595.10072478_AGCTT 16 chr19 5799262 255 20M * 0 0 * * XA:i:0 MD:Z:20 NM:i:0 UG:i:245 BX:Z:AGCTT
+SRR2057595.10072601_TTGGC 16 chr19 4078302 255 67M * 0 0 * * XA:i:2 MD:Z:39A21A5 NM:i:2 UG:i:79 BX:Z:TTGGC
+SRR2057595.10072627_AATAC 0 chr19 12046308 255 33M * 0 0 * * XA:i:1 MD:Z:23A9 NM:i:1 UG:i:343 BX:Z:AATAC
+SRR2057595.10072909_TCCAG 0 chr19 29662201 255 26M * 0 0 * * XA:i:1 MD:Z:0C25 NM:i:1 UG:i:509 BX:Z:TCCAG
+SRR2057595.10072922_TGATT 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:41 BX:Z:TGATT
+SRR2057595.10072936_TAGTA 16 chr19 61240268 255 27M * 0 0 * * XA:i:1 MD:Z:10C16 NM:i:1 UG:i:702 BX:Z:TAGTA
+SRR2057595.10073020_TGTTT 0 chr19 41595518 255 38M * 0 0 * * XA:i:1 MD:Z:25G12 NM:i:1 UG:i:579 BX:Z:TGTTT
+SRR2057595.10073067_CGTCT 0 chr19 13129329 255 35M * 0 0 * * XA:i:2 MD:Z:26C5A2 NM:i:2 UG:i:421 BX:Z:CGTCT
+SRR2057595.10073092_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.1007313_ACATT 0 chr19 8799370 255 64M * 0 0 * * XA:i:0 MD:Z:64 NM:i:0 UG:i:297 BX:Z:ACATT
+SRR2057595.10073348_CCTTG 16 chr19 4078298 255 49M * 0 0 * * XA:i:1 MD:Z:43A5 NM:i:1 UG:i:24 BX:Z:CCTTG
+SRR2057595.10073515_GGATC 16 chr19 4078298 255 61M * 0 0 * * XA:i:2 MD:Z:42G0A17 NM:i:2 UG:i:61 BX:Z:GGATC
+SRR2057595.10073784_TGATG 16 chr19 3544146 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:1 BX:Z:TGATG
+SRR2057595.10073896_TTCGT 0 chr19 36922761 255 57M * 0 0 * * XA:i:1 MD:Z:5C51 NM:i:1 UG:i:538 BX:Z:TTCGT
+SRR2057595.10073986_ATCTC 0 chr19 21910875 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:458 BX:Z:ATCTC
+SRR2057595.10074218_AGTGC 0 chr19 8798525 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:296 BX:Z:AGTGC
+SRR2057595.10074241_AAACA 16 chr19 4078299 255 49M * 0 0 * * XA:i:1 MD:Z:42A6 NM:i:1 UG:i:33 BX:Z:AAACA
+SRR2057595.10074267_GCTAC 0 chr19 13129281 255 31M * 0 0 * * XA:i:2 MD:Z:17C1T11 NM:i:2 UG:i:391 BX:Z:GCTAC
+SRR2057595.10074447_ATTAT 16 chr19 7546213 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:278 BX:Z:ATTAT
+SRR2057595.10074845_GTTGT 16 chr19 12564367 255 21M * 0 0 * * XA:i:2 MD:Z:0A12A7 NM:i:2 UG:i:380 BX:Z:GTTGT
+SRR2057595.10075349_ATGAT 16 chr19 61240306 255 36M * 0 0 * * XA:i:2 MD:Z:16A4T14 NM:i:2 UG:i:716 BX:Z:ATGAT
+SRR2057595.10075433_GGGGC 16 chr19 4078446 255 67M * 0 0 * * XA:i:1 MD:Z:66T0 NM:i:1 UG:i:98 BX:Z:GGGGC
+SRR2057595.10075536_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:53 BX:Z:GCATA
+SRR2057595.10075745_GTATT 0 chr19 47323072 255 47M * 0 0 * * XA:i:1 MD:Z:0C46 NM:i:1 UG:i:628 BX:Z:GTATT
+SRR2057595.10075769_ATTAT 16 chr19 7546213 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:278 BX:Z:ATTAT
+SRR2057595.10075776_GCTAC 16 chr19 4078446 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:97 BX:Z:GCTAC
+SRR2057595.10075922_AATAC 0 chr19 12046308 255 33M * 0 0 * * XA:i:1 MD:Z:23A9 NM:i:1 UG:i:343 BX:Z:AATAC
+SRR2057595.10075965_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:53 BX:Z:GCATA
+SRR2057595.10076063_AAATC 16 chr19 47891298 255 21M * 0 0 * * XA:i:2 MD:Z:4C11C4 NM:i:2 UG:i:633 BX:Z:AAATC
+SRR2057595.10076706_TTGCA 0 chr19 44434953 255 43M * 0 0 * * XA:i:0 MD:Z:43 NM:i:0 UG:i:602 BX:Z:TTGCA
+SRR2057595.1007711_TCCAG 0 chr19 29662201 255 26M * 0 0 * * XA:i:1 MD:Z:0C25 NM:i:1 UG:i:509 BX:Z:TCCAG
+SRR2057595.10077136_ATGTC 0 chr19 37052811 255 64M * 0 0 * * XA:i:1 MD:Z:11C52 NM:i:1 UG:i:542 BX:Z:ATGTC
+SRR2057595.10077390_GATCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:34 BX:Z:GATCA
+SRR2057595.10077550_GATCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:34 BX:Z:GATCA
+SRR2057595.10078118_AGCGC 16 chr19 27464368 255 52M * 0 0 * * XA:i:0 MD:Z:52 NM:i:0 UG:i:493 BX:Z:AGCGC
+SRR2057595.10078219_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:53 BX:Z:GCATA
+SRR2057595.10078231_ATGAT 16 chr19 61240306 255 36M * 0 0 * * XA:i:2 MD:Z:16A4T14 NM:i:2 UG:i:716 BX:Z:ATGAT
+SRR2057595.10078601_AATGC 0 chr19 8798773 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:306 BX:Z:AATGC
+SRR2057595.10079068_TTGGC 16 chr19 4078302 255 67M * 0 0 * * XA:i:2 MD:Z:39A21A5 NM:i:2 UG:i:79 BX:Z:TTGGC
+SRR2057595.10079368_GAGTG 0 chr19 8798502 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:289 BX:Z:GAGTG
+SRR2057595.10079546_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:648 BX:Z:CGGCC
+SRR2057595.10079549_TCTTA 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:705 BX:Z:TCTTA
+SRR2057595.10079658_CGAAC 0 chr19 13129273 255 36M * 0 0 * * XA:i:2 MD:Z:25C1T8 NM:i:2 UG:i:386 BX:Z:CGAAC
+SRR2057595.10080019_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:405 BX:Z:TATGG
+SRR2057595.10080347_GCAGA 0 chr19 8799844 255 53M * 0 0 * * XA:i:0 MD:Z:53 NM:i:0 UG:i:309 BX:Z:GCAGA
+SRR2057595.10080699_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10080920_GCTAT 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:706 BX:Z:GCTAT
+SRR2057595.10080946_TATAT 0 chr19 40194298 255 25M * 0 0 * * XA:i:1 MD:Z:13A11 NM:i:1 UG:i:567 BX:Z:TATAT
+SRR2057595.10081070_CGCCG 16 chr19 4078299 255 59M * 0 0 * * XA:i:1 MD:Z:42A16 NM:i:1 UG:i:58 BX:Z:CGCCG
+SRR2057595.10081274_AACGC 16 chr19 4078298 255 51M * 0 0 * * XA:i:1 MD:Z:43A7 NM:i:1 UG:i:42 BX:Z:AACGC
+SRR2057595.10081914_AATAC 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:125 BX:Z:AATAC
+SRR2057595.10082001_TCTTG 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:705 BX:Z:TCTTA
+SRR2057595.1008200_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.1008230_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10082591_ACAGA 16 chr19 4078299 255 22M * 0 0 * * XA:i:2 MD:Z:0C0C20 NM:i:2 UG:i:136 BX:Z:ACAGA
+SRR2057595.10082733_CCTTT 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:180 BX:Z:CCTTT
+SRR2057595.1008274_ATCAA 0 chr19 20547357 255 23M * 0 0 * * XA:i:0 MD:Z:23 NM:i:0 UG:i:452 BX:Z:ATCAA
+SRR2057595.100827_ACAGA 16 chr19 4078299 255 22M * 0 0 * * XA:i:2 MD:Z:0C0C20 NM:i:2 UG:i:136 BX:Z:ACAGA
+SRR2057595.10082802_GCCGT 0 chr19 30861987 255 20M * 0 0 * * XA:i:2 MD:Z:3C2T13 NM:i:2 UG:i:511 BX:Z:GCCGT
+SRR2057595.10082815_CCTCA 0 chr19 8798505 255 48M * 0 0 * * XA:i:0 MD:Z:48 NM:i:0 UG:i:292 BX:Z:CCTCA
+SRR2057595.1008318_CTATT 16 chr19 56874049 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:672 BX:Z:CTATT
+SRR2057595.10084177_ATCAA 0 chr19 20547357 255 23M * 0 0 * * XA:i:0 MD:Z:23 NM:i:0 UG:i:452 BX:Z:ATCAA
+SRR2057595.1008424_GATAA 16 chr19 47057431 255 22M * 0 0 * * XA:i:2 MD:Z:6T10T4 NM:i:2 UG:i:622 BX:Z:GATAA
+SRR2057595.10084297_CTTCA 0 chr19 13129483 255 30M * 0 0 * * XA:i:2 MD:Z:6G16A6 NM:i:2 UG:i:382 BX:Z:CTTCA
+SRR2057595.10084300_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:173 BX:Z:AGCCG
+SRR2057595.10084403_GACGT 0 chr19 40194275 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:565 BX:Z:GACGT
+SRR2057595.10084641_ACGCA 16 chr19 51217013 255 67M * 0 0 * * XA:i:2 MD:Z:3A46A16 NM:i:2 UG:i:647 BX:Z:ACGCA
+SRR2057595.10084680_CCCCG 16 chr19 4078298 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:184 BX:Z:CCCCG
+SRR2057595.1008532_CCGCG 0 chr19 8991126 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:318 BX:Z:CCGCG
+SRR2057595.1008533_AAGGT 0 chr19 8798514 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:294 BX:Z:AAGGT
+SRR2057595.10085421_CGAGA 0 chr19 6375345 255 21M * 0 0 * * XA:i:2 MD:Z:10C5G4 NM:i:2 UG:i:265 BX:Z:CGAGA
+SRR2057595.10085567_TATTC 16 chr19 5038295 255 24M * 0 0 * * XA:i:0 MD:Z:24 NM:i:0 UG:i:206 BX:Z:TATTC
+SRR2057595.10085614_AATTA 16 chr19 50733889 255 62M * 0 0 * * XA:i:2 MD:Z:56C0C4 NM:i:2 UG:i:645 BX:Z:AATTA
+SRR2057595.10085673_GAAGT 16 chr19 8360277 255 67M * 0 0 * * XA:i:2 MD:Z:10A52A3 NM:i:2 UG:i:285 BX:Z:GAAGT
+SRR2057595.10086547_TTCGT 0 chr19 47167097 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:623 BX:Z:TTCGT
+SRR2057595.10086746_TCTTC 16 chr19 4078299 255 36M * 0 0 * * XA:i:1 MD:Z:27A8 NM:i:1 UG:i:178 BX:Z:TCTGC
+SRR2057595.1008697_TTGCA 0 chr19 44434953 255 43M * 0 0 * * XA:i:0 MD:Z:43 NM:i:0 UG:i:602 BX:Z:TTGCA
+SRR2057595.10087261_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10087496_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:249 BX:Z:CACTG
+SRR2057595.10087607_ATACG 0 chr19 13129421 255 31M * 0 0 * * XA:i:1 MD:Z:11A19 NM:i:1 UG:i:393 BX:Z:ATACG
+SRR2057595.10087628_GGCGT 16 chr19 5797126 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:233 BX:Z:GGCGT
+SRR2057595.10087735_TCTGC 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:178 BX:Z:TCTGC
+SRR2057595.10088373_AAAGG 16 chr19 23347776 255 34M * 0 0 * * XA:i:1 MD:Z:9T24 NM:i:1 UG:i:467 BX:Z:AAAGG
+SRR2057595.1008837_GCGGA 16 chr19 4078298 255 48M * 0 0 * * XA:i:1 MD:Z:43A4 NM:i:1 UG:i:19 BX:Z:GCGGA
+SRR2057595.10088477_AGTCG 0 chr19 17767763 255 67M * 0 0 * * XA:i:2 MD:Z:10A4A51 NM:i:2 UG:i:440 BX:Z:AGTCG
+SRR2057595.1008854_TTCGT 0 chr19 47167097 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:623 BX:Z:TTCGT
+SRR2057595.10088899_CATAA 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:401 BX:Z:CATAA
+SRR2057595.10088953_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.10088992_TATTC 16 chr19 5038295 255 24M * 0 0 * * XA:i:0 MD:Z:24 NM:i:0 UG:i:206 BX:Z:TATTC
+SRR2057595.10089226_AAACA 16 chr19 4078299 255 49M * 0 0 * * XA:i:1 MD:Z:42A6 NM:i:1 UG:i:33 BX:Z:AAACA
