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A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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Support for generic MM tags? #235

Open ADHDrian opened 1 month ago

ADHDrian commented 1 month ago

Hello,

I have a BAM file with MM tags of the form "MM:Z:N-21891" for m6A. modkit throws the following error:

failed to get modbase info for record 2f9765ad-b38c-49f8-80e0-4f5a0656c981, Bad Input: malformed MM delta list

Is there an option to make modkit parse such a BAM file? A few sample reads are show below. Thanks a lot!

f4b69c94-578c-4fd2-b487-0edd5cc81f05    16  1   4490935 60  1S34M1D83M1D9M1D7M1D8M2D4M1I9M1D8M3D17M1D13M2D12M1D18M2D36M1D48M2D31M5D83M1D12M3D11M1D4M1D3M2D15M1D56M1D21M1D31M1D24M1D10M2D26M2D22M1D4M1D34M2D24M1D97M2D21M1D8M1D18M1D5M1D4M1D24M1I10M1D7M1D53M3D14M1I49M1D15M1D63M2I5M1D6M1D14M1D29M1D9M2D6M1I13M1D30M2D17M2I15M1D17M1I12M1D41M2D2M1D8M3I4M2D9M1D15M4D4M1D4M1D27M1D15M5I31M1I29M2D11M1D7M1D5M2I5M1D50M3D18M4D27M1I6M2D13M4D4M1D18M431N6M3D25M1I12M1D11M1D24M1I19M1I15M1D14M1D13M3I15M1I17M117S    *   0   0   AAGTCACAACACAAACTTTATTTTGATTAGTTTCTTGACTCTAAAATTGTAGGAATTAAAGGCAAATTTTGTGGGAAGTGGGATCAAGACTTTTGGAAAAAAAGACAAACTGGAAAGAATATATCTGAAAGCTCTTTGGCAGGTCGAAGATGACTGAAATCCGATTTTGAACAGCCTCATTAAGTGTACAGAATAAAACATTTACAAATCATTTTTAAAAACCAATTTGGAATGTACATAACAAGTTCATCTTTTAAGAATTTTCTCAGAACAATTATATCACATTTGAACACCCCGCTGTTTGTGTTGGGTTTCTTAGATGCATTTTCTTACCATTGTAAATGAAAATTTTACAATTAAGTATACACTTCTAATTGTATAATACTTACTGTTGATCTCAAATTTGATAAAAATCGATGCGAAGATTTTAAAAATCCAGGATTTATTAAATTGAAAACACGCATGACAAATTTCTCTAGATCAATACACTTTCAAGAAATGGAATAAGTCAGTGAGATATTTTAAACTGGCTAAAACTGGACAGGATTGTGGGGAGCAAGTCCCTCAAGGCATTTAAACAAAAATCTCGTGTAGCCCCTAACTGTTCAAGGCAGACAAAATAAATTACCATAAATTATGCCAAGGCAACTTAAAAACAAACGCTTGACGCTAAGGATTTCCTTAGCGCTTCCAGGTTGTGTAACACTGCTTCTGGCCCTAGGTCGGGACGGCAACCGTCAAATGTCGGGGTAGTTGCAATAGTAGACCGCTGAGCTAGCGTCGGACACCACGGAGGAAATGGCTCTGAGGCTGTCTGTGGTTCACTCCGCAGTCGTGCCCTGGTAGGAAGACCCATCTCGGGCTATACCAAAGGCAGATACTGTTCGAATTCCATGACGGTCCACCTCCCTAGGGCTCAGAGGGCTGGTTGGATTCCGTGCCATCCCGGCAGGGCCGTGCCTCGGGAGGCGAAGGTTGCCCGGGGGCCGTGCGCTGGGTGCTGCTGCTGCGGTGGCGGCGGCGGTGCCTGCGTTGCAGCGGCTGCTGGGATGCGCGTGGAAACCGCGCCCCGCACTTGCGGCGGGCGAGCCGATCGCGCCGTAGTACAGGTGTGCAAGCGCTGGGGGCGCCAGGATCCCGGCATCGCAGGGCCCGAGAGGTCCGGCCCACTCGCGGGGCCAAGCGGGCGGCTCTCGGACACTGCATAGTCCCAGACTGGAGCGTGTGTAGGTGCCGGCTGCCGCGGGCAGTCCCCTGGAGCGGGGCTGCAAAGAAGAGCCGGGCCCTGTCCGCGCCATCCAGCGGGAATGGGTCTGGAGTGGGCAGAGGAGCATCGAGCTTTGCGGGCGCCCAGTCCTGGCAGTCCCGATGGGGCCATAGCGGAGACATCAGCTGAGGACCGGCCGATAGCCCGGCTCCGGGAGTGGAAAGGCAGACCCAGGCCATCCATGGCCACAGCGGCCGCCCTCGGGAGCCAGCGCGCCGGTGGGGCTCGACAAAGCGTCAGGAAGAGCCTCCTCCACCCGCTTCATGCGCTTCACCTGCTTGCGCCGCCGCGGCCGGTACTAGTTGGGGAGAGCCTGCGCTGCACGCGCAGCCGCTCGGCCTCTTCCCACGAGGCCGCTTCTCTGGGTCACGCCTTCCAAGACTTGCCTAGCATGCTTAGCTCTGCGTTGTGCAGATCTTGGGTTCTGCTGGCTAACCGCTTCGTTCGTCTTTGGCCCACACCATAGAAGGCGTTCATCGGCCGCCGGGATGCAAGACTCCGTTTGGCTCGGCCCGCGTCCCAGCTGGCTTTGCCCCGCTACTCGCCAACCACCTCGCCTTTCACATCCCAGAGGCTCAGAGGCTCTCTACCTCCCCGGCCCAGCGTGCGTGAGCTGTATGGTATTGGCTGTGAGGCCAGGAAGTAGTAAGTTTGGAAAGGCGGCTGGGGCTGATGCTGCAA    *   NM:i:177    ms:i:1393   AS:i:1337   nn:i:0  ts:A:+  tp:A:P  cm:i:221    s1:i:1140   s2:i:0  de:f:0.0677 cs:Z::34-c:63*ga:11*at:7-g*ta:8-a:7-t:8-gt:4+a:9-a:8-aat:17-a:13-ta:12-g*ta:10*ga:6-at:31*ga:4-t:48-ta:31-aagaa:59*tc*ta:22-g:12-gat:11-t:4-g:3-ga:15-a:56-a:21-t:31-a:24-c:10-gt:26-ta:22-a:4-a:34-aa*gt:23-c:8*ta:77*ct:1*ta:8-ga:1*at:19-t:8-g:18-t:5-a:4-g:21*ga:2+a:10-c:7-a:6*ta:34*ac:1*at:9-ggg:14+g:49-g:15-g:3*ta:41*cg:17+gt:5-g:6-g:14-c:21*ga:7-c:9-at:6+a:13-a:17*gc:12-aa:14*ct:2+cg:15-c:17+g:7*tc:4-c:3*ag:14*ga:3*tg:3*ct:14-gt:2-c:1*ga:6+ttt:4-ga:9-c:15-agtg:4-c:4-g*ta:14*gt:11-g:15+ggagt:31+a:16*cg:1*ac:10-cc:11-g:1*ga:5-g:5+ag:5-c:50-ttg:9*ta:1*ga*tg:5-atat:27+c:6-ag:13-ccaa:4-a:18~ct431ac:6-tct:25+t:12-t:2*ct:8-g:24+g:19+g:6*ga:8-c:14-a:6*ga:6+ttt:15+a:17   rl:i:0  MM:Z:N-21891,258,55,54,214,8,41,28,32,41,47,259,16,62,6,208,43,51,196,4,5,54,126,87,26;N-17802,130,61,21,8,65,136,48,73,2,87,138,25,175,62,38,70,52,451,11,6,87,11,48,55,5; ML:B:C,7,23,245,191,235,9,254,31,141,12,27,251,164,13,112,255,8,1,94,13,188,122,50,2,13,89,222,2,11,42,71,12,87,24,0,5,36,17,56,106,6,0,168,21,248,1,49,11,113
