diff --git a/tests/dedup_paired_contig.sam b/tests/dedup_paired_contig.sam new file mode 100644 index 00000000..dfa9186e --- /dev/null +++ b/tests/dedup_paired_contig.sam @@ -0,0 +1,133 @@ +@HD VN:1.5 SO:coordinate +ILLUMINA_0179:6:1102:12470:144275|ATACTAGGGGCCCAATCAAC:CCAATTGGGCCACTTAGCAA 147 AAC73112 9 60 58M18S = 1 -66 CATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAG ADDC@C?>BB?BCACCDDCCDDDDDDDCCEEDCFDBFHHIGFIJJJIJIJIIJJIJJJIGJHIHJJJ X0:i:0 MC:Z:15S64M MD:Z:58 XE:i:44 XI:f:1 NM:i:0 MQ:i:60 XR:i:58 AS:i:580 +ILLUMINA_0179:6:1102:12470:144275|ATACTAGGGGCCCAATCAAC:CCAATTGGGCCACTTAGCAA 99 AAC73112 1 60 15S64M = 9 66 GAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCT JJJHIJJJJJJJJJJJJJJJJJJJJJJIJIIIJIJIJHHHEHHFFEFDDDEDDDCDCCDDDDD?ACCCDB@8A@>BBBB X0:i:0 MC:Z:58M18S MD:Z:64 XE:i:52 XI:f:1 NM:i:0 MQ:i:60 XR:i:64 AS:i:640 +ILLUMINA_0179:6:1102:14712:11012|GATGAGTTCGCTCCACCTCT:GGTTCCCCGAAGGTCCTCAT 147 AAC73113 1867 60 60M = 1867 -60 CTCAATGCTGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCAGGTTCGCTTTCTTAT C>C@DCDDC:>CDDDCA?<8??C@C>@A@;DDFD?>>CFFCFHHCEEEEHEAFCHGGHHF@GJIFIIIGJIHCJIIJJJJJ X0:i:0 MC:Z:77M MD:Z:49A27 XE:i:52 XI:f:0.987 NM:i:1 MQ:i:60 XR:i:77 AS:i:745 +ILLUMINA_0179:6:1104:20455:26471|CAATAAGTAGAGGAGTGGCT:CTGAGAACTCCCCGTTCATA 147 AAC73113 1229 60 67M = 1183 -113 GTGGGATCTCGGCGAAATTCTTTGCCGCGCTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCA DDCC@?DBDDDDDDDDDDDDDDBDDDDDBBDDDDHJIHHEFCHGIJJJJJJIJJIIIJIJJJJJIJJ X0:i:0 MC:Z:16M MD:Z:28A38 XE:i:42 XI:f:0.9851 NM:i:1 MQ:i:60 XR:i:67 AS:i:645 +ILLUMINA_0179:6:1104:20455:26471|CAATAAGTAGAGGAGTGGCT:CTGAGAACTCCCCGTTCATA 99 AAC73113 1183 60 16M = 1229 113 CGGCTGGCCATTATCT GCH=FGF6DDBG??*9 X0:i:0 MC:Z:67M MD:Z:16 XE:i:4 XI:f:1 NM:i:0 MQ:i:60 XR:i:16 AS:i:160 +ILLUMINA_0179:6:1104:4890:55036|GGTTCCCCGAAGGTCCTCAT:GATGAGTTCGCTCCACCTCT 163 AAC73113 1867 60 60M = 1867 60 CTCAATGCTGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCAGGTTCGCTTTCTTAT JJJJIJJJJJJHIJJJJIJJJIJJIJJJFGIIIIIJIHIFIJIJHGFFFHDFDDDCDDDC X0:i:0 MC:Z:60M MD:Z:8A35T15 XE:i:26 XI:f:0.9667 NM:i:2 MQ:i:60 XR:i:60 AS:i:550 +ILLUMINA_0179:6:1104:4890:55036|GGTTCCCCGAAGGTCCTCAT:GATGAGTTCGCTCCACCTCT 83 AAC73113 1867 60 60M = 1867 -60 CTCAATGCTGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCAGGTTCGCTTTCTTAT CADCCCDB@9CDEEDDDDDEEECDEEFFFHHIIFJJIGIIJJJJJJJJJJJJJJJJJJJJ X0:i:0 MC:Z:60M MD:Z:8A35T15 XE:i:26 XI:f:0.9667 NM:i:2 MQ:i:60 XR:i:60 AS:i:550 +ILLUMINA_0179:6:1104:4935:178202|CTATAACCTCAAGTGCACCG:GCAGTGAATTAGTTGTCCAT 163 AAC73113 922 60 70M1S = 922 70 GGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCAA JJIJJJJIIIIJJIEHGIGIHIJJIJGIIHJJJJJCHIJJJJIIEEHFFDDB;@ACCCDDDDDDCDD>DDD X0:i:0 MC:Z:70M1S MD:Z:20C20T2T20C4 XE:i:24 XI:f:0.9429 NM:i:4 MQ:i:60 XR:i:70 AS:i:600 +ILLUMINA_0179:6:1104:4935:178202|CTATAACCTCAAGTGCACCG:GCAGTGAATTAGTTGTCCAT 83 AAC73113 922 60 70M1S = 922 -70 GGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCAA @CC>:3@DCDDDCCCEDCAAC>A@>DCDDDDBDDDDCBBCCFHJGHAIIGHGGIIIGJIJJIJJJJJJIJJ X0:i:0 MC:Z:70M1S MD:Z:20C20T2T20C4 XE:i:24 XI:f:0.9429 NM:i:4 MQ:i:60 XR:i:70 AS:i:600 +ILLUMINA_0179:6:1106:2094:187039|CCAATTGGGCCACTTAGCAA:TATACTCGGGATGTCTCTTA 163 AAC73113 1638 60 47M = 1678 89 GCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGG C+2?*193::@6DAE9CH7?@;;>B X0:i:0 MC:Z:49M MD:Z:47 XE:i:35 XI:f:1 NM:i:0 MQ:i:60 XR:i:47 AS:i:470 +ILLUMINA_0179:6:1106:2094:187039|CCAATTGGGCCACTTAGCAA:TATACTCGGGATGTCTCTTA 83 AAC73113 1678 60 49M = 1638 -89 GTGGCGGATCAATATGCCGACTTCTTGCGCGAAGGTTTCCACGTTGTCA B@=5(5>3;;>ACBDDEEEC@DDB8@<@8)AFGFAFFBD::EIGCFCBA X0:i:0 MC:Z:47M MD:Z:24C24 XE:i:24 XI:f:0.9796 NM:i:1 MQ:i:60 XR:i:49 AS:i:465 +ILLUMINA_0179:6:1106:8062:182725|GCATAGTCCTAATCGTAGCA:GAACGAAAGGGGCAGCGACT 163 AAC73112 23 60 44M25S = 23 44 TTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGACAAAAG JJJJIJIJJJJJGGHHIJGIIHIIIDHIHHHHHFB?CCDBDD@BD399>BBDCDBDDDDD>@DD@BDCDDDDCCDC@CDDDDDDDDDDDBDDFFHHJJIIJIJJIDJJJJJJJJJIJIJJJJJJJIIJ X0:i:0 MC:Z:44M25S MD:Z:44 XE:i:30 XI:f:1 NM:i:0 MQ:i:60 XR:i:44 AS:i:440 +ILLUMINA_0179:6:1107:4975:132518|CCGATTCAGTCAAGCTCCAT:CTCGTGAAGCTCAACTAGTT 163 AAC73113 1576 60 1S65M = 1615 110 TGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCT JJJJJJJJJJIIJJIIIBAF;4FDJIIGFGAIIHJGHHHCGHJJHIJJJJIJJJJJJIGHFJJJJ X0:i:0 MC:Z:1S65M MD:Z:71 XE:i:59 XI:f:1 NM:i:0 MQ:i:60 XR:i:71 AS:i:710 +ILLUMINA_0179:6:1108:10721:9885|TCCTAGTTACACCCGTACGC:TTACGCCCGACCTACTTTGT 147 AAC73113 2262 60 2S65M = 2262 -65 GCCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGAAA BBBDDDBDDDDEDDDC;@@BDDDDDEEEEEFFFDFFHHHIIIIIIGJJJJJIIIIJJJIGGJJJJJJ X0:i:0 MC:Z:2S65M MD:Z:65 XE:i:53 XI:f:1 NM:i:0 MQ:i:60 XR:i:65 AS:i:650 +ILLUMINA_0179:6:1108:10721:9885|TCCTAGTTACACCCGTACGC:TTACGCCCGACCTACTTTGT 99 AAC73113 2262 60 2S65M = 2262 65 GCCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGAAA JJJJJJJIIGFGIJJJIIIJJJJIHCHFFFFF;6ACAAECDDDDD?CDDDDD>:;@CDB?C>A<<9< X0:i:0 MC:Z:2S65M MD:Z:65 XE:i:53 XI:f:1 NM:i:0 MQ:i:60 XR:i:65 AS:i:650 +ILLUMINA_0179:6:1108:17608:138109|CTGAGAACTCCCCGTTCATA:TGGCACGTACGGGAGTACAA 163 AAC73113 1680 60 51M = 1689 87 GGCGGATCAATATGCCGACTTCTTGCGCGAAGGTTTCCACGTTGTCACGCC GHD@F:?@BF8B@78=5;=B?;;@;;9=@/;/8(3>3>@AC&+8 X0:i:0 MC:Z:78M MD:Z:22C28 XE:i:26 XI:f:0.9804 NM:i:1 MQ:i:60 XR:i:51 AS:i:485 +ILLUMINA_0179:6:1108:17608:138109|CTGAGAACTCCCCGTTCATA:TGGCACGTACGGGAGTACAA 83 AAC73113 1689 60 78M = 1680 -87 ATATGCCGACTTCTTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTACTA A>DBBDB@CDDDB@5>BBDDCDBCC@BBBBDDDDBBDDDFHFHIHJJJJJJJJIJJIGDJJJIJJJJIJJJJJIHEIJ X0:i:0 MC:Z:51M MD:Z:13C64 XE:i:53 XI:f:0.9872 NM:i:1 MQ:i:60 XR:i:78 AS:i:755 +ILLUMINA_0179:6:1201:5266:97241|GGTACGCGGAGCATATCCTT:GGCGTACGATTCGCAAGCTT 147 AAC73113 2038 60 53M = 2017 -74 GCGCGTAAGCTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGC BBB?>CCCCCCC@:CDDDFFHGGGIGIIJJIGIIJJIIHDFDIIIJHIHFJII X0:i:0 MC:Z:74M MD:Z:8A44 XE:i:32 XI:f:0.9811 NM:i:1 MQ:i:60 XR:i:53 AS:i:505 +ILLUMINA_0179:6:1201:5266:97241|GGTACGCGGAGCATATCCTT:GGCGTACGATTCGCAAGCTT 99 AAC73113 2017 60 74M = 2038 74 GATCTTTCTGGTATGGATGTAGCGCGTAAGCTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGC JIJJIIJJJJIFGHIJJJJCBGHGGHHDCECCEECCCDCDCCDDBBD?B>2:>8@B>@>B@DDCCDDC?A@>?@ X0:i:0 MC:Z:53M MD:Z:20G8A44 XE:i:40 XI:f:0.973 NM:i:2 MQ:i:60 XR:i:74 AS:i:690 +ILLUMINA_0179:6:1201:8226:146783|AACTATACCCCAGAGCCAAT:GTACTCCTGTGTGAATGGGC 147 AAC73113 822 60 76M = 821 -77 CCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGCCGT ?>@>3>>44<<2@<8BA<@5:@AA=DDC@?=3A;;)CC=3E?.)B6;==F>EF:B?EBFABBF@IGFAJJJJJJJI X0:i:0 MC:Z:77M MD:Z:48A27 XE:i:51 XI:f:0.9868 NM:i:1 MQ:i:60 XR:i:76 AS:i:735 +ILLUMINA_0179:6:1201:8226:146783|AACTATACCCCAGAGCCAAT:GTACTCCTGTGTGAATGGGC 99 AAC73113 821 60 77M = 822 77 CCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGCCGT HJJGIHIIIJJJJJJJJJIJJJJIJJIIJJIJJHGHIIJIJJEHHHCFFFDEDEEEEE@BBDDDDCD>B>A:@@BB> X0:i:0 MC:Z:76M MD:Z:49A27 XE:i:52 XI:f:0.987 NM:i:1 MQ:i:60 XR:i:77 AS:i:745 +ILLUMINA_0179:6:1202:12136:144106|GGAGGTTCCCCTTAAGTTGT:CTCTACCATACTCACGGGTC 163 AAC73113 915 60 70M = 915 70 GGTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATG JJIJJJJJJJJJJIJJIJJJJJ>FIGJHHIJDCHIJJJIJJIIIIHHEHFFDCDDBBD>BDDDCC?B?9? X0:i:0 MC:Z:70M MD:Z:27C20T2T18 XE:i:29 XI:f:0.9571 NM:i:3 MQ:i:60 XR:i:70 AS:i:625 +ILLUMINA_0179:6:1202:12136:144106|GGAGGTTCCCCTTAAGTTGT:CTCTACCATACTCACGGGTC 83 AAC73113 915 60 70M = 915 -70 GGTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATG CCDDDCCCCCCC@CBCCCDCDDACFDDCDCDDDDDDEEDDFFFHHHJIJJJJJJIIIIJJJJJJJJJJJJ X0:i:0 MC:Z:70M MD:Z:27C20T2T18 XE:i:29 XI:f:0.9571 NM:i:3 MQ:i:60 XR:i:70 AS:i:625 +ILLUMINA_0179:6:1202:19717:142559|GTACTCCTGTGTGAATGGGC:ACGACTTCGGGACATCCTGT 147 AAC73113 600 60 69M = 588 -81 GGTACTTGGACGCAACGGTTCCGACTACTCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTG C>@>:3<5>999<<2005855&:3CC@DBDBBB?8;;=A=EBDFFFFHEHA=AIHIIIJIIIHEDIHCG X0:i:0 MC:Z:79M MD:Z:3G26T2T35 XE:i:37 XI:f:0.9565 NM:i:3 MQ:i:60 XR:i:69 AS:i:615 +ILLUMINA_0179:6:1202:19717:142559|GTACTCCTGTGTGAATGGGC:ACGACTTCGGGACATCCTGT 99 AAC73113 588 60 79M = 600 81 AGGCGAACTGGTGGTACTTGGACGCAACGGTTCCGACTACTCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGT JJJJJIIJJJIBGGHGIJIJIIIJJJIJJGHCBCEDABBCDCCBDDDDDD>>3@3:@CB8@?BB@D<.5??