+SRR2057595.10089360_ACCTG 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:126 BX:Z:ACCTG
+SRR2057595.10089372_CAAAC 0 chr19 34304620 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:531 BX:Z:CAAAC
+SRR2057595.10089645_CATTT 0 chr19 49059158 255 49M * 0 0 * * XA:i:2 MD:Z:30A7A10 NM:i:2 UG:i:639 BX:Z:CATTT
+SRR2057595.10089847_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10090471_ATTCT 0 chr19 3576314 255 23M * 0 0 * * XA:i:2 MD:Z:16T5T0 NM:i:2 UG:i:5 BX:Z:ATTCT
+SRR2057595.10090859_TTGCA 0 chr19 44434953 255 43M * 0 0 * * XA:i:0 MD:Z:43 NM:i:0 UG:i:602 BX:Z:TTGCA
+SRR2057595.10090930_CCTCG 0 chr19 13129273 255 46M * 0 0 * * XA:i:2 MD:Z:25C1T18 NM:i:2 UG:i:387 BX:Z:CCTCG
+SRR2057595.10090939_GATGG 0 chr19 44417644 255 23M * 0 0 * * XA:i:2 MD:Z:15T4C2 NM:i:2 UG:i:601 BX:Z:GATGG
+SRR2057595.10091088_TCGCT 16 chr19 4078298 255 64M * 0 0 * * XA:i:2 MD:Z:42G0A20 NM:i:2 UG:i:67 BX:Z:TCGCT
+SRR2057595.10091189_AGCAT 0 chr19 36976220 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:539 BX:Z:AGCAT
+SRR2057595.10091303_GTCCA 16 chr19 4078431 255 67M * 0 0 * * XA:i:1 MD:Z:11A55 NM:i:1 UG:i:107 BX:Z:GTCCA
+SRR2057595.10091425_AGCTT 16 chr19 5799262 255 20M * 0 0 * * XA:i:0 MD:Z:20 NM:i:0 UG:i:245 BX:Z:AGCTT
+SRR2057595.10091775_TAGTA 0 chr19 10274608 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:324 BX:Z:TAGTA
+SRR2057595.10091818_TCTGC 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:178 BX:Z:TCTGC
+SRR2057595.10092607_CATAA 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:401 BX:Z:CATAA
+SRR2057595.10092724_CTGAT 0 chr19 42626015 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:587 BX:Z:CTGAT
+SRR2057595.10092926_GCTAC 16 chr19 4078446 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:97 BX:Z:GCTAC
+SRR2057595.1009294_CCAAC 0 chr19 8820047 255 33M * 0 0 * * XA:i:0 MD:Z:33 NM:i:0 UG:i:315 BX:Z:CCAAC
+SRR2057595.10093528_ATACG 0 chr19 13129421 255 31M * 0 0 * * XA:i:1 MD:Z:11A19 NM:i:1 UG:i:393 BX:Z:ATACG
+SRR2057595.1009371_GCGGA 16 chr19 4078298 255 48M * 0 0 * * XA:i:1 MD:Z:43A4 NM:i:1 UG:i:19 BX:Z:GCGGA
+SRR2057595.10094012_GTGGA 16 chr19 35902240 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:535 BX:Z:GTGGA
+SRR2057595.1009415_TTAAA 16 chr19 4785463 255 21M * 0 0 * * XA:i:0 MD:Z:21 NM:i:0 UG:i:196 BX:Z:TTAAA
+SRR2057595.10094858_ATTAT 0 chr19 4755116 255 67M * 0 0 * * XA:i:2 MD:Z:42C11T12 NM:i:2 UG:i:195 BX:Z:ATTAT
+SRR2057595.10094990_TCCAG 0 chr19 29662201 255 26M * 0 0 * * XA:i:1 MD:Z:0C25 NM:i:1 UG:i:509 BX:Z:TCCAG
+SRR2057595.10095705_AACAG 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:174 BX:Z:AACAG
+SRR2057595.10095797_CGTCT 0 chr19 13129329 255 35M * 0 0 * * XA:i:2 MD:Z:26C5A2 NM:i:2 UG:i:421 BX:Z:CGTCT
+SRR2057595.10095837_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10096002_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:173 BX:Z:AGCCG
+SRR2057595.10096480_TTCGT 16 chr19 40658723 255 67M * 0 0 * * XA:i:1 MD:Z:53T13 NM:i:1 UG:i:576 BX:Z:TTCGT
+SRR2057595.10096536_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10096738_CTAGA 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:43 BX:Z:CTAGA
+SRR2057595.10096905_AATTA 16 chr19 50733890 255 61M * 0 0 * * XA:i:2 MD:Z:55C0C4 NM:i:2 UG:i:645 BX:Z:AATTA
+SRR2057595.10096962_TGTTT 0 chr19 41595518 255 38M * 0 0 * * XA:i:1 MD:Z:25G12 NM:i:1 UG:i:579 BX:Z:TGTTT
+SRR2057595.10096976_AGATC 16 chr19 24352786 255 67M * 0 0 * * XA:i:1 MD:Z:25C41 NM:i:1 UG:i:479 BX:Z:AGATC
+SRR2057595.10097042_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:249 BX:Z:CACTG
+SRR2057595.10097390_CCATC 0 chr19 5008676 255 30M * 0 0 * * XA:i:2 MD:Z:1A23G4 NM:i:2 UG:i:203 BX:Z:CCATC
+SRR2057595.10097856_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:405 BX:Z:TATGG
+SRR2057595.10097927_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:53 BX:Z:GCATA
+SRR2057595.10098678_CTCCG 0 chr19 11195966 255 43M * 0 0 * * XA:i:1 MD:Z:0T42 NM:i:1 UG:i:338 BX:Z:CTCCG
+SRR2057595.10098703_TAGTA 0 chr19 10274608 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:324 BX:Z:TAGTA
+SRR2057595.10098714_GCAGG 0 chr19 47903921 255 21M * 0 0 * * XA:i:2 MD:Z:2T0T17 NM:i:2 UG:i:634 BX:Z:GCAGG
+SRR2057595.10098837_AATTA 16 chr19 50733888 255 63M * 0 0 * * XA:i:2 MD:Z:57C0C4 NM:i:2 UG:i:645 BX:Z:AATTA
+SRR2057595.10098952_AAATC 16 chr19 47891298 255 21M * 0 0 * * XA:i:2 MD:Z:4C11C4 NM:i:2 UG:i:633 BX:Z:AAATC
+SRR2057595.10098_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10099454_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10099862_TGATT 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:41 BX:Z:TGATT
+SRR2057595.10099876_AGATC 16 chr19 24352786 255 67M * 0 0 * * XA:i:1 MD:Z:25C41 NM:i:1 UG:i:479 BX:Z:AGATC
+SRR2057595.10100225_GAAGT 16 chr19 8360277 255 67M * 0 0 * * XA:i:2 MD:Z:10A52A3 NM:i:2 UG:i:285 BX:Z:GAAGT
+SRR2057595.10100273_CCTCG 0 chr19 13129273 255 46M * 0 0 * * XA:i:2 MD:Z:25C1T18 NM:i:2 UG:i:387 BX:Z:CCTCG
+SRR2057595.10100361_AGAAT 16 chr19 24246487 255 44M * 0 0 * * XA:i:0 MD:Z:44 NM:i:0 UG:i:476 BX:Z:AGAAT
+SRR2057595.10100419_TCTTG 16 chr19 4078423 255 67M * 0 0 * * XA:i:1 MD:Z:19A47 NM:i:1 UG:i:111 BX:Z:TCTTG
+SRR2057595.10100887_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.10101063_ATGAA 0 chr19 56007800 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:666 BX:Z:ATGAA
+SRR2057595.10101443_TATAT 0 chr19 40194298 255 25M * 0 0 * * XA:i:1 MD:Z:13A11 NM:i:1 UG:i:567 BX:Z:TATAT
+SRR2057595.10101541_TCTAC 0 chr19 8798544 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:288 BX:Z:TCTAC
+SRR2057595.10101549_AAAGA 0 chr19 42921257 255 44M * 0 0 * * XA:i:2 MD:Z:4G9G29 NM:i:2 UG:i:590 BX:Z:AAAGA
+SRR2057595.10102419_GGGGC 16 chr19 4078446 255 67M * 0 0 * * XA:i:1 MD:Z:66T0 NM:i:1 UG:i:98 BX:Z:GGGGC
+SRR2057595.10102630_CTATT 16 chr19 56874049 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:672 BX:Z:CTATT
+SRR2057595.10102792_GCTAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:517 BX:Z:GCTAA
+SRR2057595.10102901_AACTT 16 chr19 4078420 255 64M * 0 0 * * XA:i:2 MD:Z:2T19A41 NM:i:2 UG:i:55 BX:Z:AACTT
+SRR2057595.10102918_ATTAT 16 chr19 7546213 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:278 BX:Z:ATTAT
+SRR2057595.10103451_GATCA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:34 BX:Z:GATCA
+SRR2057595.10103512_TCTTG 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:705 BX:Z:TCTTA
+SRR2057595.10103749_ATCAA 0 chr19 20547357 255 23M * 0 0 * * XA:i:0 MD:Z:23 NM:i:0 UG:i:452 BX:Z:ATCAA
+SRR2057595.10103791_ACGAC 16 chr19 4078298 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:186 BX:Z:ACGAC
+SRR2057595.10104373_ACAGA 16 chr19 4078299 255 22M * 0 0 * * XA:i:2 MD:Z:0C0C20 NM:i:2 UG:i:136 BX:Z:ACAGA
+SRR2057595.10104410_GCAGG 16 chr19 8963035 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:317 BX:Z:GCAGG
+SRR2057595.10104500_GTATT 0 chr19 47323072 255 47M * 0 0 * * XA:i:1 MD:Z:0C46 NM:i:1 UG:i:628 BX:Z:GTATT
+SRR2057595.10105258_CGCCG 16 chr19 4078299 255 59M * 0 0 * * XA:i:1 MD:Z:42A16 NM:i:1 UG:i:58 BX:Z:CGCCG
+SRR2057595.10105817_GCGGA 16 chr19 4078298 255 48M * 0 0 * * XA:i:1 MD:Z:43A4 NM:i:1 UG:i:19 BX:Z:GCGGA
+SRR2057595.10105818_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:1 MD:Z:0C35 NM:i:1 UG:i:173 BX:Z:AGCCG
+SRR2057595.10106002_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.10106174_CTGCC 16 chr19 3957282 255 22M * 0 0 * * XA:i:2 MD:Z:17C1G2 NM:i:2 UG:i:9 BX:Z:CTGCC
+SRR2057595.10106174_CTGCC 16 chr19 3970897 255 22M * 0 0 * * XA:i:2 MD:Z:17C1G2 NM:i:2 UG:i:10 BX:Z:CTGCC
+SRR2057595.10106212_AGCGC 16 chr19 27464368 255 52M * 0 0 * * XA:i:0 MD:Z:52 NM:i:0 UG:i:493 BX:Z:AGCGC
+SRR2057595.10106528_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.1010661_ATTAT 16 chr19 7546213 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:278 BX:Z:ATTAT
+SRR2057595.10106731_CCTCA 0 chr19 8798505 255 48M * 0 0 * * XA:i:0 MD:Z:48 NM:i:0 UG:i:292 BX:Z:CCTCA
+SRR2057595.10106761_CCTCG 0 chr19 13129273 255 46M * 0 0 * * XA:i:2 MD:Z:25C1T18 NM:i:2 UG:i:387 BX:Z:CCTCG
+SRR2057595.10106812_CCAAG 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:37 BX:Z:CCAAG
+SRR2057595.10106892_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:1 MD:Z:25T10 NM:i:1 UG:i:173 BX:Z:AGCCG
+SRR2057595.10107056_GGCAG 0 chr19 13129322 255 22M * 0 0 * * XA:i:0 MD:Z:22 NM:i:0 UG:i:409 BX:Z:GGCAG
+SRR2057595.1010759_TCTAA 0 chr19 12086447 255 46M * 0 0 * * XA:i:0 MD:Z:46 NM:i:0 UG:i:364 BX:Z:TCTAA
+SRR2057595.1010759_TCTAA 0 chr19 12086782 255 46M * 0 0 * * XA:i:0 MD:Z:46 NM:i:0 UG:i:369 BX:Z:TCTAA
+SRR2057595.10108058_TCTCG 16 chr19 6446235 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:266 BX:Z:TCTCG
+SRR2057595.10108108_TGTTT 0 chr19 41595519 255 37M * 0 0 * * XA:i:1 MD:Z:24G12 NM:i:1 UG:i:580 BX:Z:TGTTT
+SRR2057595.10108134_TCTTG 16 chr19 4078423 255 67M * 0 0 * * XA:i:1 MD:Z:19A47 NM:i:1 UG:i:111 BX:Z:TCTTG
+SRR2057595.10108322_TATTG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:404 BX:Z:TATTG
+SRR2057595.10108355_TAACA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:32 BX:Z:TAACA
+SRR2057595.10108853_GGCGT 16 chr19 5797126 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:233 BX:Z:GGCGT