8ddc0184-ef2f-4cfd-8fd8-68e8d70b2b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i:251    ms:i:872    AS:i:767    nn:i:0  ts:A:+  tp:A:P  cm:i:102    s1:i:595    s2:i:0  de:f:0.1207 cs:Z::4*at:3*ag:19-g:37-at:4-t:6-aa:7*ag:4-a*gt:21-aa:23*ct:4-cc:7*ct:3-ta:15-g:5-cct:11-g*ta:7+a:12+t*cg*at:6-a:14-t*tc:14-t*ta:25-c:3-gaa:2-g:22*ag:21-atg:3-gggta:30-g:31+c:1*tg:2+t:1*at:12*at:6-t:3*tg:3*ag:30-g:5+a:23-cc:4-c:12*at*gt*ta:7+gaa:1*ta:21-g:14*ag*ga:8+g:5*cg:2*gc:6*tg:8*ta:1*ca*tg:8*gt:1*tc:1*ga:11+c:2*ta:8*ag:5-tg:5-gt*ta:4-gt:20-g:9-a:2*ct:1*ag:8-t:7-gt:2*at:7-gg:33*ag*ga:11*ct:27-a*ct:7+atcg:11-g:5+a:5+g:2-gt:21-g:1*cg:10-g:7-aaaga:4*ca:3*tc:1~ct65ag*ct:3+aa:7+aatttt:1+gc:5-t:9-g:8-t*ga*ta:12-g:1-gg:3*ag:1*ct:16+t:2*ct:4+g*ag:2+a:21-cc:21+g:1+t:2-g:9-g:6-gacgaga:2-gtg:46*ca:1-c*ca:11-t:2-t:4-gg:11-atat:2-t:45-c:2*at:23~ct431ac:2+c*ag:4-c:17+a:9*tc:3*ta:7*ta*ga:3*ag:1*ct:9-c*ga:3*ta:15+ggc:3*ct:6+ca:6-c:1*gt:5*gt*ag:6+t*gc:1*tc*tc*ta:7-c:7+c:11-c:3*gt:5*ct:9*tc*ct:6-c*at:1*cg:1*tc*tg*ag:9-g:14-c:1*gc:27+gc*tc:3*ct:1-c:24*cg:15+a:11*ct:1-ggc:18-c:1*gt:3*ct:2*ag*ga*ct:3*ga:2-a:2-gccac:4+g:15 rl:i:0  MM:Z:N-21891,328,59,57,219,10,26,39,53,254,15,66,10,201,37,50;N-17802,72,126,59,24,7,68,139,41,69,2,172,26,169,65,37,76,43; ML:B:C,119,49,2,184,238,244,245,255,22,252,156,143,249,77,81,84,35,75,160,15,9,10,17,69,142,2,14,202,10,23,151,59
450a0665-9fd7-4697-805b-a16011b7070d    16  1   4491387 60  8S19M1D9M3D32M1D10M1D18M1D7M1D20M1D6M1I12M1D10M1D10M1I23M1D4M1D8M1D28M1D7M1D21M1D4M1D10M1I8M2D27M1I1M1I41M2D7M4I4M1I14M2D4M1D20M1D9M1I11M1I9M10S    *   0   0   ATTAAATAAAAAAAATTCCAGGATTTATTAAGATTGAAACACGCATGACAAAATTTCTCTAGATCAGTCACTTTCAAGAATGGATTAAATCAGTGAACAGTTTAAACTGGCTAAAACTGGACATGATTGAAGGGGAGCAAGTCCTCAAGGCATTAAGACAAAGAATCTCATGTAGCCCCTCAACTGTCAAAGACAGACAAATAAATTACCATAAATTATATGCCAAGCAACTTAAAACAAAACAGCTTGACGCTAGGATTCCTTAGCGCCTTCCAGGTTGTGTAACACTGCTTCTGGCCCTCAGTGATCGGGTCAGCAACTGTCAAGTGTCGGGGTAGTAGCAAATGTACCATTGTGAAAGCTAAGCGTCGGACACCAGAGGAATGGCTCCGTGGCTGTCTGGATGATCACTTCCGCAGTCGTGGTCCCTGGTTGGAAAACCT *   NM:i:60 ms:i:253    AS:i:249    nn:i:0  ts:A:+  tp:A:P  cm:i:25 s1:i:160    s2:i:0  de:f:0.1174 cs:Z::5*ga:13-t:9-aga:30*ag:1-a:10-a:6*at:3*ga:7-g:1*tc:1*tg:3-a:20-g:6+a*ta:11-c:10-t:4*ag:5+g:6*ga:16-t:4-g*ta:1*ga:5-a:28-g:7-a:21-a:4-t:10+c:8-aa*gt:26+t:1+a:7*ga:5*ct:5*ag:12*ta:4*ta*at:2-ag:3*ga*ct:2+tgaa:4+a:14-cg:4-a:20-a:2*gt:1*ta:4+t:11+g:9  rl:i:0  MM:Z:N-21891,17,18,7,256,51;N-17802,63,53,107;  ML:B:C,6,218,130,199,7,94,3,17