@ X0:i:0 MC:Z:69M MD:Z:15G26T2T33 XE:i:38 XI:f:0.962 NM:i:3 MQ:i:60 XR:i:79 AS:i:715 +ILLUMINA_0179:6:1202:9412:20310|GGTACGCGGAGCATATCCTT:GCCACTACCTAACTTAAGGA 163 AAC73112 1 60 20S56M = 1 56 TTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGG JJJJJIJJIIIJJJJIJJJJEHIGJIJJIIIJEEGGFFGHGIJIIGEHEFHFFDFEEEEEDCDCDCC??9@(>@@@ X0:i:0 MC:Z:20S56M MD:Z:56 XE:i:44 XI:f:1 NM:i:0 MQ:i:60 XR:i:56 AS:i:560 +ILLUMINA_0179:6:1202:9412:20310|GGTACGCGGAGCATATCCTT:GCCACTACCTAACTTAAGGA 83 AAC73112 1 60 20S56M = 1 -56 TTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGG >4CCAC@>CCDDDCCCCCCDECCBDDDDCDCADCDDCEAEECFDBHHHIHDJJIIHFJIGGJIJJIJJJJIHFJJJ X0:i:0 MC:Z:20S56M MD:Z:56 XE:i:44 XI:f:1 NM:i:0 MQ:i:60 XR:i:56 AS:i:560 +ILLUMINA_0179:6:1204:18042:78067|CTTCGCGTTCACGAACTAAG:CCGGCCATTCTTGTGTTGCT 147 AAC73113 18 60 62M = 18 -62 CGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATATTCTGGAAAGCA -=DBCBA>ADDCDDCEAAEEA>@C==B0<;AC>BDBB@CDAC>CCACD X0:i:0 MC:Z:62M MD:Z:39T22 XE:i:37 XI:f:0.9839 NM:i:1 MQ:i:60 XR:i:62 AS:i:595 +ILLUMINA_0179:6:1204:6488:90725|AACTATACCCCAGAGCCAAT:GATGAGTTCGCTCCACCTCT 163 AAC73113 735 60 79M = 765 87 GTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACC JJJJJJJJIJJJJIJJJIJJJJJIJJJIHIIIJJJJIIGIGEEHHGFDDDDDDDDDECDDDCCACBB99>BDBDCCD>A X0:i:0 MC:Z:57M21S MD:Z:79 XE:i:67 XI:f:1 NM:i:0 MQ:i:60 XR:i:79 AS:i:790 +ILLUMINA_0179:6:1204:6488:90725|AACTATACCCCAGAGCCAAT:GATGAGTTCGCTCCACCTCT 83 AAC73113 765 60 57M21S = 735 -87 GGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCTAAAGTTCTTCACCCCCGCAC >@@DDDDDDDCBDBDDB@BCDCCDC?CDDDA@8DDDDDDDCDDDDBBDDDDDDDDDDDDDDDDDEECA9JJJJIIIGJ X0:i:0 MC:Z:79M MD:Z:57 XE:i:45 XI:f:1 NM:i:0 MQ:i:60 XR:i:57 AS:i:570 +ILLUMINA_0179:6:1204:8876:143905|ACCCAATTGCTTGCCTATCA:AATGAGGAAATGACACGGGC 147 AAC73113 872 60 43M = 855 -60 CAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACC @:CA?9DEEHA?=>CEC1HDJIIGHCGIGIJJIGJJIIGHGII X0:i:0 MC:Z:60M MD:Z:43 XE:i:31 XI:f:1 NM:i:0 MQ:i:60 XR:i:43 AS:i:430 +ILLUMINA_0179:6:1204:8876:143905|ACCCAATTGCTTGCCTATCA:AATGAGGAAATGACACGGGC 99 AAC73113 855 60 60M = 872 60 CGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACC IIIBDE>FGGGIIEGGIJIJJDDHGGEAHGCHI@A;FHHC@AE>DE>BCECCCD@;;A>C X0:i:0 MC:Z:43M MD:Z:15A44 XE:i:35 XI:f:0.9833 NM:i:1 MQ:i:60 XR:i:60 AS:i:575 +ILLUMINA_0179:6:1205:15620:25859|CCAATTGGGCCACTTAGCAA:TCTAACGCGAGGGGTCCTAT 163 AAC73113 1802 60 78M = 1815 89 GTAAATTCCTCTATGACACCAACGTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCTGGTG JIJGJJJJJJJJJJJIIIJJIJJIHGIHGDFFDD@CCD@CBDDDDDDDCD?CCBCAACCDDDCACCCCC:@>CDACCEFFDFBEIGGIIIIIIGGHIIJIJJJIIJJJJJJJJJJJJIJJJJJJJJJJJJJJJ X0:i:0 MC:Z:78M MD:Z:60A15 XE:i:51 XI:f:0.9868 NM:i:1 MQ:i:60 XR:i:76 AS:i:735 +ILLUMINA_0179:6:1205:18696:116920|AATGAGGAAATGACACGGGC:ACGAGCCGAATACCTTGTAA 147 AAC73113 1229 60 76M = 1224 -81 GTGGGATCTCGGCGAAATTCTTTGCCGCGCTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTC BA?A@<CCDDDC?BDBBBDBBBBDDDDDFFEECGIJJJHFIJJIJJIIIIGIIGEIG@HGJJJJJJIJ X0:i:0 MC:Z:79M MD:Z:28A47 XE:i:51 XI:f:0.9868 NM:i:1 MQ:i:60 XR:i:76 AS:i:735 +ILLUMINA_0179:6:1205:18696:116920|AATGAGGAAATGACACGGGC:ACGAGCCGAATACCTTGTAA 99 AAC73113 1224 60 79M = 1229 81 CTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCGCTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCT JIJJIJJIJJJJIIJJIIJJHGFFFFFFFECCDDDDDBDAADDDDDDD9AC:C@?CCCDDDDBDDDACDDC>C><0?BCCC@BB??A<AAA?? X0:i:0 MC:Z:52M25S MD:Z:57 XE:i:43 XI:f:1 NM:i:0 MQ:i:60 XR:i:57 AS:i:570 +ILLUMINA_0179:6:1206:5081:107848|GTTACGCAACGTTAACCACG:CAGGGGTAACCAAAGACTTG 83 AAC73112 15 60 52M25S = 10 -57 CACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG 20?>4:C@>:5?@5BDCDCDCCCCC>A:?DDCDDCB?@BBBBDBDDEFFFFHJIJIHGJIIGHGDGCJJGIIJIIIH X0:i:0 MC:Z:57M19S MD:Z:52 XE:i:38 XI:f:1 NM:i:0 MQ:i:60 XR:i:52 AS:i:520 +ILLUMINA_0179:6:1206:9263:50244|GGCGTACGATTCGCAAGCTT:GGTACGCGGAGCATATCCTT 163 AAC73113 2017 60 72M = 2017 74 GATCTTTCTGGTATGGATGTAGCGCGTAAGCTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTG IIJIJJJJJJIIJJIIHIJFG>FGIEEBD@CEEEDCCE;@CABDDB?BDCDC@@<009<98++>@@CCB?8A X0:i:0 MC:Z:74M MD:Z:20G8A42 XE:i:38 XI:f:0.9722 NM:i:2 MQ:i:60 XR:i:72 AS:i:670 +ILLUMINA_0179:6:1206:9263:50244|GGCGTACGATTCGCAAGCTT:GGTACGCGGAGCATATCCTT 83 AAC73113 2017 60 74M = 2017 -74 GATCTTTCTGGTATGGATGTAGCGCGTAAGCTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGC CDC@>>A@:9(@A>>:@CDB<@BBDDCDDCADCCDDBDDDCCDDDDDDDCFFGFGJJJIEJJJJJIIHFIHHJJJJJJIIJJJJJJJIJJJJIJ X0:i:0 MC:Z:65M13S MD:Z:6A7T48 XE:i:36 XI:f:0.9683 NM:i:2 MQ:i:60 XR:i:63 AS:i:580 +ILLUMINA_0179:6:1207:10721:4345|GCCCAAACCCATACAAGCGG:TCTAGTTACGTTCAACGCCT 99 AAC73113 1764 60 65M13S = 1766 65 CTACCATCTGTTGCGTCATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGAGTGAAACGTGAG JJ>HIIJJJJIJJJJJJJJJJJJJFDDBDDDBCDDDDDD;BBBCDDDDDACCDCCDDDBDD@BCAAC:(44>ABBDDB X0:i:0 MC:Z:63M13S MD:Z:8A7T48 XE:i:36 XI:f:0.9692 NM:i:2 MQ:i:60 XR:i:65 AS:i:600 +ILLUMINA_0179:6:1207:1297:114545|ACGACTTCGGGACATCCTGT:CTATCATACATGCTCGAATC 147 AAC73113 1672 60 40M = 1616 -96 CAGGCAGTGGCGGATCAATATGCCGACTTCTTGCGCGAAG 6(ED?C9'-?2CDDC=;EGHGF@?