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Attempt to fix CGATOxford#349 by replacing unordered sets by dictiona…
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…ries (only true for python3.5+) in cases where the order of elements influences the results. Also updating test results to compensate for using dicts as ordered structures. Note that it is now not necessary to set the environment variable PYTHONHASHSEED anymore.
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@christianbioinf
christianbioinf committed Aug 22, 2019
1 parent 4253ddf commit 054b60b
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Showing 25 changed files with 16,593 additions and 9,681 deletions.
5,851 changes: 4,651 additions & 1,200 deletions tests/group_adj_py3.sam
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9,907 changes: 6,679 additions & 3,228 deletions tests/group_adj_py3.tsv
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24 changes: 12 additions & 12 deletions tests/group_cluster_py3.sam
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Original file line number Diff line number Diff line change
Expand Up @@ -8648,8 +8648,8 @@ SRR2057595.13554798_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 N
SRR2057595.13565432_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:107 BX:Z:GTCAA
SRR2057595.13574588_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:107 BX:Z:GTCAA
SRR2057595.13587786_GTCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:107 BX:Z:GTCAA
SRR2057595.12229826_GTCGA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:107 BX:Z:GTCAA
SRR2057595.1408002_GCCAA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:107 BX:Z:GTCAA
SRR2057595.12229826_GTCGA 16 chr19 4078298 255 57M * 0 0 * * XA:i:1 MD:Z:43A13 NM:i:1 UG:i:107 BX:Z:GTCAA
SRR2057595.2688_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:108 BX:Z:GCATA
SRR2057595.37339_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:108 BX:Z:GCATA
SRR2057595.41440_GCATA 16 chr19 4078298 255 57M * 0 0 * * XA:i:2 MD:Z:42G0A13 NM:i:2 UG:i:108 BX:Z:GCATA
Expand Down Expand Up @@ -9849,8 +9849,8 @@ SRR2057595.13197976_GCCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 N
SRR2057595.13267737_GCCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:2 MD:Z:28A14A20 NM:i:2 UG:i:119 BX:Z:GCCGA
SRR2057595.13294730_GCCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:119 BX:Z:GCCGA
SRR2057595.13412461_GCCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:119 BX:Z:GCCGA
SRR2057595.11740437_ACCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:119 BX:Z:GCCGA
SRR2057595.4264163_GCGGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:119 BX:Z:GCCGA
SRR2057595.11740437_ACCGA 16 chr19 4078298 255 64M * 0 0 * * XA:i:1 MD:Z:43A20 NM:i:1 UG:i:119 BX:Z:GCCGA
SRR2057595.485289_TCGCT 16 chr19 4078298 255 64M * 0 0 * * XA:i:2 MD:Z:42G0A20 NM:i:2 UG:i:120 BX:Z:TCGCT
SRR2057595.1898374_TCGCT 16 chr19 4078298 255 64M * 0 0 * * XA:i:2 MD:Z:42G0A20 NM:i:2 UG:i:120 BX:Z:TCGCT
SRR2057595.2550928_TCGCT 16 chr19 4078298 255 64M * 0 0 * * XA:i:2 MD:Z:42G0A20 NM:i:2 UG:i:120 BX:Z:TCGCT
Expand Down Expand Up @@ -12993,7 +12993,7 @@ SRR2057595.13286517_CACCG 16 chr19 4078406 255 36M * 0 0 * * XA:i:2 MD:Z:9G6T19
SRR2057595.11957120_GGTAT 16 chr19 4078406 255 36M * 0 0 * * XA:i:2 MD:Z:9G6T19 NM:i:2 UG:i:141 BX:Z:GGTAT