05b73ba3-6917-4ad9-b6f7-fdd06c6893ea    16  1   4491397 60  7S45M1I39M1D3M2I14M1D11M1D6M1D12M2D14M1D16M4D7M1I4M1D5M1D1M1D24M1I59M1D47M3D3M2D13M2D49M1I4M2D44M2I20M1I19M6D22M1I5M1I29M1D11M1D23M1D5M1D78M1D6M1I42M1D14M1D20M1D15M1D2M2D53M1D20M1I2M3D17M2D2M1D53M2D27M2D6M1I2M1D9M3D25M1D63M1D35M1I34M2D12M1D22M3D17M1I78M431N28M1I77M   *   0   0   CTTTTTTCAGGATTTATTTAAGATTGAGAAAACACGCATGACAAAATTTCTCTTAGATCAATACACTTTCAAGAAATGGAATAAGTCAGTGAATATTTTTTAAAACTGGCTAAACTGGACAGAATTGTGGGAGCAAGTCCCAAGGCATTTAAAAACAAATCTCGTGTAGCCAACTGTGTCAAAGGCAAAAAATAAATTACCATAAATTATATGGCCAAGGCAACTTAAAACAAAAACAGCTTGACGCCAAGGATTTCCTTAGCGCTTCCAGGAGTGTGTAACACTGCTTCTGGCCCTCAGGTCGGAGCAGCAACCGTCAGTCGGTGGGCCCCATAAGACCGCTGAGCTAGCGTCGGACACCACGGAGGAAATGGCTCCGTGGCTCGTCTGAGGTTCACTCCGCAGTCGTGTCCCTGGTAGGGAAGACCCATCTCGCGGGCTTATACACAAAGGGCAAGATACTGTTCGAATTCCGCCACCTCCCCTAGGAGCTCAGTGGGGCTGGGTTGGATTCCGTGCCATCCCGGCAGGTCGTGCCTCGGGAGGGGCGAAGGTTGCCCGGGGCTGGCGCTGGTGCTGCTGCTGCGGTGGCGGCGGCGGTGCCTGCGGTTGCAGCGGCTGCTGGGGATGCGCGTGGAAACCGCGCCCCGTCTTGCAGGCGGGCGAGCCCATCGCGCCGTAGTACAGGTGCATAGCGCTGGGGGCGCCAGGATCCCGGCGTCGCAGGGCCCGAGGGTCCGGCCCCACTGCGTGGACAGCGGGCGGCTCTACGGACACTGCATAGCCGGAGACTGGAGCGTAAGGTAGGTGCCGGCCGCCGGGCAAGCCTGGCAGCGGGGCTGCAGGAGCCGGAGCCTGCTCCACGCCATCCAGCGGGTATGTGTCCGGAGTGGGCAGAGTAGCCATCGAGCGCGGGAGCGCCCAGCCTGGCTAGCTCGATAGTGGCCCATGTGCGGAGACATCAGCGGGGACCGGCCGGATAGCCCGGCTCTGGAAAAGGCAGACCCAGGCCATCCATGGCCACGCGGCCGCCTCGGGACCAAGCGCGCCGGCCTGGGGCTCGACGAAGAGCGTGCAGGAAGCCTCCCTCCACCCGCTTCACGCTTCACCTGCCGCGCCGCCGCGGCCGGTACTTGTTGGGGTGGTCCTGCATTATGCTGCACGCGCAGCCGCTGGGCCTCTTCCACGAAGGGCCGCTTCTCTGCCAAAGCCAACGCCTTCCAAGACATGCCTAGCATCTTGCTTAGCTCTGCGTTGTGCCAGATCTGGGTTCTGCTGTGCCAACCGCTTGCGTTCGTCTTTGGCCCACACCATAAAGGCGTTCATCGGCCGCCGGA   *   NM:i:119    ms:i:1023   AS:i:978    nn:i:0  ts:A:+  tp:A:P  cm:i:188    s1:i:958    s2:i:0  de:f:0.0673 cs:Z::45+t:39-g:3+tt:14-a:11-t*ga:5-g:12-ct:14-c:1*ac:14-ccct:7+g:4-g*ta:4-g:1-c:24+g:17*ac*ca:15*tc:24-a:33*ga*tg:1*ga:10-aat:3-gg:3*ag:1*tg*tc*gc:1*ac:3-gt:49+c:4-ga:44+cg:20+a:19-tgcggt:22+g:5+g:27*gt:1-a:1*at:9-g:21*ct:1-t:5-g:55*ta:22-c*at:5+a:35*gt:6-g:14-c:6*ag:13-g:15-c:2-at:1*gt:2*ca:29*tc:1*cg:16-t:20+a:2-tcc:17-aa:2-a*ag:6*ga*tg:23*gt:20-gg:6*ga:20-tc:6+t:2-t:1*ct:7-ggg:25-a:23*ct:2*ga:36-c:35+a:34-tg:12-t*tc:21-gta:17+t:21*cg:33*ga:1*tc:16*ta:3~ct431ac:28+c:77    rl:i:0  MM:Z:N-21891,66,59,64,261,29,68,47,271,53,16,6,209,38,51;N-17802,21,7,70,144,52,67,91,132,25,175,65,34,76,156;  ML:B:C,5,254,5,3,253,98,15,254,217,72,12,121,243,9,46,2,11,3,10,41,160,134,187,7,11,22,20,94