*B;@HDD@6F:?IGCJ X0:i:0 MC:Z:29M MD:Z:30C9 XE:i:18 XI:f:0.975 NM:i:1 MQ:i:60 XR:i:40 AS:i:375 +ILLUMINA_0179:6:1207:1297:114545|ACGACTTCGGGACATCCTGT:CTATCATACATGCTCGAATC 99 AAC73113 1616 60 29M = 1672 96 GCCTCGTGAAAGAATATCATCTGCTGAAC CEEEIIDDIII>DCDI9D>BBDEE*=B== X0:i:0 MC:Z:40M MD:Z:29 XE:i:17 XI:f:1 NM:i:0 MQ:i:60 XR:i:29 AS:i:290 +ILLUMINA_0179:6:1207:16160:119641|ACTGCAAAGTCTAGCAGTTG:TTGGAAACTACGTTCTCGAC 147 AAC73112 1 60 24S28M = 1 -28 AAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCA DCAA=).=FGEED=;=7=)C4FFBF=GFCDFBAGGGIIGEIGE+AEHEBHGFCG:?EFGGEHGIHIGGCBHHAHID?@FAFAGGE7;CA> X0:i:0 MC:Z:24S28M MD:Z:28 XE:i:16 XI:f:1 NM:i:0 MQ:i:60 XR:i:28 AS:i:280 +ILLUMINA_0179:6:1207:20920:139349|GCCACTACCTAACTTAAGGA:GGTACGCGGAGCATATCCTT 147 AAC73112 1 60 4S56M = 1 -56 ATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGG C:@:@>@@?<8(>CC>;>BADCAEFDBFDHEBGDDGCIGHHJIIJJHJJJJJJJGIGIIH X0:i:0 MC:Z:20S56M MD:Z:56 XE:i:44 XI:f:1 NM:i:0 MQ:i:60 XR:i:56 AS:i:560 +ILLUMINA_0179:6:1207:20920:139349|GCCACTACCTAACTTAAGGA:GGTACGCGGAGCATATCCTT 99 AAC73112 1 60 20S56M = 1 56 TTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGG FJBHIJIJECHGIJJJIIJIJJJJIJICHII6FHGEHIEGIIJIJJ>C);ADFBEDEDEED@AA;;AB<<@CDCB? X0:i:0 MC:Z:4S56M MD:Z:56 XE:i:44 XI:f:1 NM:i:0 MQ:i:60 XR:i:56 AS:i:560 +ILLUMINA_0179:6:1208:16151:65050|GAGGTGTGTGAGGGATATAG:AACGGGTGTAAGAATACACC 147 AAC73113 784 60 53M19S = 741 -96 GCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCGCACCATTACCCCCATCGC @@CA@@A9A>:85&DDDBBCA>>DDDB>BDBBDDDDDDDDDDEECEEDFFHJJIIHIJIIG@JJIIJIIJJJ X0:i:0 MC:Z:76M MD:Z:53 XE:i:41 XI:f:1 NM:i:0 MQ:i:60 XR:i:53 AS:i:530 +ILLUMINA_0179:6:1208:16151:65050|GAGGTGTGTGAGGGATATAG:AACGGGTGTAAGAATACACC 99 AAC73113 741 60 76M = 784 96 GTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCC JGJJJJIIIJIJJJIJJIGIJJIGIGIIJCHHIJJIGGIIHE:AD>>=ACC@DDDDDCCBDD>BCD@CCCD> X0:i:0 MC:Z:53M19S MD:Z:76 XE:i:64 XI:f:1 NM:i:0 MQ:i:60 XR:i:76 AS:i:760 +ILLUMINA_0179:6:1208:20630:101871|CTGAGAACTCCCCGTTCATA:TTACGCCCGACCTACTTTGT 163 AAC73113 1377 14 9S25M5S = 1377 25 CGTCATTAAGTTGAATACCGATCAGGTAATCGAAATCCC JIG?GHFIIG?DCHIJIIGGIJGGGIECAE=EEAEFDD@ X0:i:0 MC:Z:9S25M5S MD:Z:3C14T6 XE:i:2 XI:f:0.92 NM:i:2 MQ:i:14 XR:i:25 AS:i:200 +ILLUMINA_0179:6:1208:20630:101871|CTGAGAACTCCCCGTTCATA:TTACGCCCGACCTACTTTGT 83 AAC73113 1377 14 9S25M5S = 1377 -25 CGTCATTAAGTTGAATACCGATCAGGTAATCGAAATCCC HGHGEHDC@:ACCCA@DDDDDDBDD@DBDDDCDDDDDBB?CDEEDFFFEDFGHHHHJIGBEFD?BJJJJJJJJJJJJJJJIJJJJJ X0:i:0 MC:Z:63M MD:Z:11C1T65 XE:i:53 XI:f:0.9747 NM:i:2 MQ:i:60 XR:i:79 AS:i:740 +ILLUMINA_0179:6:2102:16001:13833|AACTATACCCCAGAGCCAAT:GATGAGTTCGCTCCACCTCT 163 AAC73113 735 60 79M = 765 95 GTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACC JJJJJJJIJJJJJJJJIJIJJJJIJJJJIIJJJJJIJJIIHHHHHHDFCDDDDDDDEDEEDCCCCDDDBDDDDDD>CCC X0:i:0 MC:Z:57M1I8M12S MD:Z:79 XE:i:67 XI:f:1 NM:i:0 MQ:i:60 XR:i:79 AS:i:790 +ILLUMINA_0179:6:2102:16001:13833|AACTATACCCCAGAGCCAAT:GATGAGTTCGCTCCACCTCT 83 AAC73113 765 60 57M1I8M12S = 735 -95 GGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCTAAAGTTCCTCACCCCCGCAC CCCCBDDCDCC?BBDDDDDDDCDDDC@8DDDDDDDDDDDDDDDDDEEC>9JJJIGJIIJ X0:i:0 MC:Z:79M MD:Z:57CC6 XE:i:45 XI:f:0.9545 NM:i:3 MQ:i:60 XR:i:66 AS:i:580 +ILLUMINA_0179:6:2103:12957:50237|CAGGGGTAACCAAAGACTTG:GTTACGCAACGTTAACCACG 147 AAC73112 17 60 50M25S = 10 -57 CCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG ?@@DCDACBDDDDC@DDCA@@@CCDDDDDDDDDDDDDDDDDDDDEEFFEHJJJIJJJJJIJJJJJJJJIJJJJJJ X0:i:0 MC:Z:57M19S MD:Z:50 XE:i:36 XI:f:1 NM:i:0 MQ:i:60 XR:i:50 AS:i:500 +ILLUMINA_0179:6:2103:12957:50237|CAGGGGTAACCAAAGACTTG:GTTACGCAACGTTAACCACG 99 AAC73112 10 60 57M19S = 17 57 ATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGA JJJJIJJJIGIJIJJJGIJIJJJJJJJJIIBHHGGHIJGIIDHEFHFDFDDD?BBB@CBDDBBDDDCABDDCBD?C X0:i:0 MC:Z:50M25S MD:Z:57 XE:i:43 XI:f:1 NM:i:0 MQ:i:60 XR:i:57 AS:i:570 +ILLUMINA_0179:6:2103:16045:47116|GAATTAGGGGCAAACGCCTA:TTTGGGTCACTTGGAAGCCG 147 AAC73113 2248 60 79M = 2229 -98 GATGAAGATAGTGCCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGAAA :A::DCC@:9BDDDBDDDBDBDADDDDDDDB?DCEEDEDDFFFDHHHHHIGJIIJJIIJJJJJJIIJJJJJJJJJJJJI X0:i:0 MC:Z:78M MD:Z:9G1C1T65 XE:i:53 XI:f:0.962 NM:i:3 MQ:i:60 XR:i:79 AS:i:715 +ILLUMINA_0179:6:2103:16045:47116|GAATTAGGGGCAAACGCCTA:TTTGGGTCACTTGGAAGCCG 99 AAC73113 2229 60 78M = 2248 98 GCGCTATGTTGGCAATATTGATGAAGATAGTGCCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTT JIJJIIJJIJJJIJIIIJJJJJJIJJJJ@HEHJJIJJGGHDD?BBDDDDDDDDDDDDDCCDDD@@@A>CA3>A8955> X0:i:0 MC:Z:79M MD:Z:28G1C1T45 XE:i:49 XI:f:0.9615 NM:i:3 MQ:i:60 XR:i:78 AS:i:705 +ILLUMINA_0179:6:2103:17302:4450|GCATTGGAAGGTCGACAGTA:CTGCGCATAGGCCGATTCAA 147 AAC73113 922 60 76M = 916 -82 GGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCATGGCGG C@DDCCDBDDDDCEEEEDEDCCDDCDDDDCCDDDDDDDB?DDDFFHIJJJJJJJJJJJJJJJJIIJJIJJJJJJJJ X0:i:0 MC:Z:78M MD:Z:20C20T2T20C10 XE:i:24 XI:f:0.9474 NM:i:4 MQ:i:60 XR:i:76 AS:i:660 +ILLUMINA_0179:6:2103:17302:4450|GCATTGGAAGGTCGACAGTA:CTGCGCATAGGCCGATTCAA 99 AAC73113 916 60 78M = 922 82 GTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCATG JJJJJJJJIIJJJIJIJJJJIJJJJJJJJJIJJJIIHIIIJGGHJHCCHFFD>@BDDBDDDA:>ABACB?>CD@C@CA X0:i:0 MC:Z:76M MD:Z:26C20T2T20C6 XE:i:30 XI:f:0.9487 NM:i:4 MQ:i:60 XR:i:78 AS:i:680 +ILLUMINA_0179:6:2104:14055:52244|CCAATTGGGCCACTTAGCAA:ATACTAGGGGCCCAATCAAC 163 AAC73112 1 60 15S64M = 9 66 GAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCT JIJIJJIJJJJJJJJJJJJJIJJJJJJJJJIIHGIIIHHHGEHFEEFDDEEDDDDDDCDCCDDDD@CCAB>BDB<9BD7 X0:i:0 MC:Z:58M18S MD:Z:64 XE:i:52 XI:f:1 NM:i:0 MQ:i:60 XR:i:64 AS:i:640 +ILLUMINA_0179:6:2104:14055:52244|CCAATTGGGCCACTTAGCAA:ATACTAGGGGCCCAATCAAC 83 AAC73112 9 60 58M18S = 1 -66 CATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAG CC@>C>CCACCCDDDCCADDCEDEDFFFFHHIJJIHHJJJJJJIJJJJJJIJIHIIJJJ X0:i:0 MC:Z:15S64M MD:Z:58 XE:i:44 XI:f:1 NM:i:0 MQ:i:60 XR:i:58 AS:i:580 +ILLUMINA_0179:6:2105:14909:7626|GTGTGAGCTCCTTACCTCTG:GGTCTGCCCACTAACAGCGA 147 AAC73113 433 60 43M4S = 387 -89 GTTACCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCCAGC @<5<=8:<;=5'>8A@:ACCBG@=4C=GB7GF@>EIGBD?CG?9GEG X0:i:0 MC:Z:63M MD:Z:5T37 XE:i:25 XI:f:0.9767 NM:i:1 MQ:i:60 XR:i:43 AS:i:405 +ILLUMINA_0179:6:2105:14909:7626|GTGTGAGCTCCTTACCTCTG:GGTCTGCCCACTAACAGCGA 99 AAC73113 387 60 63M = 433 89 GTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTATCGATCC IIIGGGGIIEGBHIID>FEGEA>;AEEEHEEEBCCBBBBB;;CCA?3(33?@>(8<<@B?AFGIGIGGGHJGAFHGGJ;@EEEEHFFFEE@CCDCAC:ACB@8<@:555C@>445D@C?DCDDCB@?=AABBBHGEIHHBIIIJJIJIGIGGGGGFIHFBJIIGII X0:i:0 MC:Z:5S66M2S MD:Z:50 XE:i:36 XI:f:1 NM:i:0 MQ:i:60 XR:i:50 AS:i:500 +ILLUMINA_0179:6:2105:2876:52695|TTACGCCCGACCTACTTTGT:TCCTAGTTACACCCGTACGC 163 AAC73113 2262 60 2S65M = 2262 65 GCCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGAAA IJJJJJJJJJIIIJIJJJJJJJIJHEHFDFFF@CE>;>>:@???@=C<@CC>:>;AA:?(4:C@:C>5-(CA;3@@;(@@B@FEBFHGE@BHIGGGHIGIHFAIGHHGGIEGIIGHEJ X0:i:0 MC:Z:21M MD:Z:13G25T22 XE:i:24 XI:f:0.9677 NM:i:2 MQ:i:60 XR:i:62 AS:i:570 +ILLUMINA_0179:6:2106:8781:42582|GCAGTGAATTAGTTGTCCAT:CTTCGCGTTCACGAACTAAG 163 AAC73113 734 60 76M = 739 82 TGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCAT JJJJJJJJJJJJJJJJJJJJJIJJIFGIJIJHHHHFFFFDFEEEEEDDBDDDDD9>CDDEEDCACCA@BBDBBDBC X0:i:0 MC:Z:77M MD:Z:76 XE:i:64 XI:f:1 NM:i:0 MQ:i:60 XR:i:76 AS:i:760 +ILLUMINA_0179:6:2106:8781:42582|GCAGTGAATTAGTTGTCCAT:CTTCGCGTTCACGAACTAAG 83 AAC73113 739 60 77M = 734 -82 AAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCC BB8>ADDCDDDDDDDCC>CDCDDCADDDDDDDBDDDDDCDDDDDDDDDDBBFJJJJJIGJJIHEFJJJJ X0:i:0 MC:Z:76M MD:Z:77 XE:i:65 XI:f:1 NM:i:0 MQ:i:60 XR:i:77 AS:i:770 +ILLUMINA_0179:6:2107:10923:24726|TGTCTTCAGTGCACAGTTTA:GCAGTGAATTAGTTGTCCAT 163 AAC73113 364 60 44M = 365 79 CTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGG JJJJIJJJJJJIIIIJJIIAEHHGFGFFIJJIIHHHHHEDFFCA X0:i:0 MC:Z:78M MD:Z:44 XE:i:32 XI:f:1 NM:i:0 MQ:i:60 XR:i:44 AS:i:440 +ILLUMINA_0179:6:2107:10923:24726|TGTCTTCAGTGCACAGTTTA:GCAGTGAATTAGTTGTCCAT 83 AAC73113 365 60 78M = 364 -79 TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTA @CCA5B>55BDBDDCDDDDCB@BBB?BDDBDDCDDCBDDD@CEDFHHHGFHJJJJJJJIGJIJIJIIJIHHEJHIGJJ X0:i:0 MC:Z:44M MD:Z:73T4 XE:i:61 XI:f:0.9872 NM:i:1 MQ:i:60 XR:i:78 AS:i:755 +ILLUMINA_0179:6:2107:13259:173360|GATGAGTTCGCTCCACCTCT:AACTATACCCCAGAGCCAAT 147 AAC73113 783 60 12S24M = 735 -72 CATTACCCCCATCGCTAAAGTTCTTCACCCCCGCAC C@C>3;>>?C@A>?65B?8EEHGIF X0:i:0 MC:Z:79M MD:Z:24 XE:i:12 XI:f:1 NM:i:0 MQ:i:60 XR:i:24 AS:i:240 +ILLUMINA_0179:6:2107:13259:173360|GATGAGTTCGCTCCACCTCT:AACTATACCCCAGAGCCAAT 99 AAC73113 735 60 79M = 783 72 GTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACC IIGIFGE?FHCGIHGI@BGHIIIIIIIECHG<@F>?