+SRR2057595.10108990_TTGGC 16 chr19 36085526 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:536 BX:Z:TTGGC
+SRR2057595.10109290_TATGA 16 chr19 4797429 255 49M * 0 0 * * XA:i:0 MD:Z:49 NM:i:0 UG:i:197 BX:Z:TATGA
+SRR2057595.10109512_CTCTT 16 chr19 10761035 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:332 BX:Z:CTCTT
+SRR2057595.10109901_ATGAA 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:175 BX:Z:ATAAA
+SRR2057595.10110057_TTGTT 16 chr19 61240268 255 24M * 0 0 * * XA:i:1 MD:Z:10C13 NM:i:1 UG:i:696 BX:Z:TTGTT
+SRR2057595.10110159_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10110319_TAGTA 16 chr19 61240268 255 27M * 0 0 * * XA:i:1 MD:Z:10C16 NM:i:1 UG:i:702 BX:Z:TAGTA
+SRR2057595.10110664_TATTG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:404 BX:Z:TATTG
+SRR2057595.10110928_ATCCG 16 chr19 37369602 255 35M * 0 0 * * XA:i:0 MD:Z:35 NM:i:0 UG:i:544 BX:Z:ATCCG
+SRR2057595.10111198_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.10111819_CCTTT 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:180 BX:Z:CCTTT
+SRR2057595.1011210_GCTAC 16 chr19 4078446 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:97 BX:Z:GCTAC
+SRR2057595.10112142_GATCT 16 chr19 4078433 255 67M * 0 0 * * XA:i:1 MD:Z:9A57 NM:i:1 UG:i:90 BX:Z:GATCT
+SRR2057595.10112493_TCTGT 16 chr19 45885126 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:608 BX:Z:TCTGT
+SRR2057595.10112719_GATTG 0 chr19 8799830 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:314 BX:Z:GATTG
+SRR2057595.10113412_TGTTT 0 chr19 41595518 255 38M * 0 0 * * XA:i:1 MD:Z:25G12 NM:i:1 UG:i:579 BX:Z:TGTTT
+SRR2057595.1011350_CATGC 16 chr19 42000773 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:584 BX:Z:CATGC
+SRR2057595.10113554_TGACC 0 chr19 12086441 255 52M * 0 0 * * XA:i:0 MD:Z:52 NM:i:0 UG:i:362 BX:Z:TGACC
+SRR2057595.10113554_TGACC 0 chr19 12086776 255 52M * 0 0 * * XA:i:0 MD:Z:52 NM:i:0 UG:i:367 BX:Z:TGACC
+SRR2057595.10113832_CTAGA 0 chr19 7609388 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:279 BX:Z:CTAGA
+SRR2057595.10113868_ATGAA 0 chr19 56007800 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:666 BX:Z:ATGAA
+SRR2057595.10113897_CATGC 16 chr19 42000773 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:584 BX:Z:CATGC
+SRR2057595.10114178_TTAAA 16 chr19 4785463 255 21M * 0 0 * * XA:i:0 MD:Z:21 NM:i:0 UG:i:196 BX:Z:TTAAA
+SRR2057595.10114345_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10114548_GATGA 16 chr19 55763541 255 22M * 0 0 * * XA:i:2 MD:Z:2C14G4 NM:i:2 UG:i:662 BX:Z:GATGA
+SRR2057595.10114848_GTTGT 16 chr19 12564367 255 21M * 0 0 * * XA:i:2 MD:Z:0A12A7 NM:i:2 UG:i:380 BX:Z:GTTGT
+SRR2057595.10115148_CTATT 16 chr19 56874049 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:672 BX:Z:CTATT
+SRR2057595.10115906_TGGAC 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:127 BX:Z:TGGAC
+SRR2057595.10116129_GACTC 16 chr19 25016726 255 31M * 0 0 * * XA:i:0 MD:Z:31 NM:i:0 UG:i:483 BX:Z:GACTC
+SRR2057595.10116129_GACTC 16 chr19 60850233 255 31M * 0 0 * * XA:i:0 MD:Z:31 NM:i:0 UG:i:693 BX:Z:GACTC
+SRR2057595.10116527_CTTAC 16 chr19 4078298 255 54M * 0 0 * * XA:i:2 MD:Z:42G0A10 NM:i:2 UG:i:49 BX:Z:CTTAC
+SRR2057595.10116529_GTCCT 16 chr19 59694502 255 21M * 0 0 * * XA:i:2 MD:Z:8T0A11 NM:i:2 UG:i:688 BX:Z:GTCCT
+SRR2057595.1011687_TAACA 16 chr19 4078298 255 50M * 0 0 * * XA:i:2 MD:Z:42G0A6 NM:i:2 UG:i:32 BX:Z:TAACA
+SRR2057595.10116904_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10117105_CGCTT 0 chr19 13129322 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:406 BX:Z:CGCTT
+SRR2057595.10117768_TATCA 16 chr19 60837460 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:691 BX:Z:TATCA
+SRR2057595.1011778_TGTTT 0 chr19 41595518 255 38M * 0 0 * * XA:i:1 MD:Z:25G12 NM:i:1 UG:i:579 BX:Z:TGTTT
+SRR2057595.10117819_CTAGC 16 chr19 4078298 255 62M * 0 0 * * XA:i:2 MD:Z:21C21A18 NM:i:2 UG:i:63 BX:Z:CTAGC
+SRR2057595.10117947_AATCG 16 chr19 4078303 255 67M * 0 0 * * XA:i:2 MD:Z:38A21A6 NM:i:2 UG:i:88 BX:Z:AATCG
+SRR2057595.10118173_TTCGT 0 chr19 36922761 255 57M * 0 0 * * XA:i:1 MD:Z:5C51 NM:i:1 UG:i:538 BX:Z:TTCGT
+SRR2057595.10118916_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:173 BX:Z:AGCCG
+SRR2057595.10119454_TGTTT 0 chr19 41595518 255 38M * 0 0 * * XA:i:1 MD:Z:25G12 NM:i:1 UG:i:579 BX:Z:TGTTT
+SRR2057595.10119776_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:52 BX:Z:GTCAA
+SRR2057595.10119820_CAGAC 0 chr19 5493782 255 41M * 0 0 * * XA:i:0 MD:Z:41 NM:i:0 UG:i:218 BX:Z:CAGAC
+SRR2057595.10119919_GAATG 16 chr19 33191616 255 28M * 0 0 * * XA:i:2 MD:Z:1G17G8 NM:i:2 UG:i:526 BX:Z:GAATG
+SRR2057595.10120218_TGGTA 16 chr19 28085954 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:498 BX:Z:TGGTA
+SRR2057595.10120257_TCAGG 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:407 BX:Z:TCAGG
+SRR2057595.10120271_GTCCC 0 chr19 12347657 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:372 BX:Z:GTCCC
+SRR2057595.10120271_GTCCC 0 chr19 12348043 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:374 BX:Z:GTCCC
+SRR2057595.10120271_GTCCC 16 chr19 15035071 255 32M * 0 0 * * XA:i:1 MD:Z:29T2 NM:i:1 UG:i:428 BX:Z:GTCCC
+SRR2057595.10120377_TATTC 16 chr19 5038295 255 24M * 0 0 * * XA:i:0 MD:Z:24 NM:i:0 UG:i:206 BX:Z:TATTC
+SRR2057595.10120569_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:53 BX:Z:GCATA
+SRR2057595.10120734_AGTAA 16 chr19 4078423 255 67M * 0 0 * * XA:i:2 MD:Z:19A24T22 NM:i:2 UG:i:110 BX:Z:AGTAA
+SRR2057595.10120758_AACGC 16 chr19 4078298 255 51M * 0 0 * * XA:i:1 MD:Z:43A7 NM:i:1 UG:i:42 BX:Z:AACGC
+SRR2057595.10120905_ACCTG 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:126 BX:Z:ACCTG
+SRR2057595.10121117_TGTTC 0 chr19 61241963 255 27M * 0 0 * * XA:i:2 MD:Z:20A5G0 NM:i:2 UG:i:719 BX:Z:TGTTC
+SRR2057595.10121638_AATTA 16 chr19 50733888 255 63M * 0 0 * * XA:i:2 MD:Z:57C0C4 NM:i:2 UG:i:645 BX:Z:AATTA
+SRR2057595.10122214_TATTG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:404 BX:Z:TATTG
+SRR2057595.10122328_TAAAG 16 chr19 61240268 255 28M * 0 0 * * XA:i:1 MD:Z:10C17 NM:i:1 UG:i:710 BX:Z:TAAAG
+SRR2057595.10122369_AGCTT 16 chr19 5799262 255 20M * 0 0 * * XA:i:0 MD:Z:20 NM:i:0 UG:i:245 BX:Z:AGCTT
+SRR2057595.10122580_AAGGT 0 chr19 8798514 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:294 BX:Z:AAGGT
+SRR2057595.101226_AACTT 16 chr19 4078420 255 64M * 0 0 * * XA:i:2 MD:Z:2T19A41 NM:i:2 UG:i:55 BX:Z:AACTT
+SRR2057595.10123331_ATTAT 16 chr19 7546213 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:278 BX:Z:ATTAT
+SRR2057595.10123377_CTAAT 0 chr19 40194243 255 44M * 0 0 * * XA:i:2 MD:Z:5T20A17 NM:i:2 UG:i:562 BX:Z:CTAAT
+SRR2057595.1012355_CAACT 16 chr19 4078298 255 49M * 0 0 * * XA:i:2 MD:Z:42G0A5 NM:i:2 UG:i:25 BX:Z:CAACT
+SRR2057595.10123626_TCTAC 0 chr19 8798544 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:288 BX:Z:TCTAC
+SRR2057595.10124059_GATGA 16 chr19 55763541 255 22M * 0 0 * * XA:i:2 MD:Z:2C14G4 NM:i:2 UG:i:662 BX:Z:GATGA
+SRR2057595.1012426_CATTT 0 chr19 49059158 255 49M * 0 0 * * XA:i:2 MD:Z:30A7A10 NM:i:2 UG:i:639 BX:Z:CATTT
+SRR2057595.10125107_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:405 BX:Z:TATGG
+SRR2057595.1012543_GGATC 16 chr19 4078298 255 61M * 0 0 * * XA:i:2 MD:Z:42G0A17 NM:i:2 UG:i:61 BX:Z:GGATC
+SRR2057595.10125580_TGCTA 0 chr19 10830415 255 21M * 0 0 * * XA:i:2 MD:Z:0A10C9 NM:i:2 UG:i:334 BX:Z:TGCTA
+SRR2057595.1012559_TGATT 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:41 BX:Z:TGATT
+SRR2057595.10125877_CTATT 16 chr19 56874049 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:672 BX:Z:CTATT
+SRR2057595.10125930_ATCGG 0 chr19 8799853 255 44M * 0 0 * * XA:i:0 MD:Z:44 NM:i:0 UG:i:310 BX:Z:ATCGG
+SRR2057595.10125966_GATGA 16 chr19 55763541 255 22M * 0 0 * * XA:i:2 MD:Z:2C14G4 NM:i:2 UG:i:662 BX:Z:GATGA
+SRR2057595.10126475_TCAGG 0 chr19 38669715 255 54M * 0 0 * * XA:i:0 MD:Z:54 NM:i:0 UG:i:550 BX:Z:TCAGG
+SRR2057595.10126817_CAGAC 0 chr19 5493782 255 41M * 0 0 * * XA:i:0 MD:Z:41 NM:i:0 UG:i:218 BX:Z:CAGAC
+SRR2057595.1012699_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10127386_GCAGA 0 chr19 8799844 255 53M * 0 0 * * XA:i:0 MD:Z:53 NM:i:0 UG:i:309 BX:Z:GCAGA
+SRR2057595.10127482_AAGGT 0 chr19 8798514 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:294 BX:Z:AAGGT
+SRR2057595.10127633_GGACC 16 chr19 4078298 255 28M * 0 0 * * XA:i:1 MD:Z:18C9 NM:i:1 UG:i:143 BX:Z:GGACC
+SRR2057595.10127800_CCTTT 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:180 BX:Z:CCTTT
+SRR2057595.10127806_TTTTC 16 chr19 4078296 255 67M * 0 0 * * XA:i:2 MD:Z:0T44A21 NM:i:2 UG:i:69 BX:Z:TTTTC
+SRR2057595.10127925_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10127969_TCAGC 16 chr19 4078298 255 49M * 0 0 * * XA:i:1 MD:Z:43A5 NM:i:1 UG:i:23 BX:Z:TCAGC
+SRR2057595.10128074_TATTC 16 chr19 5038295 255 24M * 0 0 * * XA:i:0 MD:Z:24 NM:i:0 UG:i:206 BX:Z:TATTC
+SRR2057595.10128154_CTAGG 16 chr19 5798663 255 67M * 0 0 * * XA:i:2 MD:Z:0G0G65 NM:i:2 UG:i:242 BX:Z:CTAGG
+SRR2057595.10128297_ATAAA 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:175 BX:Z:ATAAA