4c718cef-9dbc-449e-b6b6-1ae47507d721    16  1   4774301 60  1S17M1I17M1D3M1D23M1I82M3D39M2D2M1I2M2D22M3008N2M2I29M1D12M3I34M1D16M1D3M1D9M3D12M4919N16M1I14M1D6M1I6M1I46M2D25M2D5M1D12M1I30M1217N38M8D46M1I19M1I25M1I7M1I12M1467N48M1D4M1I28M1I1M1I4M2D11M   *   0   0TATAACAAAAGTTTCCCTCCTTACTTTAGAAATGGGTGTGGGGCAGATGCAGGCACACATGGAAGGCCAGATGCAGGCACACATGGAGACCAGATGCAGGCACACATGGAGGCCAGATGCTGGTCAGATGTCTTTTCTCAATGGCTTTATTATTTTATGTGTATTGAGTATCTGGCCGAAAGTCTGTGATCAAAAGAGTGCATCAAGTGCCCTGAAGACTTCTGGGGTCATAGAAGGCTGTAGTACAACACCGCCATTTTTTTTTTCAATGGCAGCAATGGCTAATTCTGAAGCAGCTGCACTTCAATATAATTTTGCTTGAGTATCAGCACCCTCTTCAACCAGCTGGAACTCCATAATCCCTTTAAGCAGGCTGGAATGGTCACACCTCTCCCATTCACAAGCTGGGTTAGGTCAATAGGTTGTTGGATCAACTCGACCTAAATCAAAAATATGTAGTCTCCTGAAGACTCAAAGGCTGATACTGGTGCCTGAAACTATGTCCTTCATTAAATCCATATTTTGGGATTCGTATGAGTCTGCCCTCCCTCAAAGCCTAGCCTTGGCCGGGTTCCTCTCTGCCCTTTCTCCTTTATGGCCTCCTGCCACACTTCCTACCTCTTCTCCTGATCTCTGAGGACGTCTTTCCCGTTTTCTTGAGTTAGGACTGGGCTTCAGGTTGGCCAGGCTCACTCTGGCAGAGGACCGCAGCAGGTCCAGGCTGGTCCCTGCCAGCCGCGCCGTGCC    *   NM:i:60 ms:i:595    AS:i:457    nn:i:0  ts:A:+  tp:A:P  cm:i:103    s1:i:479    s2:i:83 de:f:0.0539 cs:Z::17+c:17-a:3-g:23+a:82-ttt:28*tg:7*ag:2-ca:2+t:2-ag:3*ga:18~ct3008ac:2+ga:8*tg:20-a:12+ttt:34-c:16-t:3-t:9-aaa:12~ct4919ac:16+a:14-c:6+a:6+a:46-ga:25-tg:1*ga:3-c:12+a:30~ct1217ac:38-gtaaaatg:22*ct:23+c:19+c:25+t:7+g*ta:11~ct1467ac:9*gt:38-c:4+g:28+t:1+c:4-cg:11  rl:i:14 MM:Z:N-21891,21,9,53,89,32,35,42,44,4,26,154,37,58,6,111;N-17802,42,96,12,215,176,44,46,45; ML:B:C,20,153,48,143,53,6,2,81,9,30,56,20,77,120,24,14,28,83,17,29,22,2,9
ArtRand commented 1 month ago

Hello @ADHDrian,

This has been a long-standing limitation but is easy enough to remove. I'll look into getting it into the next release. What caller is producing MM:Z:N-21891 tags?

ADHDrian commented 1 month ago

Hello @ArtRand , thank you very much for your reply. It would be extremely helpful if you can indeed add this generic feature. The caller that produces these tags is not an official software release, but some research code that attempts mod base calling other than m6A and psi.