&59@DB<8@CCC> X0:i:0 MC:Z:12S24M MD:Z:79 XE:i:67 XI:f:1 NM:i:0 MQ:i:60 XR:i:79 AS:i:790 +ILLUMINA_0179:6:2107:13988:44881|TCCGAGGGTGGACTTAAGCC:GGTACGCGGAGCATATCCTT 163 AAC73113 1418 60 37M = 1450 88 TCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAA HHGGBFGGHIE???032>>(: X0:i:0 MC:Z:56M MD:Z:37 XE:i:25 XI:f:1 NM:i:0 MQ:i:60 XR:i:37 AS:i:370 +ILLUMINA_0179:6:2107:13988:44881|TCCGAGGGTGGACTTAAGCC:GGTACGCGGAGCATATCCTT 83 AAC73113 1450 60 56M = 1418 -88 CTGAAGCGTCAACAAAGCTGGCTTAAGAATAAACATATCGACTTACGTGTCTGCGG A@;5'88CCA=C;;6;B@9>;;;)EEHHC?D>EC4C@;F=8FBBGGHCGA6882 X0:i:0 MC:Z:49M25S MD:Z:55 XE:i:43 XI:f:1 NM:i:0 MQ:i:60 XR:i:55 AS:i:550 +ILLUMINA_0179:6:2107:14054:142127|GGTTCCCCGAAGGTCCTCAT:CAATAAGTAGAGGAGTGGCT 83 AAC73112 18 60 49M25S = 10 -57 CACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG CCCAB?BBBDDDDFFHAHJIJIIFJJJJJIHGGDHFIJJJJIJJJJ X0:i:0 MC:Z:55M MD:Z:49 XE:i:35 XI:f:1 NM:i:0 MQ:i:60 XR:i:49 AS:i:490 +ILLUMINA_0179:6:2108:11303:87616|CAGGCAGGTGTGTGGGCTTT:TGTCTTCAGTGCACAGTTTA 163 AAC73113 16 60 54M = 16 57 TTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATATT JJEHIIID@FDFGHGDCGHIJJG4@CGCHHFH.?BEDECCBDD8<;5>;300FHE?ECDIIJJJIIHIGJIIJIHGIIIHG>J X0:i:0 MC:Z:54M MD:Z:41T15 XE:i:32 XI:f:0.9825 NM:i:1 MQ:i:60 XR:i:57 AS:i:545 +ILLUMINA_0179:6:2108:15145:94396|GGTACGCGGAGCATATCCTT:TCCGAGGGTGGACTTAAGCC 147 AAC73113 1437 60 69M = 1418 -88 GCTGCTGGAGCAACTGAAGCGTCAACAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGG BB<9@ADDDDBDDDDDDCEEEDCFFFFFHHHGHHGIHEJIIJJIHFHGJIJJIJJJJIJJJ X0:i:0 MC:Z:76M MD:Z:24G44 XE:i:44 XI:f:0.9855 NM:i:1 MQ:i:60 XR:i:69 AS:i:665 +ILLUMINA_0179:6:2108:15145:94396|GGTACGCGGAGCATATCCTT:TCCGAGGGTGGACTTAAGCC 99 AAC73113 1418 60 76M = 1437 88 TCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAACAAAGCTGGCTGAAGAATAAACATATCGACTT IJJJHIJEHEHJJGGFDCDDDDDDDDDDDDDDDDDDDDDDBDDDDDDBDDCCDDDDBCDDCCDCCDDDDDCDBDD8 X0:i:0 MC:Z:69M MD:Z:43G32 XE:i:51 XI:f:0.9868 NM:i:1 MQ:i:60 XR:i:76 AS:i:735 +ILLUMINA_0179:6:2108:18425:62382|TTGGAAACTACGTTCTCGAC:ACTGCAAAGTCTAGCAGTTG 163 AAC73112 1 60 24S28M = 1 28 AAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCA JJJJJIJJIIJJHIGIJJJJJJJJJJJHJJJFIJIIEHEHIGGGGJIGHHHG X0:i:0 MC:Z:24S28M MD:Z:28 XE:i:16 XI:f:1 NM:i:0 MQ:i:60 XR:i:28 AS:i:280 +ILLUMINA_0179:6:2108:18425:62382|TTGGAAACTACGTTCTCGAC:ACTGCAAAGTCTAGCAGTTG 83 AAC73112 1 60 24S28M = 1 -28 AAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCA FHHHGHHHGJJIJIIIIJIJJJJJJIIJJJJJJJJJJIIHIGFJIGIHEJJJ X0:i:0 MC:Z:24S28M MD:Z:28 XE:i:16 XI:f:1 NM:i:0 MQ:i:60 XR:i:28 AS:i:280 +ILLUMINA_0179:6:2201:10713:65111|GCCCAAACCCATACAAGCGG:GGTCTGCCCACTAACAGCGA 163 AAC73113 481 29 48M1I4M1D3M5S = 481 56 CTCGAATCTACCGTCGATATTGCTGAGTCCACCCGTCGTATCGCGGCACAGTCCATCGGTG JIJJJJIIJIIJJHIIGIJIIIGIJIGGIHIIHHFDFA>C???B=BDDDC9:C@(4@@>02 X0:i:0 MC:Z:48M1I4M1D3M5S MD:Z:35C5T8C1^G3 XE:i:23 XI:f:0.9123 NM:i:5 MQ:i:29 XR:i:56 AS:i:435 +ILLUMINA_0179:6:2201:10713:65111|GCCCAAACCCATACAAGCGG:GGTCTGCCCACTAACAGCGA 83 AAC73113 481 29 48M1I4M1D3M5S = 481 -56 CTCGAATCTACCGTCGATATTGCTGAGTCCACCCGTCGTATCGCGGCACAGTCCATCGGTG CC8@A@:<<0;BDBB>CCACCA@DB;BB>B=FFFFDGJJJIIHJJIIIHGFJJIJJ X0:i:0 MC:Z:48M1I4M1D3M5S MD:Z:35C5T8C1^G3 XE:i:23 XI:f:0.9123 NM:i:5 MQ:i:29 XR:i:56 AS:i:435 +ILLUMINA_0179:6:2202:18309:12773|GCAGTGAATTAGTTGTCCAT:CTATAACCTCAAGTGCACCG 147 AAC73113 922 60 70M1S = 922 -70 GGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCAA ++::>::(:>@4CB>DDCEDDCC@A:(>:::?BBDBC:DBCDBBE;0CDCGEEHDEIHHGGHEIFFDE:II X0:i:0 MC:Z:65M1S MD:Z:20C20T2T20C4 XE:i:24 XI:f:0.9429 NM:i:4 MQ:i:60 XR:i:70 AS:i:600 +ILLUMINA_0179:6:2202:18309:12773|GCAGTGAATTAGTTGTCCAT:CTATAACCTCAAGTGCACCG 99 AAC73113 922 60 65M1S = 922 70 GGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTT EHBGE@EB9??CBGEFBC?