+SRR2057595.10128465_TTGCA 0 chr19 44434953 255 43M * 0 0 * * XA:i:0 MD:Z:43 NM:i:0 UG:i:602 BX:Z:TTGCA
+SRR2057595.10128496_AGCCG 16 chr19 4078298 255 39M * 0 0 * * XA:i:0 MD:Z:39 NM:i:0 UG:i:11 BX:Z:AGCCG
+SRR2057595.1012868_AAACA 16 chr19 4078299 255 49M * 0 0 * * XA:i:1 MD:Z:42A6 NM:i:1 UG:i:33 BX:Z:AAACA
+SRR2057595.1012871_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.10128720_CCTCA 0 chr19 8798505 255 48M * 0 0 * * XA:i:0 MD:Z:48 NM:i:0 UG:i:292 BX:Z:CCTCA
+SRR2057595.10128783_TTGCA 0 chr19 44434953 255 43M * 0 0 * * XA:i:0 MD:Z:43 NM:i:0 UG:i:602 BX:Z:TTGCA
+SRR2057595.10128887_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.10128931_AGCCG 16 chr19 4078299 255 36M * 0 0 * * XA:i:0 MD:Z:36 NM:i:0 UG:i:173 BX:Z:AGCCG
+SRR2057595.10129033_ACAGA 16 chr19 4078299 255 22M * 0 0 * * XA:i:2 MD:Z:0C0C20 NM:i:2 UG:i:136 BX:Z:ACAGA
+SRR2057595.10129046_TCAAA 16 chr19 4078298 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:185 BX:Z:TCAAA
+SRR2057595.10129405_ATGAA 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:175 BX:Z:ATAAA
+SRR2057595.1012950_GGGAT 0 chr19 13129424 255 25M * 0 0 * * XA:i:1 MD:Z:8A16 NM:i:1 UG:i:394 BX:Z:GGGAT
+SRR2057595.10129521_CGCCG 16 chr19 4078299 255 59M * 0 0 * * XA:i:1 MD:Z:42A16 NM:i:1 UG:i:58 BX:Z:CGCCG
+SRR2057595.10129734_TATTG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:404 BX:Z:TATTG
+SRR2057595.10130199_GGCAG 0 chr19 13129322 255 22M * 0 0 * * XA:i:0 MD:Z:22 NM:i:0 UG:i:409 BX:Z:GGCAG
+SRR2057595.10130333_GTCGC 0 chr19 12080548 255 51M * 0 0 * * XA:i:2 MD:Z:28C20G1 NM:i:2 UG:i:345 BX:Z:GTCGC
+SRR2057595.10130333_GTCGC 16 chr19 12084189 255 51M * 0 0 * * XA:i:2 MD:Z:1C20G28 NM:i:2 UG:i:352 BX:Z:GTCGC
+SRR2057595.10130767_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.10130878_TTAGT 16 chr19 4078302 255 67M * 0 0 * * XA:i:2 MD:Z:39A21A5 NM:i:2 UG:i:81 BX:Z:TTAGT
+SRR2057595.10131031_AGCTT 16 chr19 5799262 255 20M * 0 0 * * XA:i:0 MD:Z:20 NM:i:0 UG:i:245 BX:Z:AGCTT
+SRR2057595.10131148_CAGCA 16 chr19 5801892 255 47M * 0 0 * * XA:i:0 MD:Z:47 NM:i:0 UG:i:258 BX:Z:CAGCA
+SRR2057595.10131269_CATGC 0 chr19 13129570 255 22M * 0 0 * * XA:i:1 MD:Z:9A12 NM:i:1 UG:i:392 BX:Z:CATGC
+SRR2057595.10131482_CTTTC 16 chr19 4078298 255 53M * 0 0 * * XA:i:2 MD:Z:42G0A9 NM:i:2 UG:i:47 BX:Z:CTTTC
+SRR2057595.10132002_CCCGT 16 chr19 47349292 255 19M * 0 0 * * XA:i:2 MD:Z:8A3G6 NM:i:2 UG:i:629 BX:Z:CCCGT
+SRR2057595.10132034_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:534 BX:Z:ATACC
+SRR2057595.10132108_TCTAC 0 chr19 8798544 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:288 BX:Z:TCTAC
+SRR2057595.10132494_CGAAC 0 chr19 13129273 255 36M * 0 0 * * XA:i:2 MD:Z:25C1T8 NM:i:2 UG:i:386 BX:Z:CGAAC
+SRR2057595.10133086_TCTTA 16 chr19 61240268 255 27M * 0 0 * * XA:i:1 MD:Z:10C16 NM:i:1 UG:i:705 BX:Z:TCTTA
+SRR2057595.10133357_GTCGC 0 chr19 12080548 255 51M * 0 0 * * XA:i:2 MD:Z:28C20G1 NM:i:2 UG:i:345 BX:Z:GTCGC
+SRR2057595.10133357_GTCGC 16 chr19 12084189 255 51M * 0 0 * * XA:i:2 MD:Z:1C20G28 NM:i:2 UG:i:352 BX:Z:GTCGC
+SRR2057595.1013336_TTGTT 16 chr19 61240268 255 24M * 0 0 * * XA:i:1 MD:Z:10C13 NM:i:1 UG:i:696 BX:Z:TTGTT
+SRR2057595.10133381_AGAGT 16 chr19 24180225 255 55M * 0 0 * * XA:i:1 MD:Z:41C13 NM:i:1 UG:i:474 BX:Z:AGAGT
+SRR2057595.10133440_CTGCG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:712 BX:Z:CTGCG
+SRR2057595.10134016_GACAC 0 chr19 12348541 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:378 BX:Z:GACAC
+SRR2057595.10134016_GACAC 16 chr19 15034579 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:429 BX:Z:GACAC
+SRR2057595.10134072_GCAGG 16 chr19 8963035 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:317 BX:Z:GCAGG
+SRR2057595.1013452_ATATA 0 chr19 13129330 255 22M * 0 0 * * XA:i:1 MD:Z:0T21 NM:i:1 UG:i:422 BX:Z:ATATA
+SRR2057595.10134979_AGTAT 0 chr19 10600420 255 29M * 0 0 * * XA:i:0 MD:Z:29 NM:i:0 UG:i:328 BX:Z:AGTAT
+SRR2057595.10135304_GTCCA 16 chr19 4078431 255 67M * 0 0 * * XA:i:1 MD:Z:11A55 NM:i:1 UG:i:107 BX:Z:GTCCA
+SRR2057595.1013548_TGTTT 16 chr19 50526830 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:643 BX:Z:TGTTT
+SRR2057595.10135758_TTGCA 0 chr19 44434953 255 43M * 0 0 * * XA:i:0 MD:Z:43 NM:i:0 UG:i:602 BX:Z:TTGCA
+SRR2057595.10135807_CCCGT 16 chr19 47349292 255 19M * 0 0 * * XA:i:2 MD:Z:8A3G6 NM:i:2 UG:i:629 BX:Z:CCCGT
+SRR2057595.1013613_GATTG 0 chr19 55501486 255 31M * 0 0 * * XA:i:1 MD:Z:8A22 NM:i:1 UG:i:659 BX:Z:GATTG
+SRR2057595.1013616_ATAGA 0 chr19 38795805 255 62M * 0 0 * * XA:i:1 MD:Z:46A15 NM:i:1 UG:i:553 BX:Z:ATAGA
+SRR2057595.10136267_TTCGC 16 chr19 4078428 255 67M * 0 0 * * XA:i:2 MD:Z:14A24T27 NM:i:2 UG:i:74 BX:Z:TTCGC
+SRR2057595.10136714_ATCCG 16 chr19 37369602 255 35M * 0 0 * * XA:i:0 MD:Z:35 NM:i:0 UG:i:544 BX:Z:ATCCG
+SRR2057595.10136765_GCTAT 0 chr19 57701750 255 67M * 0 0 * * XA:i:2 MD:Z:34T1T30 NM:i:2 UG:i:677 BX:Z:GCTAT
+SRR2057595.10137151_ATTCT 0 chr19 3576314 255 23M * 0 0 * * XA:i:2 MD:Z:16T5T0 NM:i:2 UG:i:5 BX:Z:ATTCT
+SRR2057595.10137262_ACAAA 16 chr19 4078298 255 49M * 0 0 * * XA:i:1 MD:Z:43A5 NM:i:1 UG:i:27 BX:Z:ACAAA
+SRR2057595.10137317_GATTG 0 chr19 8799830 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:314 BX:Z:GATTG
+SRR2057595.10137603_GCTAT 16 chr19 61240267 255 28M * 0 0 * * XA:i:1 MD:Z:11C16 NM:i:1 UG:i:706 BX:Z:GCTAT
+SRR2057595.10137788_TAGTA 0 chr19 10274608 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:324 BX:Z:TAGTA
+SRR2057595.1013793_GCGCA 0 chr19 8798523 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:295 BX:Z:GCGCA
+SRR2057595.10138029_GTTGT 16 chr19 12564367 255 21M * 0 0 * * XA:i:2 MD:Z:0A12A7 NM:i:2 UG:i:380 BX:Z:GTTGT
+SRR2057595.10138656_CTAGC 16 chr19 4078298 255 62M * 0 0 * * XA:i:1 MD:Z:43A18 NM:i:1 UG:i:63 BX:Z:CTAGC
+SRR2057595.10138697_GCCGT 0 chr19 30861987 255 20M * 0 0 * * XA:i:2 MD:Z:3C2T13 NM:i:2 UG:i:511 BX:Z:GCCGT
+SRR2057595.10138764_GATGG 0 chr19 44417644 255 23M * 0 0 * * XA:i:2 MD:Z:15T4C2 NM:i:2 UG:i:601 BX:Z:GATGG
+SRR2057595.10138897_TGATT 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:41 BX:Z:TGATT
+SRR2057595.10139239_GAGTG 0 chr19 8798502 255 51M * 0 0 * * XA:i:0 MD:Z:51 NM:i:0 UG:i:289 BX:Z:GAGTG
+SRR2057595.10139499_AGTCT 0 chr19 13129558 255 37M * 0 0 * * XA:i:1 MD:Z:21A15 NM:i:1 UG:i:398 BX:Z:AGTCT
+SRR2057595.10139596_GCTAC 16 chr19 4078446 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:97 BX:Z:GCTAC
+SRR2057595.10139652_GGATG 0 chr19 13129322 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:402 BX:Z:GGATG
+SRR2057595.10139674_ATGAA 16 chr19 4078298 255 37M * 0 0 * * XA:i:0 MD:Z:37 NM:i:0 UG:i:175 BX:Z:ATAAA
+SRR2057595.10139952_TAGTA 16 chr19 61240268 255 27M * 0 0 * * XA:i:1 MD:Z:10C16 NM:i:1 UG:i:702 BX:Z:TAGTA
+SRR2057595.10140058_ATATA 0 chr19 13129330 255 22M * 0 0 * * XA:i:1 MD:Z:0T21 NM:i:1 UG:i:422 BX:Z:ATATA
+SRR2057595.10141122_GTCCC 0 chr19 12347657 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:372 BX:Z:GTCCC
+SRR2057595.10141122_GTCCC 0 chr19 12348043 255 32M * 0 0 * * XA:i:0 MD:Z:32 NM:i:0 UG:i:374 BX:Z:GTCCC
+SRR2057595.10141122_GTCCC 16 chr19 15035071 255 32M * 0 0 * * XA:i:1 MD:Z:29T2 NM:i:1 UG:i:428 BX:Z:GTCCC
+SRR2057595.10141295_TAGTA 0 chr19 10274608 255 34M * 0 0 * * XA:i:0 MD:Z:34 NM:i:0 UG:i:324 BX:Z:TAGTA
+SRR2057595.10142441_GTCTA 16 chr19 4078420 255 67M * 0 0 * * XA:i:2 MD:Z:2T19A44 NM:i:2 UG:i:124 BX:Z:GTCTA
+SRR2057595.10142482_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:274 BX:Z:GCCGA
+SRR2057595.10143102_AAGTA 16 chr19 31326011 255 57M * 0 0 * * XA:i:1 MD:Z:23A33 NM:i:1 UG:i:512 BX:Z:AAGTA
+SRR2057595.10143387_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:53 BX:Z:GCATA
+SRR2057595.10143631_ATTTT 0 chr19 45095257 255 57M * 0 0 * * XA:i:0 MD:Z:57 NM:i:0 UG:i:606 BX:Z:ATTTT
+SRR2057595.10143687_CGCTT 0 chr19 13129322 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:406 BX:Z:CGCTT
+SRR2057595.10143772_TGATT 16 chr19 4078299 255 50M * 0 0 * * XA:i:2 MD:Z:41G0A7 NM:i:2 UG:i:41 BX:Z:TGATT
+SRR2057595.10143909_CAGAC 0 chr19 5493782 255 41M * 0 0 * * XA:i:0 MD:Z:41 NM:i:0 UG:i:218 BX:Z:CAGAC
+SRR2057595.10143972_CTTAC 16 chr19 4078298 255 54M * 0 0 * * XA:i:2 MD:Z:42G0A10 NM:i:2 UG:i:49 BX:Z:CTTAC
+SRR2057595.10144216_CATAA 0 chr19 13129322 255 35M * 0 0 * * XA:i:1 MD:Z:33C1 NM:i:1 UG:i:401 BX:Z:CATAA
+SRR2057595.10144367_ATGAT 16 chr19 61240306 255 36M * 0 0 * * XA:i:2 MD:Z:16A4T14 NM:i:2 UG:i:716 BX:Z:ATGAT
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_in2.bam
Binary file test-data/group_in2.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_in3.bam
Binary file test-data/group_in3.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_in4.bam
Binary file test-data/group_in4.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_in5.bam
Binary file test-data/group_in5.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_in6.bam
Binary file test-data/group_in6.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out1.bam
Binary file test-data/group_out1.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out2.bam
Binary file test-data/group_out2.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out3.bam