SRR2057595.3802859_AGTAA 16 chr19 4078409 255 33M * 0 0 * * XA:i:2 MD:Z:6G6T19 NM:i:2 UG:i:142 BX:Z:AGTAA
SRR2057595.2310264_GCCTT 16 chr19 4078412 255 30M * 0 0 * * XA:i:2 MD:Z:3G6T19 NM:i:2 UG:i:143 BX:Z:GCCTT
SRR2057595.6226935_TATCC 16 chr19 4078412 255 67M * 0 0 * * XA:i:2 MD:Z:3G26A36 NM:i:2 UG:i:152 BX:Z:CATCC
SRR2057595.6226935_TATCC 16 chr19 4078412 255 67M * 0 0 * * XA:i:2 MD:Z:3G26A36 NM:i:2 UG:i:152 BX:Z:TATCC
SRR2057595.8572651_CAAAC 16 chr19 4078418 255 35M * 0 0 * * XA:i:2 MD:Z:4T19A10 NM:i:2 UG:i:144 BX:Z:CAAAC
SRR2057595.8000802_GTGCG 16 chr19 4078418 255 60M * 0 0 * * XA:i:2 MD:Z:4T19A35 NM:i:2 UG:i:149 BX:Z:GTGCG
SRR2057595.2487465_AACTT 16 chr19 4078418 255 66M * 0 0 * * XA:i:2 MD:Z:4T19A41 NM:i:2 UG:i:159 BX:Z:AACTT
Expand Down Expand Up @@ -15211,7 +15211,7 @@ SRR2057595.534130_GATCT 16 chr19 4078434 255 66M * 0 0 * * XA:i:1 MD:Z:8A57 NM:i
SRR2057595.11513813_GCGAT 16 chr19 4078434 255 67M * 0 0 * * XA:i:2 MD:Z:8A24T33 NM:i:2 UG:i:180 BX:Z:GCGAT
SRR2057595.5436928_GTGCG 16 chr19 4078437 255 41M * 0 0 * * XA:i:1 MD:Z:5A35 NM:i:1 UG:i:149 BX:Z:GTGCG
SRR2057595.11681356_GATAC 16 chr19 4078437 255 42M * 0 0 * * XA:i:1 MD:Z:5A36 NM:i:1 UG:i:150 BX:Z:GATAC
SRR2057595.13577605_CATCC 16 chr19 4078437 255 42M * 0 0 * * XA:i:1 MD:Z:5A36 NM:i:1 UG:i:152 BX:Z:CATCC
SRR2057595.13577605_CATCC 16 chr19 4078437 255 42M * 0 0 * * XA:i:1 MD:Z:5A36 NM:i:1 UG:i:152 BX:Z:TATCC
SRR2057595.13051052_AGTAA 16 chr19 4078438 255 52M * 0 0 * * XA:i:2 MD:Z:4A24T22 NM:i:2 UG:i:171 BX:Z:AGTAA
SRR2057595.9848177_TGGTC 16 chr19 4078439 255 47M * 0 0 * * XA:i:1 MD:Z:3A43 NM:i:1 UG:i:162 BX:Z:TGGTC
SRR2057595.1226182_TCTTG 16 chr19 4078439 255 51M * 0 0 * * XA:i:1 MD:Z:3A47 NM:i:1 UG:i:172 BX:Z:TCTTG
Expand Down Expand Up @@ -19763,8 +19763,8 @@ SRR2057595.13496462_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i
SRR2057595.13514063_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:238 BX:Z:CACTG
SRR2057595.13521988_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:238 BX:Z:CACTG
SRR2057595.13523213_CACTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:238 BX:Z:CACTG
SRR2057595.13444863_CACAG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:238 BX:Z:CACTG
SRR2057595.8311794_CATTG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:238 BX:Z:CACTG
SRR2057595.13444863_CACAG 16 chr19 5798673 255 42M * 0 0 * * XA:i:0 MD:Z:42 NM:i:0 UG:i:238 BX:Z:CACTG
SRR2057595.299231_TGAAC 16 chr19 5798677 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:239 BX:Z:TGAAC
SRR2057595.318697_TGAAC 16 chr19 5798677 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:239 BX:Z:TGAAC
SRR2057595.573016_TGAAC 16 chr19 5798677 255 38M * 0 0 * * XA:i:0 MD:Z:38 NM:i:0 UG:i:239 BX:Z:TGAAC
Expand Down Expand Up @@ -21747,8 +21747,8 @@ SRR2057595.13595347_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM
SRR2057595.13609810_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.13610242_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.13648468_GCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.8637529_GGCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.8139214_GCTGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.8637529_GGCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.13256411_CCCGA 16 chr19 7389994 255 48M * 0 0 * * XA:i:1 MD:Z:47C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.2019660_GCCGA 16 chr19 7389996 255 46M * 0 0 * * XA:i:1 MD:Z:45C0 NM:i:1 UG:i:270 BX:Z:GCCGA