@GHBB?F3FGEFHA7CGEGIGB@E84=B;;?A>C@ABB9?B>A X0:i:0 MC:Z:70M1S MD:Z:20C20T2T20 XE:i:24 XI:f:0.9538 NM:i:3 MQ:i:60 XR:i:65 AS:i:575 +ILLUMINA_0179:6:2202:19511:189557|TGGCACGTACGGGAGTACAA:CTGAGAACTCCCCGTTCATA 147 AAC73113 1689 60 78M = 1680 -87 ATATGCCGACTTCTTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTACTA CC>DDBBCCCC?BDBDB@DDDDDDDDDDDDDDDDBDDDDEFHHJIIJJJIHJJGIGFD@JIJJJIJJJJJJJIJHJJJ X0:i:0 MC:Z:76M MD:Z:13C64 XE:i:53 XI:f:0.9872 NM:i:1 MQ:i:60 XR:i:78 AS:i:755 +ILLUMINA_0179:6:2202:19511:189557|TGGCACGTACGGGAGTACAA:CTGAGAACTCCCCGTTCATA 99 AAC73113 1680 60 76M = 1689 87 GGCGGATCAATATGCCGACTTCTTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCG HIGGIGGGHIJIJDGIIIGHHFFFFFDDBBB?B:ACCDEDB8?B@>AC@<8>9BDBDBDD5@ABBDDDBDDB@A?< X0:i:0 MC:Z:78M MD:Z:22C53 XE:i:51 XI:f:0.9868 NM:i:1 MQ:i:60 XR:i:76 AS:i:735 +ILLUMINA_0179:6:2203:10197:115616|TATACTCGGGATGTCTCTTA:CCAATTGGGCCACTTAGCAA 147 AAC73113 1655 60 72M = 1638 -89 TTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCTTGCGCGAAGGTTTCCACGTTGTCA @CA>CCCC>933>CA=;?;A;@:EEC>ABBFECC==GEGEHA?6EGHIHEHHFCIIIIJIGHFG X0:i:0 MC:Z:70M MD:Z:47C24 XE:i:47 XI:f:0.9861 NM:i:1 MQ:i:60 XR:i:72 AS:i:695 +ILLUMINA_0179:6:2203:10197:115616|TATACTCGGGATGTCTCTTA:CCAATTGGGCCACTTAGCAA 99 AAC73113 1638 60 70M = 1655 89 GCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCTTGCGC IIGGCFCFHEHGHIGHIDEGIIGCHGIEEHGIID@EHECHDB;BCCDD:89:>CCA>><<><>@ X0:i:0 MC:Z:72M MD:Z:64C5 XE:i:52 XI:f:0.9857 NM:i:1 MQ:i:60 XR:i:70 AS:i:675 +ILLUMINA_0179:6:2203:19573:26850|GGTCTGCCCACTAACAGCGA:GTGTGAGCTCCTTACCTCTG 163 AAC73113 387 60 21M = 402 89 GTCGATCGCCATTATGGCCGG IIJJJJIIJJJJJJJIGGJEH X0:i:0 MC:Z:74M4S MD:Z:21 XE:i:9 XI:f:1 NM:i:0 MQ:i:60 XR:i:21 AS:i:210 +ILLUMINA_0179:6:2203:19573:26850|GGTCTGCCCACTAACAGCGA:GTGTGAGCTCCTTACCTCTG 83 AAC73113 402 60 74M4S = 387 -89 GGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCCAGC @90&D@?@CCA:@959DBBBD@ACA8?BA?BC????<5?BDDDDBDDAHDIEHHEHFBIJJJJIHIIJJJJJJJIJJI X0:i:0 MC:Z:21M MD:Z:36T37 XE:i:49 XI:f:0.9865 NM:i:1 MQ:i:60 XR:i:74 AS:i:715 +ILLUMINA_0179:6:2203:7432:5904|CTGCGCATAGGCCGATTCAA:GCATTGGAAGGTCGACAGTA 163 AAC73113 916 60 71M1S = 922 82 GTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCCGGGATGAAAGGGATGGTT IGGGGGIJ?BGII@FFHIIIIGIJIJJGDGHIIJIJIJEHIIIHGH?EEFFDD';;B/9BA>>>?B1<@B@@ X0:i:0 MC:Z:76M MD:Z:26C20T2T2G17 XE:i:27 XI:f:0.9437 NM:i:4 MQ:i:60 XR:i:71 AS:i:610 +ILLUMINA_0179:6:2203:7432:5904|CTGCGCATAGGCCGATTCAA:GCATTGGAAGGTCGACAGTA 83 AAC73113 922 60 76M = 916 -82 GGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCATGGCGG @@CC>:@B@@>CCC@DC?BDDDDDDCDBDDCDC@FFDDB?HFHHHEJIHJIHIGHFIJJJJJJJIJJJIJJJ X0:i:0 MC:Z:19S53M MD:Z:66 XE:i:52 XI:f:1 NM:i:0 MQ:i:60 XR:i:66 AS:i:660 +ILLUMINA_0179:6:2204:13281:166416|GTGACAAACTTCGGTATAGG:ACGGTCAATTGCAGAGCCCC 163 AAC73112 10 60 1S51M = 38 51 TATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCG JGJJJJJJJJJIIJJJJJHIIIIIJFHIIJJJIJJJIJIJGGEFEFHEDDCC X0:i:0 MC:Z:23M MD:Z:51 XE:i:39 XI:f:1 NM:i:0 MQ:i:60 XR:i:51 AS:i:510 +ILLUMINA_0179:6:2204:13281:166416|GTGACAAACTTCGGTATAGG:ACGGTCAATTGCAGAGCCCC 83 AAC73112 38 60 23M = 10 -51 CCATTACCACAGGTAACGGTGCG B==B)/F???9D8):00D?8?8I X0:i:0 MC:Z:1S51M MD:Z:23 XE:i:11 XI:f:1 NM:i:0 MQ:i:60 XR:i:23 AS:i:230 +ILLUMINA_0179:6:2204:1547:101925|CGCCTTACGAATAAGGGAGT:TATCACAGCCAATGTAGTGT 147 AAC73112 20 60 47M25S = 1 -66 CCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG ACA>:>ACCCCACDCDDDDDDDDDFFHHJJJIJJJJJIJIIIJJJIJJJJJJIIJJJJJI X0:i:0 MC:Z:5S66M7S MD:Z:47 XE:i:33 XI:f:1 NM:i:0 MQ:i:60 XR:i:47 AS:i:470 +ILLUMINA_0179:6:2204:1547:101925|CGCCTTACGAATAAGGGAGT:TATCACAGCCAATGTAGTGT 99 AAC73112 1 60 5S66M7S = 20 66 CATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTAC JJJJJJJJIJJIIJJJJIIJIIJJJJJJJJIHGI@EGIJHFHHHFDFFFEDEDEDCCDDDD?BB;5+(>:A@9=6BB>AB?;>E?