Binary file test-data/group_out3.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out3.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group_out3.tab Tue Aug 29 17:37:07 2017 -0400
@@ -0,0 +1,498 @@
+read_id contig position gene umi umi_count final_umi final_umi_count unique_id
+chrM_81_583_3:0:0_2:0:0_f4/1_TT chrM 80 NA TT 1 TT 1 0
+chrM_110_732_3:0:0_2:0:0_160/1_CC chrM 109 NA CC 1 CC 1 1
+chrM_118_613_6:0:0_4:0:0_169/1_AG chrM 117 NA AG 1 AG 1 2
+chrM_149_684_2:0:0_2:0:0_6e/1_TA chrM 148 NA TA 1 TA 1 3
+chrM_152_616_6:0:0_2:0:0_84/1_GC chrM 151 NA GC 1 GC 1 4
+chrM_247_748_8:0:0_1:0:0_1b7/1_GC chrM 246 NA GC 1 GC 1 5
+chrM_280_772_1:0:0_9:0:0_31/1_CG chrM 279 NA CG 1 CG 1 6
+chrM_292_819_2:0:0_1:0:0_18d/1_CA chrM 291 NA CA 1 CA 1 7
+chrM_390_890_3:0:0_6:0:0_bf/1_CA chrM 389 NA CA 1 CA 1 8
+chrM_447_921_2:0:0_3:0:0_1cc/1_AC chrM 446 NA AC 1 AC 1 9
+chrM_469_983_2:0:0_1:0:0_121/1_AC chrM 468 NA AC 1 AC 1 10
+chrM_541_1074_3:0:0_8:1:0_22/1_AC chrM 540 NA AC 1 AC 1 11
+chrM_8_556_3:0:0_2:0:0_1b1/1_AC chrM 556 NA AC 1 AC 1 12
+chrM_112_577_2:0:0_4:0:0_17b/1_CG chrM 577 NA CG 1 CG 1 13
+chrM_627_1063_6:0:0_4:1:0_12a/1_AA chrM 626 NA AA 1 AA 1 14
+chrM_164_650_5:0:0_3:0:0_164/1_AC chrM 650 NA AC 1 AC 1 15
+chrM_200_695_6:0:0_2:0:0_5a/1_TA chrM 695 NA TA 3 TA 3 16
+chrM_168_695_5:0:0_2:0:0_1af/1_TA chrM 695 NA TA 3 TA 3 16
+chrM_170_695_1:0:0_6:0:0_1e3/1_TA chrM 695 NA TA 3 TA 3 16
+chrM_209_705_3:0:0_2:0:0_1b3/1_TA chrM 705 NA TA 1 TA 1 17
+chrM_288_807_3:0:0_5:0:0_8e/1_AG chrM 807 NA AG 1 AG 1 18
+chrM_818_1274_1:1:0_4:0:0_124/1_TC chrM 817 NA TC 1 TC 1 19
+chrM_442_872_4:0:0_6:0:0_146/1_AT chrM 872 NA AT 1 AT 1 20
+chrM_460_919_3:0:0_1:0:0_0/1_GA chrM 919 NA GA 1 GA 1 21
+chrM_384_950_5:0:0_2:0:0_34/1_GG chrM 950 NA GG 1 GG 1 22
+chrM_476_980_5:0:0_2:0:0_133/1_TA chrM 980 NA TA 1 TA 1 23
+chrM_552_999_4:0:0_5:0:0_bb/1_AT chrM 999 NA AT 1 AT 1 24
+chrM_512_1030_5:0:0_7:1:0_a5/1_AC chrM 1030 NA AC 1 AC 1 25
+chrM_1103_1634_5:0:0_3:0:0_36/1_TA chrM 1102 NA TA 1 TA 1 26
+chrM_648_1148_3:0:0_3:1:0_1d1/1_TT chrM 1148 NA TT 1 TT 1 27
+chrM_1167_1797_8:0:0_2:1:0_14e/1_GT chrM 1166 NA GT 1 GT 1 28
+chrM_619_1169_3:0:0_5:1:0_33/1_CC chrM 1169 NA CC 1 CC 1 29
+chrM_668_1248_0:0:0_4:0:0_fa/1_TT chrM 1248 NA TT 1 TT 1 30
+chrM_1288_1759_4:0:0_2:1:0_a1/1_TA chrM 1287 NA TA 1 TA 1 31
+chrM_1327_1786_4:0:0_3:1:0_1ad/1_CA chrM 1326 NA CA 1 CA 1 32
+chrM_866_1351_5:1:0_6:0:0_1c9/1_TA chrM 1351 NA TA 1 TA 1 33
+chrM_853_1366_6:1:0_4:0:0_13b/1_TC chrM 1366 NA TC 1 TC 1 34
+chrM_1399_1851_2:0:0_11:1:0_85/1_AT chrM 1398 NA AT 1 AT 1 35
+chrM_946_1444_4:1:0_6:0:0_113/1_TT chrM 1444 NA TT 1 TT 1 36
+chrM_943_1485_2:1:0_5:0:0_1e2/1_AT chrM 1485 NA AT 1 AT 1 37
+chrM_1022_1501_4:0:0_5:0:0_132/1_GA chrM 1501 NA GA 1 GA 1 38
+chrM_1504_2013_4:1:0_3:0:0_10b/1_AT chrM 1503 NA AT 1 AT 1 39
+chrM_1505_1934_1:1:0_5:0:0_157/1_TC chrM 1504 NA TC 1 TC 1 40
+chrM_997_1511_2:1:0_1:0:0_1d8/1_AT chrM 1511 NA AT 1 AT 1 41
+chrM_1521_2070_5:1:0_3:0:0_1a/1_TA chrM 1520 NA TA 1 TA 1 42
+chrM_1575_2126_5:1:0_2:1:0_18c/1_TA chrM 1574 NA TA 1 TA 1 43
+chrM_1063_1598_5:0:0_5:0:0_f5/1_TG chrM 1598 NA TG 1 TG 1 44
+chrM_1605_2128_3:1:0_4:1:0_1ea/1_TT chrM 1604 NA TT 1 TT 1 45
+chrM_1065_1609_3:0:0_5:0:0_18e/1_TA chrM 1609 NA TA 1 TA 1 46
+chrM_1140_1619_1:0:0_4:0:0_74/1_TT chrM 1619 NA TT 1 TT 1 47
+chrM_1111_1626_4:0:0_2:0:0_186/1_AC chrM 1626 NA AC 1 AC 1 48
+chrM_1664_2135_0:1:0_3:1:0_179/1_TT chrM 1663 NA TT 1 TT 1 49
+chrM_1699_2147_1:0:0_7:0:0_10c/1_AA chrM 1698 NA AA 1 AA 1 50
+chrM_1706_2240_3:0:0_6:0:0_99/1_GT chrM 1705 NA GT 1 GT 1 51
+chrM_1756_2309_0:0:0_3:0:0_c3/1_AT chrM 1755 NA AT 1 AT 1 52
+chrM_1344_1758_4:0:0_3:1:0_75/1_TT chrM 1758 NA TT 1 TT 1 53
+chrM_1223_1777_5:0:0_6:1:0_42/1_TG chrM 1777 NA TG 1 TG 1 54
+chrM_1790_2351_4:0:0_4:0:0_f3/1_CC chrM 1789 NA CC 1 CC 1 55
+chrM_1308_1807_4:0:0_4:1:0_45/1_TA chrM 1807 NA TA 1 TA 1 56
+chrM_1814_2315_6:0:0_3:0:0_12d/1_AA chrM 1813 NA AA 1 AA 1 57
+chrM_1862_2304_4:0:0_1:0:0_19d/1_AA chrM 1861 NA AA 1 AA 1 58
+chrM_1363_1869_5:0:0_3:1:0_aa/1_TA chrM 1869 NA TA 1 TA 1 59
+chrM_1363_1887_2:0:0_3:0:0_d3/1_CA chrM 1887 NA CA 1 CA 1 60
+chrM_1428_1904_7:0:0_1:0:0_1b0/1_AC chrM 1904 NA AC 1 AC 1 61
+chrM_1480_1975_4:0:0_6:0:0_cd/1_CT chrM 1975 NA CT 1 CT 1 62
+chrM_1998_2552_3:0:0_2:0:0_35/1_AC chrM 1997 NA AC 1 AC 1 63
+chrM_1427_2035_6:0:0_1:0:0_7d/1_TA chrM 2035 NA TA 1 TA 1 64
+chrM_2065_2529_4:1:0_2:0:0_69/1_CG chrM 2064 NA CG 1 CG 1 65
+chrM_2079_2546_5:1:0_2:0:0_37/1_TA chrM 2078 NA TA 1 TA 1 66
+chrM_1576_2102_2:1:0_1:0:0_3/1_CT chrM 2102 NA CT 1 CT 1 67
+chrM_2118_2553_2:0:0_6:0:0_e6/1_CC chrM 2117 NA CC 1 CC 1 68
+chrM_1707_2180_3:0:0_2:0:0_152/1_TT chrM 2180 NA TT 1 TT 1 69
+chrM_1950_2421_3:0:0_3:0:0_13/1_TC chrM 2421 NA TC 1 TC 1 70
+chrM_2426_2953_5:0:0_5:0:0_83/1_AT chrM 2425 NA AT 1 AT 1 71
+chrM_2497_3082_1:0:0_6:0:0_1a4/1_AG chrM 2496 NA AG 1 AG 1 72
+chrM_2021_2503_3:1:0_4:0:0_4d/1_AC chrM 2503 NA AC 1 AC 1 73
+chrM_2510_3002_4:0:0_1:0:0_1d/1_AA chrM 2509 NA AA 1 AA 1 74
+chrM_2528_3123_6:1:0_4:0:0_122/1_AT chrM 2527 NA AT 1 AT 1 75
+chrM_2646_3108_4:1:0_3:0:0_68/1_GA chrM 2645 NA GA 1 GA 1 76
+chrM_2063_2659_1:1:0_8:0:0_93/1_GG chrM 2659 NA GG 1 GG 1 77
+chrM_2160_2679_2:0:0_4:0:0_177/1_TC chrM 2679 NA TC 1 TC 1 78
+chrM_2823_3302_7:0:0_9:0:0_de/1_CC chrM 2822 NA CC 1 CC 1 79
+chrM_2441_2926_5:0:0_3:0:0_25/1_AA chrM 2926 NA AA 1 AA 1 80
+chrM_2958_3490_6:0:0_5:1:0_192/1_TT chrM 2957 NA TT 1 TT 1 81
+chrM_2988_3473_2:0:0_4:1:0_c6/1_GT chrM 2987 NA GT 1 GT 1 82
+chrM_3032_3426_3:0:0_3:1:0_17c/1_AG chrM 3031 NA AG 1 AG 1 83
+chrM_2563_3061_1:1:0_3:0:0_70/1_GG chrM 3061 NA GG 1 GG 1 84
+chrM_2692_3152_1:1:0_4:0:0_5d/1_TC chrM 3152 NA TC 1 TC 1 85
+chrM_2612_3153_2:1:0_1:0:0_1df/1_AT chrM 3153 NA AT 1 AT 1 86
+chrM_3202_3692_4:0:0_2:0:0_95/1_AA chrM 3201 NA AA 1 AA 1 87
+chrM_2733_3206_4:0:0_1:0:0_4e/1_GT chrM 3206 NA GT 1 GT 1 88
+chrM_2706_3256_4:0:0_9:0:0_16e/1_GA chrM 3256 NA GA 1 GA 1 89
+chrM_2864_3323_4:0:0_5:0:0_fb/1_CT chrM 3323 NA CT 1 CT 1 90
+chrM_2856_3324_2:0:0_6:0:0_4/1_GC chrM 3324 NA GC 1 GC 1 91
+chrM_2902_3333_5:0:0_3:0:0_4a/1_CC chrM 3333 NA CC 1 CC 1 92
+chrM_2890_3410_3:0:0_6:1:0_1b5/1_TA chrM 3410 NA TA 1 TA 1 93
+chrM_2875_3422_5:0:0_7:1:0_c5/1_GG chrM 3422 NA GG 1 GG 1 94
+chrM_2890_3430_4:0:0_8:1:0_19a/1_TT chrM 3430 NA TT 1 TT 1 95
+chrM_2949_3443_10:0:0_6:1:0_139/1_CT chrM 3443 NA CT 1 CT 1 96
+chrM_2872_3457_8:0:0_3:1:0_134/1_TG chrM 3457 NA TG 1 TG 1 97
+chrM_2948_3460_5:0:0_7:1:0_1c1/1_TG chrM 3460 NA TG 1 TG 1 98
+chrM_3015_3496_4:0:0_5:1:0_137/1_AT chrM 3496 NA AT 1 AT 1 99
+chrM_2965_3521_2:0:0_2:1:0_eb/1_TA chrM 3521 NA TA 1 TA 1 100
+chrM_3561_4058_2:0:0_2:0:0_14d/1_TG chrM 3560 NA TG 1 TG 1 101
+chrM_3590_4068_6:0:0_6:1:0_b8/1_GG chrM 3589 NA GG 1 GG 1 102
+chrM_3123_3605_5:0:0_4:0:0_14/1_AG chrM 3605 NA AG 1 AG 1 103
+chrM_3158_3635_7:0:0_0:0:0_1c/1_AG chrM 3635 NA AG 1 AG 1 104
+chrM_3253_3640_6:1:0_8:0:0_10a/1_GT chrM 3640 NA GT 1 GT 1 105
+chrM_3663_4221_4:0:0_1:0:0_1a9/1_TA chrM 3662 NA TA 1 TA 1 106
+chrM_3679_4214_3:1:0_4:0:0_54/1_AG chrM 3678 NA AG 1 AG 1 107
+chrM_3688_4175_3:1:0_8:0:0_fd/1_AA chrM 3687 NA AA 1 AA 1 108
+chrM_3216_3691_4:1:0_4:0:0_110/1_TT chrM 3691 NA TT 1 TT 1 109
+chrM_3701_4211_4:0:0_3:0:0_e0/1_TA chrM 3700 NA TA 1 TA 1 110
+chrM_3213_3703_4:1:0_6:0:0_199/1_AG chrM 3703 NA AG 1 AG 1 111
+chrM_3738_4170_4:1:0_3:0:0_3b/1_CA chrM 3737 NA CA 1 CA 1 112
+chrM_3752_4208_9:1:0_5:0:0_11f/1_CA chrM 3751 NA CA 1 CA 1 113
+chrM_3171_3761_4:0:0_6:0:0_38/1_AT chrM 3761 NA AT 1 AT 1 114
+chrM_3213_3785_3:1:0_10:0:0_ed/1_GT chrM 3785 NA GT 1 GT 1 115
+chrM_3793_4298_6:0:0_5:0:0_51/1_TC chrM 3792 NA TC 1 TC 1 116
+chrM_3805_4310_4:1:0_3:0:0_161/1_TA chrM 3804 NA TA 1 TA 1 117
+chrM_3817_4309_3:1:0_3:0:0_86/1_AT chrM 3816 NA AT 1 AT 1 118
+chrM_3863_4305_5:0:0_5:0:0_e9/1_AC chrM 3862 NA AC 1 AC 1 119
+chrM_3399_3957_5:1:0_2:1:0_43/1_AT chrM 3957 NA AT 1 AT 1 120
+chrM_3449_3959_6:0:0_3:1:0_16a/1_GA chrM 3959 NA GA 1 GA 1 121
+chrM_3971_4563_4:0:0_5:0:0_150/1_GG chrM 3970 NA GG 1 GG 1 122
+chrM_3541_3989_4:0:0_2:1:0_90/1_GA chrM 3989 NA GA 1 GA 1 123
+chrM_3597_3996_3:0:0_7:0:0_62/1_GT chrM 3996 NA GT 1 GT 1 124
+chrM_3450_3998_6:0:0_2:0:0_1ba/1_GC chrM 3998 NA GC 1 GC 1 125
+chrM_3637_4061_5:0:0_2:1:0_111/1_AT chrM 4061 NA AT 1 AT 1 126
+chrM_4068_4556_3:0:0_3:0:0_6a/1_CA chrM 4067 NA CA 1 CA 1 127
+chrM_4074_4533_2:0:0_2:0:0_9e/1_TA chrM 4073 NA TA 1 TA 1 128
+chrM_4082_4621_7:0:0_3:0:0_198/1_AA chrM 4081 NA AA 1 AA 1 129
+chrM_4160_4692_5:0:0_4:1:0_1f0/1_AT chrM 4159 NA AT 1 AT 1 130
+chrM_4199_4751_2:0:0_1:1:0_15c/1_GC chrM 4198 NA GC 1 GC 1 131
+chrM_4229_4769_4:0:0_6:0:0_cc/1_GA chrM 4228 NA GA 1 GA 1 132
+chrM_3770_4283_1:0:0_8:0:0_13f/1_AA chrM 4283 NA AA 1 AA 1 133
+chrM_4374_4823_2:0:0_5:0:0_dc/1_TA chrM 4373 NA TA 1 TA 1 134
+chrM_4382_4881_2:0:0_5:0:0_195/1_AT chrM 4381 NA AT 1 AT 1 135
+chrM_4384_4922_5:0:0_4:1:0_1e1/1_TA chrM 4383 NA TA 1 TA 1 136
+chrM_4056_4522_5:0:0_4:0:0_e3/1_AT chrM 4522 NA AT 1 AT 1 137
+chrM_4553_5058_6:0:0_4:0:0_a3/1_AT chrM 4552 NA AT 1 AT 1 138
+chrM_4565_5190_3:0:0_4:0:0_19c/1_AC chrM 4564 NA AC 1 AC 1 139
+chrM_4106_4574_6:0:0_2:0:0_64/1_TC chrM 4574 NA TC 1 TC 1 140
+chrM_4705_5072_2:0:0_2:1:0_b7/1_TT chrM 4704 NA TT 1 TT 1 141