SRR2057595.9119459_ACGCA 0 chr19 7507314 255 25M * 0 0 * * XA:i:2 MD:Z:8A9A6 NM:i:2 UG:i:271 BX:Z:ACGCA
Expand Down Expand Up @@ -32805,8 +32805,8 @@ SRR2057595.13626245_TATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16
SRR2057595.2931220_TACGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:391 BX:Z:TATTG
SRR2057595.4971514_TACGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:391 BX:Z:TATTG
SRR2057595.2867945_CATTG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:391 BX:Z:TATTG
SRR2057595.13255450_AATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:391 BX:Z:TATTG
SRR2057595.11618608_TAATG 0 chr19 13129322 255 28M * 0 0 * * XA:i:0 MD:Z:28 NM:i:0 UG:i:391 BX:Z:TATTG
SRR2057595.13255450_AATGG 0 chr19 13129322 255 56M * 0 0 * * XA:i:2 MD:Z:33C5A16 NM:i:2 UG:i:391 BX:Z:TATTG
SRR2057595.116977_CGCTT 0 chr19 13129322 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:392 BX:Z:CGCTT
SRR2057595.223450_CGCTT 0 chr19 13129322 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:392 BX:Z:CGCTT
SRR2057595.241741_CGCTT 0 chr19 13129322 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:392 BX:Z:CGCTT
Expand Down Expand Up @@ -33374,8 +33374,8 @@ SRR2057595.1266554_GAGGG 0 chr19 13129323 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:
SRR2057595.9571141_GAGGG 0 chr19 13129323 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:404 BX:Z:GAGGG
SRR2057595.4859358_ATGCG 0 chr19 13129323 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:405 BX:Z:ATGCG
SRR2057595.9874047_ATGCG 0 chr19 13129323 255 26M * 0 0 * * XA:i:0 MD:Z:26 NM:i:0 UG:i:405 BX:Z:ATGCG
SRR2057595.12595914_ATGAG 0 chr19 13129323 255 34M * 0 0 * * XA:i:1 MD:Z:32C1 NM:i:1 UG:i:405 BX:Z:ATGCG
SRR2057595.9121885_ATGGG 0 chr19 13129323 255 27M * 0 0 * * XA:i:0 MD:Z:27 NM:i:0 UG:i:405 BX:Z:ATGCG
SRR2057595.12595914_ATGAG 0 chr19 13129323 255 34M * 0 0 * * XA:i:1 MD:Z:32C1 NM:i:1 UG:i:405 BX:Z:ATGCG
SRR2057595.7181004_TCAGC 0 chr19 13129324 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:406 BX:Z:TCAGC
SRR2057595.32462_CGTCT 0 chr19 13129329 255 35M * 0 0 * * XA:i:2 MD:Z:26C5A2 NM:i:2 UG:i:407 BX:Z:CGTCT
SRR2057595.126970_CGTCT 0 chr19 13129329 255 35M * 0 0 * * XA:i:2 MD:Z:26C5A2 NM:i:2 UG:i:407 BX:Z:CGTCT
Expand Down Expand Up @@ -39760,9 +39760,9 @@ SRR2057595.13401504_GCTAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:
SRR2057595.13421676_GCTAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:512 BX:Z:GCTAA
SRR2057595.13463857_GCTAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:512 BX:Z:GCTAA
SRR2057595.13584467_GCTAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:512 BX:Z:GCTAA
SRR2057595.9833878_GCCAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:512 BX:Z:GCTAA
SRR2057595.12488286_GCAAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:512 BX:Z:GCTAA
SRR2057595.13441427_GCTGA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:512 BX:Z:GCTAA
SRR2057595.9833878_GCCAA 16 chr19 32596026 255 56M * 0 0 * * XA:i:0 MD:Z:56 NM:i:0 UG:i:512 BX:Z:GCTAA
SRR2057595.1134582_GATGT 0 chr19 32850824 255 54M * 0 0 * * XA:i:0 MD:Z:54 NM:i:0 UG:i:513 BX:Z:GATGT