=?8HHGEHGFD?HD;CFD?GHEFA8DA@HC X0:i:0 MC:Z:46M MD:Z:50T4 XE:i:38 XI:f:0.9818 NM:i:1 MQ:i:60 XR:i:55 AS:i:525 +ILLUMINA_0179:6:2206:19549:53890|GCAGTGAATTAGTTGTCCAT:TGTCTTCAGTGCACAGTTTA 99 AAC73113 364 60 46M = 388 79 CTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCG HHIECHGHIH?FHGIGFAA@GCGABBFEGIIAEHEEH@EEB3=A:B X0:i:0 MC:Z:55M MD:Z:46 XE:i:34 XI:f:1 NM:i:0 MQ:i:60 XR:i:46 AS:i:460 +ILLUMINA_0179:6:2206:4663:9561|CTTCGCGTTCACGAACTAAG:GCAGTGAATTAGTTGTCCAT 147 AAC73113 739 60 77M = 734 -82 AAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCC DDDDDDC?A>?DCAACDDDDBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBFJJIJIHGJJIIHEJJJJ X0:i:0 MC:Z:76M MD:Z:77 XE:i:65 XI:f:1 NM:i:0 MQ:i:60 XR:i:77 AS:i:770 +ILLUMINA_0179:6:2206:4663:9561|CTTCGCGTTCACGAACTAAG:GCAGTGAATTAGTTGTCCAT 99 AAC73113 734 60 76M = 739 82 TGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCAT JJJJJJJJHIJIJJJJJJJJJIJIJIIJJJJHHHHFFFFFFEEEEEEDDDBBDDDDDDCDDCCDDDDDB><5>B@@ X0:i:0 MC:Z:77M MD:Z:76 XE:i:64 XI:f:1 NM:i:0 MQ:i:60 XR:i:76 AS:i:760 +ILLUMINA_0179:6:2206:6489:9115|CAGGGGTAACCAAAGACTTG:CTCTACCATACTCACGGGTC 163 AAC73113 1660 60 51M = 1660 58 TGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCTTGCGCGAA JJJJJJJJJJJJJJJJJJJHJIJJJ@;:6=;@;7;@3'8>@@@A558=;&5 X0:i:0 MC:Z:58M MD:Z:42C8 XE:i:30 XI:f:0.9804 NM:i:1 MQ:i:60 XR:i:51 AS:i:485 +ILLUMINA_0179:6:2206:6489:9115|CAGGGGTAACCAAAGACTTG:CTCTACCATACTCACGGGTC 83 AAC73113 1660 60 58M = 1660 -58 TGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCTTGCGCGAAGGTTTCC CDCACCDBDDDDCDDDCDDDDDDFFFFFFHHHHJJJHGJJIJJIJJJJJJJJJJHIJJ X0:i:0 MC:Z:51M MD:Z:42C15 XE:i:33 XI:f:0.9828 NM:i:1 MQ:i:60 XR:i:58 AS:i:555 +ILLUMINA_0179:6:2207:2766:119480|CTCTACCATACTCACGGGTC:CAGGGGTAACCAAAGACTTG 147 AAC73113 1660 60 58M = 1660 -58 TGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCTTGCGCGAAGGTTTCC C@DCDDBBBCA?DDDDCDDDDDDEFFFFFHHEEIGJIHIJJJJJJJJJJJIIJJJJJI X0:i:0 MC:Z:58M MD:Z:42C15 XE:i:33 XI:f:0.9828 NM:i:1 MQ:i:60 XR:i:58 AS:i:555 +ILLUMINA_0179:6:2207:2766:119480|CTCTACCATACTCACGGGTC:CAGGGGTAACCAAAGACTTG 99 AAC73113 1660 60 58M = 1660 58 TGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCTTGCGCGAAGGTTTCC JJJJJJJJJJJJJIJJIIJHJGIJJGIGHFDFBDFF@CDDDDDDDC=BD;>B@>CA@A X0:i:0 MC:Z:58M MD:Z:42C15 XE:i:33 XI:f:0.9828 NM:i:1 MQ:i:60 XR:i:58 AS:i:555 +ILLUMINA_0179:6:2208:11779:164502|ATACTAGGGGCCCAATCAAC:ACGAGCCGAATACCTTGTAA 163 AAC73113 1240 60 71M = 1240 71 GCGAAATTCTTTGCCGCGCTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACG GIJIJJIIGIIJJJIIIGHGHIFFA>A@BBBBAACFDDDDDDDDDDB>AA X0:i:0 MC:Z:71M MD:Z:17A53 XE:i:46 XI:f:0.9859 NM:i:1 MQ:i:60 XR:i:71 AS:i:685 +ILLUMINA_0179:6:2208:11779:164502|ATACTAGGGGCCCAATCAAC:ACGAGCCGAATACCTTGTAA 83 AAC73113 1240 60 71M = 1240 -71 GCGAAATTCTTTGCCGCGCTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACG DDCC@CBDDDDDBDBDDBBB>BB;B?A@BC>GHEEFECGJIGJJIIGCIGJJIGGIIJJJIIGIIGGHGII X0:i:0 MC:Z:71M MD:Z:17A53 XE:i:46 XI:f:0.9859 NM:i:1 MQ:i:60 XR:i:71 AS:i:685 +ILLUMINA_0179:6:2208:12628:54706|AATGAGGAAATGACACGGGC:ACCCAATTGCTTGCCTATCA 163 AAC73113 855 60 60M = 855 60 CGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACC GGGGIIIBFIGHJIIJEHEDGHGG6FFGFGAF@;@F@FG X0:i:0 MC:Z:60M MD:Z:15A44 XE:i:35 XI:f:0.9833 NM:i:1 MQ:i:60 XR:i:60 AS:i:575 +ILLUMINA_0179:6:2208:12628:54706|AATGAGGAAATGACACGGGC:ACCCAATTGCTTGCCTATCA 83 AAC73113 855 60 60M = 855 -60 CGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACC <:>:::>A:2>5(A?;=:C=CABEEHCA@HHC@E=BHEABHDFDBBBAAA?9?7<@4>>A X0:i:0 MC:Z:69M MD:Z:15G26T2T20 XE:i:25 XI:f:0.9545 NM:i:3 MQ:i:60 XR:i:66 AS:i:585 +ILLUMINA_0179:6:2208:5468:160341|ACGACTTCGGGACATCCTGT:GTACTCCTGTGTGAATGGGC 83 AAC73113 600 60 69M = 588 -81 GGTACTTGGACGCAACGGTTCCGACTACTCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTG CC>(>@BDD@BDB@B>B98&BDCC@9+@>DDDBDDB@DDDEEDFFFFGHHHJIJJJJJJIIIIJJJJJJ X0:i:0 MC:Z:66M MD:Z:3G26T2T35 XE:i:37 XI:f:0.9565 NM:i:3 MQ:i:60 XR:i:69 AS:i:615 +@SQ SN:AAC73112 LN:66 +@SQ SN:AAC73113 LN:2463 diff --git a/tests/tests.yaml b/tests/tests.yaml index d8e55ce7..0b6e4d57 100644 --- a/tests/tests.yaml +++ b/tests/tests.yaml @@ -226,6 +226,14 @@ dedup_single_gene_tag: references: [single_gene_tag.sam] options: dedup -L test.log --out-sam --random-seed=123456789 --method=directional --per-gene --gene-tag=XF --skip-tags-regex="^[__|Unassigned]" +dedup_paired_contig: + skip_python: 3 + sort: True + stdin: paired_contig.bam + outputs: [stdout] + references: [dedup_paired_contig.sam] + options: dedup -L test.log --out-sam --random-seed=123456789 --method=directional --umi-separator="|" --paired + group_directional_unmapped: skip_python: 3 sort: True