+chrM_4724_5279_5:0:0_8:0:0_2e/1_AA chrM 4723 NA AA 1 AA 1 142
+chrM_4840_5344_4:1:0_4:0:0_3c/1_GT chrM 4839 NA GT 1 GT 1 143
+chrM_4509_4974_5:0:0_3:0:0_ea/1_CT chrM 4974 NA CT 1 CT 1 144
+chrM_4444_5010_5:1:0_5:1:0_119/1_TG chrM 5010 NA TG 1 TG 1 145
+chrM_4491_5013_5:1:0_6:1:0_1b/1_GA chrM 5013 NA GA 1 GA 1 146
+chrM_4490_5017_8:0:0_4:0:0_8d/1_AG chrM 5017 NA AG 1 AG 1 147
+chrM_5058_5566_6:0:0_5:0:0_1c6/1_AG chrM 5057 NA AG 1 AG 1 148
+chrM_5062_5522_7:0:0_5:0:0_e8/1_TC chrM 5061 NA TC 1 TC 1 149
+chrM_4566_5086_5:1:0_6:1:0_19/1_AT chrM 5086 NA AT 1 AT 1 150
+chrM_5119_5706_5:0:0_4:0:0_140/1_TG chrM 5118 NA TG 1 TG 1 151
+chrM_5121_5635_3:0:0_3:0:0_165/1_AG chrM 5120 NA AG 1 AG 1 152
+chrM_5166_5697_4:0:0_4:0:0_ec/1_TC chrM 5165 NA TC 1 TC 1 153
+chrM_4583_5175_2:0:0_4:0:0_10d/1_TT chrM 5175 NA TT 1 TT 1 154
+chrM_5184_5616_6:0:0_4:0:0_1ee/1_AA chrM 5183 NA AA 1 AA 1 155
+chrM_4713_5198_5:0:0_1:0:0_f0/1_TA chrM 5198 NA TA 1 TA 1 156
+chrM_4833_5239_3:1:0_3:0:0_56/1_AG chrM 5239 NA AG 1 AG 1 157
+chrM_5292_5797_3:0:0_3:0:0_130/1_CC chrM 5291 NA CC 1 CC 1 158
+chrM_5315_5855_2:0:0_5:0:0_136/1_TA chrM 5314 NA TA 1 TA 1 159
+chrM_5342_5909_5:0:0_5:0:0_5/1_GC chrM 5341 NA GC 1 GC 1 160
+chrM_4886_5348_5:0:0_3:0:0_d7/1_TC chrM 5348 NA TC 1 TC 1 161
+chrM_5355_5797_0:0:0_5:0:0_1d3/1_TA chrM 5354 NA TA 1 TA 1 162
+chrM_5362_5890_4:0:0_3:0:0_1dd/1_AT chrM 5361 NA AT 1 AT 1 163
+chrM_4974_5463_3:0:0_4:0:0_8/1_CT chrM 5463 NA CT 1 CT 1 164
+chrM_5125_5611_2:0:0_2:0:0_11b/1_AT chrM 5611 NA AT 1 AT 1 165
+chrM_5163_5634_8:0:0_3:0:0_1bf/1_TT chrM 5634 NA TT 1 TT 1 166
+chrM_5185_5662_3:0:0_4:0:0_a4/1_AT chrM 5662 NA AT 1 AT 1 167
+chrM_5683_6115_5:0:0_5:0:0_b5/1_CT chrM 5682 NA CT 1 CT 1 168
+chrM_5306_5717_1:0:0_4:0:0_1ab/1_TT chrM 5717 NA TT 1 TT 1 169
+chrM_5181_5752_4:0:0_4:0:0_128/1_GT chrM 5752 NA GT 1 GT 1 170
+chrM_5828_6286_5:0:0_4:0:0_17f/1_TT chrM 5827 NA TT 1 TT 1 171
+chrM_5310_5842_3:0:0_6:0:0_1d0/1_TA chrM 5842 NA TA 1 TA 1 172
+chrM_5845_6332_2:0:0_3:0:0_db/1_AA chrM 5844 NA AA 1 AA 1 173
+chrM_5856_6361_4:0:0_4:0:0_1d4/1_AA chrM 5855 NA AA 1 AA 1 174
+chrM_5410_5865_9:0:0_5:0:0_57/1_TA chrM 5865 NA TA 1 TA 1 175
+chrM_5411_5901_3:0:0_2:0:0_197/1_TT chrM 5901 NA TT 1 TT 1 176
+chrM_5423_5960_2:0:0_6:0:0_1ca/1_TA chrM 5960 NA TA 1 TA 1 177
+chrM_5461_5962_4:0:0_8:0:0_1a8/1_AT chrM 5962 NA AT 1 AT 1 178
+chrM_5990_6598_5:0:0_2:0:0_16f/1_TC chrM 5989 NA TC 1 TC 1 179
+chrM_6047_6502_2:0:0_6:0:0_1f3/1_CA chrM 6046 NA CA 1 CA 1 180
+chrM_6078_6610_7:0:0_6:0:0_29/1_GG chrM 6077 NA GG 1 GG 1 181
+chrM_5565_6084_3:0:0_3:0:0_194/1_TC chrM 6084 NA TC 1 TC 1 182
+chrM_6087_6574_4:0:0_2:0:0_12e/1_CC chrM 6086 NA CC 1 CC 1 183
+chrM_5710_6256_2:0:0_6:0:0_12/1_CT chrM 6256 NA CT 2 CT 2 184
+chrM_5852_6256_2:0:0_4:0:0_58/1_CT chrM 6256 NA CT 2 CT 2 184
+chrM_5770_6275_1:0:0_3:0:0_a6/1_AG chrM 6275 NA AG 1 AG 1 185
+chrM_5839_6288_5:0:0_5:0:0_1c0/1_GG chrM 6288 NA GG 1 GG 1 186
+chrM_5829_6293_3:0:0_1:0:0_bd/1_GC chrM 6293 NA GC 1 GC 1 187
+chrM_5793_6362_4:0:0_5:0:0_1a5/1_CC chrM 6362 NA CC 1 CC 1 188
+chrM_5942_6425_5:0:0_1:0:0_16d/1_AC chrM 6425 NA AC 1 AC 1 189
+chrM_5989_6468_5:0:0_1:0:0_16c/1_TG chrM 6468 NA TG 1 TG 1 190
+chrM_5994_6492_3:0:0_3:0:0_153/1_TA chrM 6492 NA TA 1 TA 1 191
+chrM_6011_6514_3:0:0_7:0:0_1ef/1_TG chrM 6514 NA TG 1 TG 1 192
+chrM_6134_6610_4:0:0_2:0:0_d6/1_GG chrM 6610 NA GG 1 GG 1 193
+chrM_6073_6613_4:0:0_6:0:0_e/1_CT chrM 6613 NA CT 1 CT 1 194
+chrM_6655_7146_3:0:0_6:0:0_55/1_TT chrM 6654 NA TT 1 TT 1 195
+chrM_6155_6684_4:0:0_6:0:0_156/1_GG chrM 6684 NA GG 1 GG 1 196
+chrM_6698_7198_5:0:1_4:0:0_19e/1_AT chrM 6697 NA AT 1 AT 1 197
+chrM_6222_6744_5:0:0_2:0:0_116/1_CA chrM 6744 NA CA 1 CA 1 198
+chrM_6258_6750_3:0:0_2:0:0_b0/1_TT chrM 6750 NA TT 1 TT 1 199
+chrM_6331_6811_6:0:0_5:0:0_b6/1_GT chrM 6811 NA GT 1 GT 1 200
+chrM_6370_6852_5:0:0_4:0:0_5c/1_AT chrM 6852 NA AT 1 AT 1 201
+chrM_6507_6920_3:0:0_5:0:1_1d2/1_AA chrM 6920 NA AA 1 AA 1 202
+chrM_6479_6981_2:0:0_5:0:1_18f/1_TG chrM 6981 NA TG 1 TG 1 203
+chrM_6530_7006_2:0:0_2:0:1_101/1_TA chrM 7006 NA TA 1 TA 1 204
+chrM_7048_7515_9:0:0_4:0:0_7e/1_AT chrM 7047 NA AT 1 AT 1 205
+chrM_7081_7575_3:0:0_0:0:0_10/1_CC chrM 7080 NA CC 1 CC 1 206
+chrM_7119_7629_5:0:0_7:0:0_1cf/1_GC chrM 7118 NA GC 1 GC 1 207
+chrM_7270_7705_10:0:0_4:0:0_b4/1_GC chrM 7269 NA GC 1 GC 1 208
+chrM_7272_7803_5:0:0_4:0:0_fe/1_TA chrM 7271 NA TA 1 TA 1 209
+chrM_6787_7349_2:0:1_1:0:0_141/1_TG chrM 7349 NA TG 1 TG 1 210
+chrM_7365_7794_3:0:0_5:0:0_1c7/1_GA chrM 7364 NA GA 1 GA 1 211
+chrM_7413_7973_6:0:0_5:0:0_158/1_TC chrM 7412 NA TC 1 TC 1 212
+chrM_6786_7414_0:0:1_6:0:0_1b6/1_AT chrM 7414 NA AT 1 AT 1 213
+chrM_7472_7886_4:0:0_4:0:0_8b/1_GG chrM 7471 NA GG 1 GG 1 214
+chrM_7505_7965_4:0:0_2:0:0_3a/1_CT chrM 7504 NA CT 1 CT 1 215
+chrM_7095_7547_2:0:0_3:0:0_149/1_GG chrM 7547 NA GG 1 GG 1 216
+chrM_7564_8021_3:0:0_2:0:0_1/1_AA chrM 7563 NA AA 1 AA 1 217
+chrM_7067_7564_4:0:0_5:0:0_107/1_AA chrM 7564 NA AA 1 AA 1 218
+chrM_7016_7567_4:0:0_5:0:0_27/1_TT chrM 7567 NA TT 1 TT 1 219
+chrM_7200_7687_2:0:0_6:0:0_c/1_TA chrM 7687 NA TA 1 TA 1 220
+chrM_7267_7793_1:0:0_4:0:0_41/1_AC chrM 7793 NA AC 1 AC 1 221
+chrM_7797_8230_4:0:0_5:0:0_f6/1_GC chrM 7796 NA GC 1 GC 1 222
+chrM_7821_8285_3:0:0_3:0:0_1f1/1_TT chrM 7820 NA TT 1 TT 1 223
+chrM_7859_8392_2:0:0_3:0:0_114/1_TT chrM 7858 NA TT 1 TT 1 224
+chrM_7881_8395_3:0:0_2:0:0_173/1_CT chrM 7880 NA CT 1 CT 1 225
+chrM_7339_7893_4:0:0_3:0:0_19b/1_TA chrM 7893 NA TA 1 TA 1 226
+chrM_7424_7912_5:0:0_4:0:0_ba/1_GG chrM 7912 NA GG 1 GG 1 227
+chrM_7467_7949_6:0:0_9:0:0_7f/1_AT chrM 7949 NA AT 1 AT 1 228
+chrM_7956_8469_8:0:0_5:1:0_14a/1_AA chrM 7955 NA AA 1 AA 1 229
+chrM_7963_8508_6:0:0_5:1:0_73/1_AC chrM 7962 NA AC 1 AC 1 230
+chrM_8018_8547_2:0:0_2:1:0_39/1_TA chrM 8017 NA TA 1 TA 1 231
+chrM_8039_8593_3:0:0_3:1:0_71/1_AG chrM 8038 NA AG 1 AG 1 232
+chrM_7594_8044_3:0:0_5:0:0_e1/1_TT chrM 8044 NA TT 1 TT 1 233
+chrM_7570_8062_4:0:0_1:0:0_1ed/1_TC chrM 8062 NA TC 1 TC 1 234
+chrM_7576_8099_6:0:0_4:0:0_1bc/1_GT chrM 8099 NA GT 1 GT 1 235
+chrM_8114_8625_4:0:0_3:1:0_17a/1_AT chrM 8113 NA AT 1 AT 1 236
+chrM_7655_8131_5:0:0_7:0:0_19f/1_CG chrM 8131 NA CG 1 CG 1 237
+chrM_8139_8619_2:0:0_5:1:0_166/1_CC chrM 8138 NA CC 1 CC 1 238
+chrM_7825_8191_3:0:0_2:0:0_1ec/1_CT chrM 8191 NA CT 1 CT 1 239
+chrM_7641_8206_4:0:0_5:0:0_13a/1_GT chrM 8206 NA GT 1 GT 1 240
+chrM_7613_8208_2:0:0_5:0:0_52/1_AT chrM 8208 NA AT 1 AT 1 241
+chrM_7752_8261_10:0:0_5:0:0_142/1_GA chrM 8261 NA GA 1 GA 1 242
+chrM_7739_8294_7:0:0_2:0:0_144/1_CC chrM 8294 NA CC 1 CC 1 243
+chrM_8303_8710_5:1:0_6:0:0_87/1_CA chrM 8302 NA CA 1 CA 1 244
+chrM_8309_8842_3:1:0_5:0:0_115/1_GA chrM 8308 NA GA 1 GA 1 245
+chrM_7965_8408_4:0:0_0:0:0_143/1_CC chrM 8408 NA CC 1 CC 1 246
+chrM_8031_8436_7:0:0_5:0:0_c0/1_TC chrM 8436 NA TC 1 TC 1 247
+chrM_8438_8973_3:1:0_2:0:0_1d5/1_AA chrM 8437 NA AA 1 AA 1 248
+chrM_8511_8920_4:0:0_3:0:0_ca/1_AT chrM 8510 NA AT 1 AT 1 249
+chrM_8532_8954_3:0:0_4:0:0_cb/1_TT chrM 8531 NA TT 1 TT 1 250
+chrM_8565_8973_6:0:0_1:0:0_66/1_GA chrM 8564 NA GA 1 GA 1 251
+chrM_8575_9003_7:0:0_2:0:0_c7/1_TA chrM 8574 NA TA 1 TA 1 252
+chrM_8125_8594_2:0:0_2:1:0_187/1_TA chrM 8594 NA TA 1 TA 1 253
+chrM_8144_8650_4:0:0_3:1:0_14b/1_GG chrM 8650 NA GG 1 GG 1 254
+chrM_8117_8669_3:0:0_5:0:0_16b/1_AG chrM 8669 NA AG 1 AG 1 255
+chrM_8296_8802_4:1:0_9:0:0_1db/1_GC chrM 8802 NA GC 1 GC 1 256
+chrM_8807_9277_3:0:0_4:0:1_108/1_TG chrM 8806 NA TG 1 TG 1 257
+chrM_8825_9275_3:0:0_5:0:1_1da/1_AA chrM 8824 NA AA 1 AA 1 258
+chrM_8868_9400_4:0:0_3:0:1_1e8/1_AC chrM 8867 NA AC 1 AC 1 259
+chrM_8885_9340_4:0:0_5:0:1_c8/1_TT chrM 8884 NA TT 1 TT 1 260
+chrM_8938_9405_8:0:0_2:0:1_1c3/1_CG chrM 8937 NA CG 1 CG 1 261
+chrM_8396_8947_8:1:0_2:0:0_155/1_AC chrM 8947 NA AC 1 AC 1 262
+chrM_8461_8951_7:0:0_1:0:0_1cb/1_TG chrM 8951 NA TG 1 TG 1 263
+chrM_8987_9581_3:0:0_3:0:0_1cd/1_TA chrM 8986 NA TA 1 TA 1 264
+chrM_9007_9456_2:0:0_4:0:0_23/1_AA chrM 9006 NA AA 1 AA 1 265
+chrM_8520_9009_2:0:0_7:0:0_193/1_TA chrM 9009 NA TA 1 TA 1 266
+chrM_8547_9016_5:0:0_4:0:0_32/1_TG chrM 9016 NA TG 1 TG 1 267
+chrM_9075_9551_5:0:1_3:0:0_4b/1_CC chrM 9074 NA CC 1 CC 1 268
+chrM_9102_9561_3:0:1_3:0:0_2b/1_TA chrM 9101 NA TA 1 TA 1 269
+chrM_9113_9686_4:0:1_1:0:0_78/1_CA chrM 9112 NA CA 1 CA 1 270
+chrM_8621_9133_8:0:0_5:0:0_145/1_GC chrM 9133 NA GC 1 GC 1 271
+chrM_9166_9651_6:0:1_4:0:0_15b/1_TT chrM 9165 NA TT 1 TT 1 272
+chrM_9168_9638_4:0:1_5:0:0_175/1_TC chrM 9167 NA TC 1 TC 1 273
+chrM_9172_9645_0:0:1_5:0:0_e7/1_CA chrM 9171 NA CA 1 CA 1 274
+chrM_9233_9739_3:0:1_5:0:0_91/1_CT chrM 9232 NA CT 1 CT 1 275
+chrM_9249_9749_6:0:1_2:0:0_12c/1_TA chrM 9247 NA TA 1 TA 1 276
+chrM_9338_9899_1:0:0_2:0:0_a8/1_TT chrM 9337 NA TT 1 TT 1 277
+chrM_8914_9385_2:0:0_3:0:1_135/1_GC chrM 9385 NA GC 1 GC 1 278
+chrM_8829_9414_6:0:0_2:0:1_1bd/1_GT chrM 9414 NA GT 1 GT 1 279
+chrM_8916_9457_5:0:0_5:0:0_167/1_AC chrM 9457 NA AC 1 AC 1 280
+chrM_8970_9471_5:0:0_6:0:0_1ac/1_CT chrM 9471 NA CT 1 CT 1 281
+chrM_8928_9477_3:0:0_6:0:0_48/1_GG chrM 9477 NA GG 2 GG 2 282
+chrM_8929_9477_7:0:0_5:0:0_f9/1_GG chrM 9477 NA GG 2 GG 2 282
