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Attempt to fix #349. #365

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Attempt to fix #349. #365

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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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