SRR2057595.8708447_GATGT 0 chr19 32850824 255 54M * 0 0 * * XA:i:0 MD:Z:54 NM:i:0 UG:i:513 BX:Z:GATGT
SRR2057595.965130_GACAG 16 chr19 32981855 255 18M * 0 0 * * XA:i:2 MD:Z:1G10C5 NM:i:2 UG:i:514 BX:Z:GACAG
Expand Down Expand Up @@ -40242,8 +40242,8 @@ SRR2057595.13290815_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10
SRR2057595.13313064_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:529 BX:Z:ATACC
SRR2057595.13322565_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:529 BX:Z:ATACC
SRR2057595.13476968_ATACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:529 BX:Z:ATACC
SRR2057595.6413612_ATCCC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:529 BX:Z:ATACC
SRR2057595.4829989_ACACC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:529 BX:Z:ATACC
SRR2057595.6413612_ATCCC 16 chr19 35673152 255 21M * 0 0 * * XA:i:2 MD:Z:7T2A10 NM:i:2 UG:i:529 BX:Z:ATACC
SRR2057595.308008_GTGGA 16 chr19 35902240 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:530 BX:Z:GTGGA
SRR2057595.311184_GTGGA 16 chr19 35902240 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:530 BX:Z:GTGGA
SRR2057595.360154_GTGGA 16 chr19 35902240 255 30M * 0 0 * * XA:i:0 MD:Z:30 NM:i:0 UG:i:530 BX:Z:GTGGA
Expand Down Expand Up @@ -49396,8 +49396,8 @@ SRR2057595.13466598_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4
SRR2057595.13508294_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:643 BX:Z:CGGCC
SRR2057595.13524099_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:643 BX:Z:CGGCC
SRR2057595.13639209_CGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:643 BX:Z:CGGCC
SRR2057595.10208347_CGGCG 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:643 BX:Z:CGGCC
SRR2057595.4719584_TGGCC 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:643 BX:Z:CGGCC
SRR2057595.10208347_CGGCG 16 chr19 52641725 255 20M * 0 0 * * XA:i:2 MD:Z:1C13A4 NM:i:2 UG:i:643 BX:Z:CGGCC
SRR2057595.12041_ACGTG 16 chr19 52844257 255 21M * 0 0 * * XA:i:2 MD:Z:15C0T4 NM:i:2 UG:i:644 BX:Z:ACGTG
SRR2057595.47279_TGCTA 16 chr19 52985168 255 20M * 0 0 * * XA:i:2 MD:Z:8T4A6 NM:i:2 UG:i:645 BX:Z:TGCTA
SRR2057595.105673_GGTCG 0 chr19 53686815 255 67M * 0 0 * * XA:i:0 MD:Z:67 NM:i:0 UG:i:646 BX:Z:GGTCG
Expand Down Expand Up @@ -54749,8 +54749,8 @@ SRR2057595.13576443_CTGCG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T1
SRR2057595.13581746_CTGCG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:707 BX:Z:CTGCG
SRR2057595.13623055_CTGCG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:707 BX:Z:CTGCG
SRR2057595.4284087_CTGTG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:707 BX:Z:CTGCG
SRR2057595.8361213_AAGCG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:707 BX:Z:CTGCG
SRR2057595.10713055_CAGCG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:707 BX:Z:CTGCG
SRR2057595.8361213_AAGCG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:707 BX:Z:CTGCG
SRR2057595.7685011_GTACG 16 chr19 61240305 255 36M * 0 0 * * XA:i:2 MD:Z:17A4T13 NM:i:2 UG:i:709 BX:Z:GTACG
SRR2057595.2364090_TGGTT 16 chr19 61240306 255 35M * 0 0 * * XA:i:2 MD:Z:16A4T13 NM:i:2 UG:i:708 BX:Z:TGGTT
SRR2057595.2489631_TGGTT 16 chr19 61240306 255 35M * 0 0 * * XA:i:2 MD:Z:16A4T13 NM:i:2 UG:i:708 BX:Z:TGGTT
Expand Down
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