+chrM_9536_10046_5:0:0_1:0:0_d5/1_TA chrM 9535 NA TA 1 TA 1 283
+chrM_9579_10013_2:0:0_3:0:0_9/1_AC chrM 9578 NA AC 1 AC 1 284
+chrM_9672_10188_5:0:0_9:0:0_11/1_CG chrM 9671 NA CG 1 CG 1 285
+chrM_9689_10220_2:0:0_2:0:0_151/1_AA chrM 9688 NA AA 1 AA 1 286
+chrM_9159_9700_2:0:1_4:0:0_2/1_GA chrM 9700 NA GA 1 GA 1 287
+chrM_9103_9709_4:0:1_5:0:0_24/1_AT chrM 9709 NA AT 1 AT 1 288
+chrM_9768_10236_5:0:0_4:0:0_1d9/1_GT chrM 9767 NA GT 1 GT 1 289
+chrM_9271_9836_3:0:0_2:0:0_77/1_CT chrM 9836 NA CT 1 CT 1 290
+chrM_9847_10370_4:0:0_5:0:0_bc/1_CA chrM 9846 NA CA 1 CA 1 291
+chrM_9856_10428_4:0:0_4:1:0_120/1_GC chrM 9855 NA GC 1 GC 1 292
+chrM_9866_10380_3:0:0_5:0:0_8f/1_CC chrM 9865 NA CC 1 CC 1 293
+chrM_9895_10412_1:0:0_7:1:0_7a/1_AT chrM 9894 NA AT 1 AT 1 294
+chrM_9904_10380_7:0:0_3:0:0_1e0/1_TG chrM 9903 NA TG 1 TG 1 295
+chrM_9917_10459_5:0:0_6:0:0_9c/1_CG chrM 9916 NA CG 1 CG 1 296
+chrM_9489_9919_2:0:0_2:0:0_b9/1_GG chrM 9919 NA GG 1 GG 1 297
+chrM_9452_9927_4:0:0_5:0:0_190/1_GA chrM 9927 NA GA 1 GA 1 298
+chrM_9932_10484_3:0:0_5:0:0_148/1_CT chrM 9931 NA CT 1 CT 1 299
+chrM_9983_10519_5:0:0_2:0:0_dd/1_AC chrM 9982 NA AC 1 AC 1 300
+chrM_9402_10032_4:0:0_5:0:0_a2/1_GG chrM 10032 NA GG 1 GG 1 301
+chrM_10074_10591_1:0:0_0:0:0_14c/1_TA chrM 10073 NA TA 1 TA 1 302
+chrM_10103_10594_8:0:0_6:1:0_1e9/1_AT chrM 10102 NA AT 1 AT 1 303
+chrM_10141_10683_4:0:0_4:0:0_6f/1_TA chrM 10140 NA TA 1 TA 1 304
+chrM_10226_10692_5:1:0_4:0:0_103/1_CT chrM 10225 NA CT 1 CT 1 305
+chrM_9669_10227_5:0:0_4:0:0_4f/1_TG chrM 10227 NA TG 1 TG 1 306
+chrM_9735_10257_0:0:0_7:0:0_b2/1_TA chrM 10257 NA TA 1 TA 1 307
+chrM_10326_10838_5:0:0_3:0:0_f2/1_TT chrM 10325 NA TT 1 TT 1 308
+chrM_9825_10334_2:0:0_6:0:0_123/1_AC chrM 10334 NA AC 1 AC 1 309
+chrM_10009_10476_0:0:0_5:0:0_176/1_CA chrM 10476 NA CA 1 CA 1 310
+chrM_9995_10574_6:0:0_4:1:0_7c/1_GG chrM 10574 NA GG 1 GG 1 311
+chrM_10582_11133_4:0:0_3:0:0_21/1_GC chrM 10581 NA GC 1 GC 1 312
+chrM_10590_11016_2:0:0_6:0:0_81/1_AA chrM 10589 NA AA 1 AA 1 313
+chrM_10607_11150_5:0:0_2:0:0_8a/1_CC chrM 10606 NA CC 1 CC 1 314
+chrM_10041_10610_6:0:0_4:0:0_ef/1_GG chrM 10610 NA GG 1 GG 1 315
+chrM_10679_11090_2:0:0_6:0:0_1b4/1_GA chrM 10678 NA GA 1 GA 1 316
+chrM_10690_11211_4:0:0_3:0:0_184/1_AC chrM 10689 NA AC 1 AC 1 317
+chrM_10692_11227_2:0:0_4:0:0_49/1_TG chrM 10691 NA TG 1 TG 1 318
+chrM_10325_10814_5:1:0_6:0:0_129/1_GC chrM 10814 NA GC 1 GC 1 319
+chrM_10834_11259_4:0:0_3:0:0_47/1_GA chrM 10833 NA GA 1 GA 1 320
+chrM_10846_11368_1:0:0_6:0:0_fc/1_TG chrM 10845 NA TG 1 TG 1 321
+chrM_10850_11370_7:0:0_4:0:0_15e/1_TT chrM 10849 NA TT 1 TT 1 322
+chrM_10491_10996_4:0:0_6:0:0_1a6/1_AG chrM 10996 NA AG 1 AG 1 323
+chrM_11001_11542_4:0:0_9:0:0_15/1_GT chrM 11000 NA GT 1 GT 1 324
+chrM_11067_11640_2:0:0_7:0:0_d2/1_TT chrM 11066 NA TT 1 TT 1 325
+chrM_10600_11115_3:0:0_3:0:0_10f/1_TT chrM 11115 NA TT 1 TT 1 326
+chrM_11179_11645_6:0:1_1:0:0_181/1_TC chrM 11178 NA TC 1 TC 1 327
+chrM_10716_11197_6:0:0_5:0:0_67/1_CA chrM 11197 NA CA 1 CA 1 328
+chrM_10649_11218_5:0:0_8:0:0_50/1_GT chrM 11218 NA GT 1 GT 1 329
+chrM_10624_11233_2:0:0_3:0:0_2f/1_CT chrM 11233 NA CT 1 CT 1 330
+chrM_11239_11740_6:0:0_1:0:0_3e/1_CT chrM 11238 NA CT 1 CT 1 331
+chrM_10825_11310_5:0:0_6:0:0_1ce/1_TA chrM 11310 NA TA 1 TA 1 332
+chrM_11423_11976_7:0:0_3:0:0_189/1_GA chrM 11422 NA GA 1 GA 1 333
+chrM_11522_12121_5:0:0_2:0:0_13d/1_GG chrM 11521 NA GG 1 GG 1 334
+chrM_11080_11521_6:0:0_7:0:0_ff/1_GT chrM 11521 NA GT 1 GT 1 335
+chrM_11076_11558_1:0:0_3:0:0_92/1_AT chrM 11558 NA AT 1 AT 1 336
+chrM_11197_11674_1:0:0_3:0:0_c1/1_TT chrM 11674 NA TT 1 TT 1 337
+chrM_11227_11680_5:0:1_3:0:0_76/1_GT chrM 11680 NA GT 1 GT 1 338
+chrM_11759_12257_5:0:0_8:0:0_9b/1_TT chrM 11758 NA TT 1 TT 1 339
+chrM_11236_11767_1:0:0_2:0:0_e2/1_TT chrM 11767 NA TT 1 TT 1 340
+chrM_11780_12326_4:0:0_7:0:0_10e/1_GG chrM 11779 NA GG 1 GG 1 341
+chrM_11789_12313_6:0:0_5:0:0_1f2/1_CG chrM 11788 NA CG 1 CG 1 342
+chrM_11815_12366_6:0:0_1:0:0_1be/1_AA chrM 11814 NA AA 1 AA 1 343
+chrM_11829_12278_5:0:0_8:0:0_11a/1_CA chrM 11828 NA CA 1 CA 1 344
+chrM_11834_12212_5:0:0_4:0:0_131/1_CC chrM 11833 NA CC 1 CC 1 345
+chrM_11305_11834_4:0:0_5:0:0_5e/1_TA chrM 11834 NA TA 1 TA 1 346
+chrM_11315_11842_2:0:0_8:0:0_126/1_TA chrM 11842 NA TA 1 TA 1 347
+chrM_11890_12397_8:0:0_2:0:0_30/1_CC chrM 11889 NA CC 1 CC 1 348
+chrM_11898_12351_4:0:0_1:0:0_a9/1_AC chrM 11897 NA AC 1 AC 1 349
+chrM_11902_12409_3:0:0_4:0:0_ad/1_AA chrM 11901 NA AA 1 AA 1 350
+chrM_11932_12361_4:0:0_6:0:0_44/1_TC chrM 11931 NA TC 1 TC 1 351
+chrM_11938_12488_7:0:0_6:0:0_ee/1_GG chrM 11937 NA GG 1 GG 1 352
+chrM_11949_12385_7:0:0_5:0:0_118/1_TT chrM 11948 NA TT 1 TT 1 353
+chrM_11551_11956_7:0:0_5:0:0_d0/1_CT chrM 11956 NA CT 1 CT 1 354
+chrM_11468_11961_6:0:0_4:0:0_c9/1_TA chrM 11961 NA TA 1 TA 1 355
+chrM_11495_11994_2:0:0_5:0:0_100/1_AG chrM 11994 NA AG 1 AG 1 356
+chrM_11413_12020_5:0:0_2:0:0_4c/1_AG chrM 12020 NA AG 1 AG 1 357
+chrM_11598_12060_3:0:0_5:0:0_89/1_AT chrM 12060 NA AT 1 AT 1 358
+chrM_11616_12104_4:0:0_7:0:0_6/1_TG chrM 12104 NA TG 1 TG 1 359
+chrM_12150_12654_2:0:0_3:0:0_12b/1_CA chrM 12149 NA CA 1 CA 1 360
+chrM_12160_12669_8:0:0_2:0:0_1ae/1_CC chrM 12159 NA CC 1 CC 1 361
+chrM_11701_12198_5:0:0_2:0:0_96/1_AA chrM 12198 NA AA 1 AA 1 362
+chrM_11745_12199_2:0:0_3:0:0_7/1_CA chrM 12199 NA CA 1 CA 1 363
+chrM_11818_12273_4:0:0_4:0:0_196/1_TA chrM 12273 NA TA 1 TA 1 364
+chrM_11791_12301_5:0:0_6:0:0_17d/1_GA chrM 12301 NA GA 1 GA 1 365
+chrM_12330_12776_4:0:0_4:0:0_63/1_AT chrM 12329 NA AT 1 AT 1 366
+chrM_12336_12829_5:0:0_5:0:0_f/1_AC chrM 12335 NA AC 1 AC 1 367
+chrM_11746_12340_4:0:0_2:0:0_6c/1_GG chrM 12340 NA GG 1 GG 1 368
+chrM_12356_12830_4:0:0_5:0:0_104/1_AA chrM 12355 NA AA 1 AA 1 369
+chrM_12371_12852_6:0:0_5:0:0_28/1_CT chrM 12370 NA CT 1 CT 1 370
+chrM_12405_12863_2:0:0_3:0:0_154/1_AC chrM 12404 NA AC 1 AC 1 371
+chrM_12413_12965_5:0:0_6:0:0_174/1_AT chrM 12412 NA AT 1 AT 1 372
+chrM_12006_12431_4:0:0_4:0:0_15a/1_AT chrM 12431 NA AT 1 AT 1 373
+chrM_11969_12486_5:0:0_4:0:0_2a/1_AC chrM 12486 NA AC 1 AC 1 374
+chrM_12495_12966_1:0:0_3:0:0_18a/1_TT chrM 12494 NA TT 1 TT 1 375
+chrM_12089_12585_1:0:0_7:0:0_1e4/1_TT chrM 12585 NA TT 1 TT 1 376
+chrM_12621_13150_2:0:0_4:0:0_9a/1_CA chrM 12620 NA CA 1 CA 1 377
+chrM_12209_12659_3:0:0_3:0:0_1a7/1_GT chrM 12659 NA GT 1 GT 1 378
+chrM_12702_13164_4:0:0_3:0:0_88/1_AC chrM 12701 NA AC 1 AC 1 379
+chrM_12712_13263_5:0:0_6:0:0_1a3/1_AT chrM 12711 NA AT 1 AT 1 380
+chrM_12284_12729_4:0:0_4:0:0_61/1_TA chrM 12729 NA TA 1 TA 1 381
+chrM_12259_12743_4:0:0_2:0:0_1a2/1_TT chrM 12743 NA TT 1 TT 1 382
+chrM_12260_12784_5:0:0_2:0:0_6d/1_TG chrM 12784 NA TG 1 TG 1 383
+chrM_12316_12791_2:0:0_3:0:0_1d6/1_TT chrM 12791 NA TT 1 TT 1 384
+chrM_12262_12819_3:0:0_5:0:0_ce/1_AT chrM 12819 NA AT 1 AT 1 385
+chrM_12329_12832_4:0:0_4:0:0_1c5/1_TC chrM 12832 NA TC 1 TC 1 386
+chrM_12323_12847_3:0:0_3:0:0_163/1_GA chrM 12847 NA GA 1 GA 1 387
+chrM_12350_12855_4:0:0_3:0:0_3f/1_AG chrM 12855 NA AG 1 AG 1 388
+chrM_12495_12939_2:0:0_4:0:0_117/1_TC chrM 12939 NA TC 1 TC 1 389
+chrM_12949_13437_4:0:0_3:0:0_1a0/1_GG chrM 12948 NA GG 1 GG 1 390
+chrM_12449_12988_5:0:0_4:0:0_79/1_AA chrM 12988 NA AA 1 AA 1 391
+chrM_13032_13560_5:0:0_4:0:0_b1/1_GC chrM 13031 NA GC 1 GC 1 392
+chrM_12548_13045_4:0:0_3:0:0_be/1_TA chrM 13045 NA TA 1 TA 1 393
+chrM_12698_13119_5:0:0_3:0:0_a/1_GC chrM 13119 NA GC 1 GC 1 394
+chrM_12657_13157_3:0:0_2:0:0_a0/1_TG chrM 13157 NA TG 1 TG 1 395
+chrM_12629_13160_5:0:0_5:0:0_125/1_GG chrM 13160 NA GG 1 GG 1 396
+chrM_12642_13191_2:0:0_5:0:0_1dc/1_AT chrM 13191 NA AT 1 AT 1 397
+chrM_13236_13695_2:0:0_9:0:0_1c8/1_TT chrM 13235 NA TT 1 TT 1 398
+chrM_13271_13696_3:0:0_5:0:0_188/1_AC chrM 13270 NA AC 1 AC 1 399
+chrM_12763_13284_4:0:0_1:0:0_d1/1_AG chrM 13284 NA AG 1 AG 1 400
+chrM_13300_13825_6:0:0_3:0:0_ac/1_AA chrM 13299 NA AA 2 AA 2 401
+chrM_13300_13872_3:0:0_5:1:0_c2/1_AA chrM 13299 NA AA 2 AA 2 401
+chrM_12845_13364_2:0:0_5:0:0_109/1_AG chrM 13364 NA AG 1 AG 1 402
+chrM_13502_13977_3:0:0_5:0:0_ae/1_TT chrM 13501 NA TT 1 TT 1 403
+chrM_13627_14137_3:0:0_3:0:0_162/1_AC chrM 13626 NA AC 1 AC 1 404
+chrM_13055_13651_7:0:0_3:0:0_8c/1_TA chrM 13651 NA TA 1 TA 1 405
+chrM_13676_14200_0:1:0_4:0:0_2d/1_CA chrM 13675 NA CA 1 CA 1 406
+chrM_13138_13709_5:0:0_7:0:0_72/1_TT chrM 13709 NA TT 1 TT 1 407
+chrM_13242_13718_6:0:0_4:0:0_11d/1_AT chrM 13718 NA AT 1 AT 1 408
+chrM_13287_13740_4:0:0_5:1:0_1b8/1_GT chrM 13740 NA GT 1 GT 1 409
+chrM_13767_14345_8:0:0_5:0:0_f8/1_GC chrM 13766 NA GC 1 GC 1 410
+chrM_13776_14348_5:0:0_6:0:0_12f/1_GG chrM 13775 NA GG 1 GG 1 411
+chrM_13243_13775_6:0:0_5:1:0_1e/1_TG chrM 13775 NA TG 1 TG 1 412
+chrM_13792_14355_3:0:0_5:0:0_d/1_CA chrM 13791 NA CA 1 CA 1 413
+chrM_13799_14307_7:0:0_6:0:0_82/1_TT chrM 13798 NA TT 1 TT 1 414
+chrM_13306_13843_4:0:0_6:0:0_b/1_AT chrM 13843 NA AT 1 AT 1 415
+chrM_13398_13896_7:0:0_5:1:0_1e5/1_GC chrM 13896 NA GC 1 GC 1 416
+chrM_13409_13926_6:0:0_2:0:0_13c/1_AG chrM 13926 NA AG 1 AG 1 417
+chrM_13997_14575_4:0:0_2:0:0_97/1_AC chrM 13996 NA AC 1 AC 1 418
+chrM_13416_13997_2:0:0_2:0:0_d9/1_TA chrM 13997 NA TA 1 TA 1 419
+chrM_13540_14114_4:1:0_4:0:0_1b2/1_TC chrM 14114 NA TC 1 TC 1 420
+chrM_14120_14578_4:0:0_4:0:0_26/1_CG chrM 14119 NA CG 1 CG 1 421
+chrM_14134_14579_3:0:0_5:0:0_da/1_CA chrM 14133 NA CA 1 CA 1 422
+chrM_13711_14180_4:0:0_8:0:0_13e/1_GG chrM 14180 NA GG 1 GG 1 423
+chrM_14205_14774_5:0:0_5:0:0_105/1_CT chrM 14204 NA CT 1 CT 1 424
+chrM_13714_14222_2:0:0_1:0:0_182/1_GA chrM 14222 NA GA 1 GA 1 425
+chrM_13745_14261_7:0:0_4:0:0_b3/1_TA chrM 14261 NA TA 1 TA 1 426
+chrM_13794_14264_5:0:0_5:0:0_102/1_TA chrM 14264 NA TA 1 TA 1 427
+chrM_13867_14400_3:0:0_1:0:0_14f/1_AA chrM 14400 NA AA 1 AA 1 428
+chrM_13938_14449_2:0:0_6:0:0_1eb/1_GT chrM 14449 NA GT 1 GT 1 429
+chrM_13943_14452_3:0:0_4:0:0_11c/1_GT chrM 14452 NA GT 1 GT 1 430
+chrM_14006_14481_5:0:0_3:0:0_df/1_TA chrM 14481 NA TA 1 TA 1 431
+chrM_14135_14581_5:0:0_5:0:0_1de/1_AT chrM 14581 NA AT 1 AT 1 432
+chrM_14612_15169_2:0:0_5:0:0_e4/1_TT chrM 14611 NA TT 1 TT 1 433
+chrM_14668_15109_2:0:0_3:0:0_3d/1_TG chrM 14667 NA TG 1 TG 1 434
+chrM_14696_15126_2:0:0_2:0:0_a7/1_AA chrM 14695 NA AA 1 AA 1 435
+chrM_14727_15156_4:0:0_4:0:0_178/1_GA chrM 14726 NA GA 1 GA 1 436
+chrM_14245_14783_3:0:0_1:0:0_9d/1_GG chrM 14783 NA GG 1 GG 1 437
+chrM_14314_14802_5:0:0_3:0:0_191/1_GG chrM 14802 NA GG 1 GG 1 438
+chrM_14817_15261_5:0:0_4:0:0_65/1_AT chrM 14816 NA AT 1 AT 1 439
+chrM_14863_15320_2:0:0_4:0:0_d8/1_AA chrM 14862 NA AA 1 AA 1 440
+chrM_14869_15387_2:0:0_7:0:0_1f/1_AC chrM 14868 NA AC 1 AC 1 441
+chrM_14888_15340_3:0:0_3:0:0_112/1_GG chrM 14887 NA GG 1 GG 1 442
+chrM_14368_14894_6:0:0_5:0:0_40/1_TC chrM 14894 NA TC 1 TC 1 443
+chrM_14410_14941_6:0:0_3:0:0_e5/1_TA chrM 14941 NA TA 1 TA 1 444
+chrM_14962_15543_5:0:0_8:0:0_46/1_CA chrM 14961 NA CA 1 CA 1 445
+chrM_14456_14987_3:0:0_5:0:0_ab/1_GT chrM 14987 NA GT 1 GT 1 446
+chrM_15070_15569_5:0:0_5:0:0_cf/1_CA chrM 15069 NA CA 1 CA 1 447
+chrM_15140_15686_2:0:0_5:0:0_185/1_CC chrM 15139 NA CC 1 CC 1 448
+chrM_15142_15661_7:0:0_3:0:0_11e/1_CT chrM 15141 NA CT 1 CT 1 449
+chrM_15192_15694_5:0:0_2:0:0_f7/1_CA chrM 15191 NA CA 1 CA 1 450
+chrM_15211_15685_5:0:0_2:0:0_1d7/1_AC chrM 15210 NA AC 1 AC 1 451
+chrM_15225_15786_3:0:0_6:0:0_17e/1_TT chrM 15224 NA TT 1 TT 1 452
+chrM_15258_15810_4:0:0_6:0:0_5f/1_TT chrM 15257 NA TT 1 TT 1 453
+chrM_14817_15317_5:0:0_2:0:0_59/1_GC chrM 15317 NA GC 1 GC 1 454
+chrM_15324_15836_4:0:0_3:0:0_94/1_AC chrM 15323 NA AC 1 AC 1 455
+chrM_15365_15880_4:1:0_3:0:0_80/1_CA chrM 15364 NA CA 1 CA 1 456
+chrM_15408_15863_2:1:0_3:0:0_1e6/1_AG chrM 15407 NA AG 1 AG 1 457
+chrM_15439_15924_0:0:0_4:0:0_172/1_TG chrM 15438 NA TG 1 TG 1 458
+chrM_14931_15457_2:0:0_4:1:0_1a1/1_AA chrM 15457 NA AA 1 AA 1 459
+chrM_15547_16054_5:0:0_1:0:0_af/1_GA chrM 15546 NA GA 1 GA 1 460
+chrM_15134_15560_3:0:0_4:0:0_1c4/1_GG chrM 15560 NA GG 1 GG 1 461
+chrM_15575_16118_5:0:0_4:0:0_1aa/1_GC chrM 15574 NA GC 1 GC 1 462
+chrM_15052_15629_7:0:0_9:0:0_15f/1_GA chrM 15629 NA GA 1 GA 1 463
+chrM_15698_16224_5:0:0_6:0:0_138/1_AC chrM 15697 NA AC 1 AC 1 464
+chrM_15247_15721_2:1:0_6:0:0_17/1_TC chrM 15721 NA TC 1 TC 1 465
+chrM_15218_15763_2:0:0_2:0:0_171/1_AG chrM 15763 NA AG 1 AG 1 466
+chrM_15860_16419_5:0:0_8:0:0_53/1_TA chrM 15859 NA TA 1 TA 1 467
+chrM_15864_16329_3:0:0_3:0:0_18b/1_CG chrM 15863 NA CG 1 CG 1 468
+chrM_15507_15962_3:0:0_0:0:0_5b/1_GT chrM 15962 NA GT 1 GT 1 469
+chrM_15430_15985_5:0:0_3:0:0_2c/1_AT chrM 15985 NA AT 1 AT 1 470
+chrM_15706_16238_6:0:0_7:0:0_7b/1_AG chrM 16238 NA AG 1 AG 1 471
+chrM_16252_16701_2:1:0_5:0:0_147/1_TA chrM 16251 NA TA 1 TA 1 472
+chrM_15753_16280_5:0:0_6:0:0_180/1_TG chrM 16280 NA TG 1 TG 1 473
+chrM_15777_16347_2:0:0_6:0:0_16/1_AT chrM 16347 NA AT 1 AT 1 474
+chrM_16366_16911_6:1:0_6:1:1_168/1_CC chrM 16365 NA CC 1 CC 1 475
+chrM_16370_16833_6:1:0_6:0:1_1bb/1_AC chrM 16369 NA AC 1 AC 1 476
+chrM_16402_16876_2:0:0_1:0:1_98/1_CA chrM 16401 NA CA 1 CA 1 477
+chrM_16426_16953_3:0:0_2:2:0_60/1_AA chrM 16425 NA AA 1 AA 1 478
+chrM_15986_16442_3:0:0_7:0:0_15d/1_TG chrM 16442 NA TG 1 TG 1 479
+chrM_16030_16460_6:0:0_4:1:0_20/1_AT chrM 16460 NA AT 1 AT 1 480
+chrM_15909_16463_3:0:0_7:1:0_106/1_GT chrM 16463 NA GT 1 GT 1 481
+chrM_15984_16500_4:0:0_1:0:0_6b/1_GT chrM 16500 NA GT 1 GT 1 482
+chrM_16070_16513_3:0:0_7:1:0_1e7/1_TA chrM 16513 NA TA 1 TA 1 483
+chrM_16064_16572_4:0:0_6:1:0_f1/1_TG chrM 16572 NA TG 1 TG 1 484
+chrM_16245_16740_4:1:0_2:0:1_127/1_TA chrM 16742 NA TA 1 TA 1 485
+chrM_16315_16834_5:0:0_3:0:1_18/1_TT chrM 16834 NA TT 1 TT 1 486
+chrM_16229_16843_2:1:0_2:0:1_c4/1_GC chrM 16843 NA GC 1 GC 1 487
+chrM_16420_16905_5:0:0_2:0:1_159/1_GT chrM 16905 NA GT 2 GT 2 488
+chrM_16420_16905_5:0:0_2:0:1_159/1_GT chrM 16905 NA GT 2 GT 2 488
+chrM_16419_16923_3:0:0_3:0:1_183/1_CG chrM 16923 NA CG 1 CG 1 489
+chrM_16585_16993_5:0:1_5:1:0_1b9/1_GA chrM 16993 NA GA 1 GA 1 490
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out4.bam
Binary file test-data/group_out4.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out4.tab
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out5.bam
Binary file test-data/group_out5.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out6.bam
Binary file test-data/group_out6.bam has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/out_R1.fastq.gz
Binary file test-data/out_R1.fastq.gz has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/out_R2.fastq.gz
Binary file test-data/out_R2.fastq.gz has changed
diff -r 418b961e0576 -r 79436b3019e9 test-data/out_paired.log
--- a/test-data/out_paired.log Thu Aug 10 06:37:09 2017 -0400
+++ b/test-data/out_paired.log Tue Aug 29 17:37:07 2017 -0400
@@ -1,116 +1,36 @@
-# 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
+# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/tmp/tmpREDhtd/files/003/dataset_3773.dat
+# job started at Tue Aug 29 14:20:44 2017 on gaius -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd
+# pid: 21437, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64
+# blacklist : None
+# compresslevel : 6
+# error_correct_cell : False
+# extract_method : string
+# filter_cell_barcode : None
+# filter_cell_barcodes : False
# log2stderr : False
# loglevel : 1
# pattern : NNNXXX
# pattern2 : None
-# prime3 : False
+# prime3 : None
# quality_encoding : None
+# quality_filter_mask : None
# quality_filter_threshold : None
# random_seed : None
# read2_in : input_read2.gz
# read2_out : out2.gz
+# read2_stdout : False
+# reads_subset : None
+# reconcile : False
# short_help : None
-# split : False
-# stats : True
# stderr : <_io.TextIOWrapper name='' 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'>
+# stdlog : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3773.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
+# whitelist : None
+2017-08-29 14:20:44,451 INFO Starting barcode extraction
+2017-08-29 14:20:44,461 INFO Input Reads: 100
+2017-08-29 14:20:44,461 INFO Reads output: 100
+# job finished in 0 seconds at Tue Aug 29 14:20:44 2017 -- 0.73 0.05 0.00 0.00 -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd
diff -r 418b961e0576 -r 79436b3019e9 test-data/out_single.log
--- a/test-data/out_single.log Thu Aug 10 06:37:09 2017 -0400
+++ b/test-data/out_single.log Tue Aug 29 17:37:07 2017 -0400
@@ -1,92 +1,37 @@
-# 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
+# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpREDhtd/files/003/dataset_3766.dat --stdout /tmp/tmpREDhtd/files/003/dataset_3767.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpREDhtd/files/003/dataset_3768.dat
+# job started at Tue Aug 29 14:20:26 2017 on gaius -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393
+# pid: 21338, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64
+# blacklist : None
+# compresslevel : 6
+# error_correct_cell : False
+# extract_method : string
+# filter_cell_barcode : None
+# filter_cell_barcodes : False
# log2stderr : False
# loglevel : 1
# pattern : XXXNNN
# pattern2 : None
# prime3 : True
# quality_encoding : phred33
+# quality_filter_mask : None
# quality_filter_threshold : 10
# random_seed : None
# read2_in : None
-# read2_out : None
+# read2_out : False
+# read2_stdout : False
+# reads_subset : None
+# reconcile : False
# short_help : None
-# split : False
-# stats : True
# stderr : <_io.TextIOWrapper name='' 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'>
+# stdin : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3766.dat' mode='r' encoding='UTF-8'>
+# stdlog : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3768.dat' mode='a' encoding='UTF-8'>
+# stdout : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3767.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
+# whitelist : None
+2017-08-29 14:20:26,493 INFO Starting barcode extraction
+2017-08-29 14:20:26,495 INFO Input Reads: 100
+2017-08-29 14:20:26,495 INFO Reads output: 72
+2017-08-29 14:20:26,495 INFO filtered: umi quality: 28
+# job finished in 0 seconds at Tue Aug 29 14:20:26 2017 -- 0.75 0.02 0.00 0.00 -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393
diff -r 418b961e0576 -r 79436b3019e9 umi-tools_extract.xml
--- a/umi-tools_extract.xml Thu Aug 10 06:37:09 2017 -0400
+++ b/umi-tools_extract.xml Tue Aug 29 17:37:07 2017 -0400
@@ -1,8 +1,9 @@
-