{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":97612481,"defaultBranch":"master","name":"minimap2","ownerLogin":"lh3","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2017-07-18T15:04:53.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/480346?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1711551543.0","currentOid":""},"activityList":{"items":[{"before":"0cc3cdca27f050fb80a19c90d25ecc6ab0b0907b","after":"69e36299168d739dded1c5549f662793af10da83","ref":"refs/heads/master","pushedAt":"2024-05-22T19:58:33.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Mention in man page that CIGAR strings in SA tags are approximate (#1213)\n\n* Mention approx CIGAR strings in man page #724\r\n\r\n* Fix FAQ typo","shortMessageHtmlLink":"Mention in man page that CIGAR strings in SA tags are approximate (#1213"}},{"before":"8170693de39b667d11c8931d343c94a23a7690d2","after":"0cc3cdca27f050fb80a19c90d25ecc6ab0b0907b","ref":"refs/heads/master","pushedAt":"2024-04-07T21:12:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"ignore filtered SVs in sveval","shortMessageHtmlLink":"ignore filtered SVs in sveval"}},{"before":"e3d8c708acfe8f2eeaf32daf6183dd11c111a5be","after":"8170693de39b667d11c8931d343c94a23a7690d2","ref":"refs/heads/master","pushedAt":"2024-03-27T14:57:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Release minimap2-2.28 (r1209)","shortMessageHtmlLink":"Release minimap2-2.28 (r1209)"}},{"before":"119bdc602967d036f6d606ae3651e1b7c70d7f6b","after":"e3d8c708acfe8f2eeaf32daf6183dd11c111a5be","ref":"refs/heads/master","pushedAt":"2024-03-27T12:49:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1208: reverted RMQ gap coefficient\n\nSuch that minimap2 can give the same alignment in other modes","shortMessageHtmlLink":"r1208: reverted RMQ gap coefficient"}},{"before":"89d4d219cd93c778c9053c322babfe1f6e6c1329","after":"119bdc602967d036f6d606ae3651e1b7c70d7f6b","ref":"refs/heads/master","pushedAt":"2024-03-20T19:53:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1207: reduced cap_kalloc from 1G to 500M\n\nThis reduces the peak memory.","shortMessageHtmlLink":"r1207: reduced cap_kalloc from 1G to 500M"}},{"before":"c881b14ba5506e6437257596c56674efe7036d2d","after":"89d4d219cd93c778c9053c322babfe1f6e6c1329","ref":"refs/heads/master","pushedAt":"2024-03-20T19:30:48.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1206: enabled RMQ for lr:hqae\n\nAlso fixed a bug in determining inner_dist for RMQ. It should have no effect on\nprevious presets.","shortMessageHtmlLink":"r1206: enabled RMQ for lr:hqae"}},{"before":"f18dadb1c432598fa8bc05367035e08de8fef1a9","after":"c881b14ba5506e6437257596c56674efe7036d2d","ref":"refs/heads/master","pushedAt":"2024-03-20T04:26:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1203: added preset lr:hqae","shortMessageHtmlLink":"r1203: added preset lr:hqae"}},{"before":"a83b8fe7cc09b5c5c74b5684cabd879c864d6fe1","after":"f18dadb1c432598fa8bc05367035e08de8fef1a9","ref":"refs/heads/master","pushedAt":"2024-03-20T03:48:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1202: halved RMQ gap cost","shortMessageHtmlLink":"r1202: halved RMQ gap cost"}},{"before":"12d441ea22ca4f781c4d0b0b05440262c8c1d5ca","after":"a83b8fe7cc09b5c5c74b5684cabd879c864d6fe1","ref":"refs/heads/master","pushedAt":"2024-03-20T01:53:33.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1201: renamed --dbg-seed-freq to --dbg-seed-occ","shortMessageHtmlLink":"r1201: renamed --dbg-seed-freq to --dbg-seed-occ"}},{"before":"5279377544a36f690e8aa34fec856c6106d259e5","after":"12d441ea22ca4f781c4d0b0b05440262c8c1d5ca","ref":"refs/heads/master","pushedAt":"2024-03-20T01:47:55.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/master'","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/master'"}},{"before":"acab05781e4f371346841a7aae305b243ec446bb","after":"5279377544a36f690e8aa34fec856c6106d259e5","ref":"refs/heads/master","pushedAt":"2024-03-19T23:20:21.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Fix MD generation check in SAM writing (#1181)\n\nThe existing logic checked for is_MD == 1, but\r\nthe function is called with a bitwise operator check\r\nwhich does not evaluate to 1.","shortMessageHtmlLink":"Fix MD generation check in SAM writing (#1181)"}},{"before":"9b0ff2418c298f5b5d0df12b137896e5c3fb0ef4","after":"acab05781e4f371346841a7aae305b243ec446bb","ref":"refs/heads/master","pushedAt":"2024-03-19T13:56:19.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'remotes/origin/master'","shortMessageHtmlLink":"Merge remote-tracking branch 'remotes/origin/master'"}},{"before":"b6762503a9c9af34ae02f56784035ff852ed04a5","after":"9b0ff2418c298f5b5d0df12b137896e5c3fb0ef4","ref":"refs/heads/master","pushedAt":"2024-03-14T02:15:46.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Fix mm_mapopt_t in Mappy (#1177)\n\nAdd transition. Related to #1069","shortMessageHtmlLink":"Fix mm_mapopt_t in Mappy (#1177)"}},{"before":"9667468e89d5c7702d4749381b883f8292bfac25","after":"b6762503a9c9af34ae02f56784035ff852ed04a5","ref":"refs/heads/master","pushedAt":"2024-03-12T17:20:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Release minimap2-2.27 (r1193)","shortMessageHtmlLink":"Release minimap2-2.27 (r1193)"}},{"before":"ba60aac6f6a1085b05eb2099d8d7b6303b285297","after":"9667468e89d5c7702d4749381b883f8292bfac25","ref":"refs/heads/master","pushedAt":"2024-03-12T02:46:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"NEWS draft","shortMessageHtmlLink":"NEWS draft"}},{"before":"fcd4df2a734cbb89bb1936dbded8ce89aa48d16c","after":"ba60aac6f6a1085b05eb2099d8d7b6303b285297","ref":"refs/heads/master","pushedAt":"2024-03-12T02:09:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1191: fixed wrong reverse() and revcomp()\n\ndue to k8 incompatibility. Resolves #1161","shortMessageHtmlLink":"r1191: fixed wrong reverse() and revcomp()"}},{"before":"0efc88601259c57830ec66ac43cae8b24dcc5a33","after":"fcd4df2a734cbb89bb1936dbded8ce89aa48d16c","ref":"refs/heads/master","pushedAt":"2024-03-11T21:27:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1190: output unadjusted dp_max to ms:i\n\nThis was an oversight affecting v2.22+. The latest minimap2 ranks hits and\nestimates mapping quality with an adjusted alignment score (see the minimap2\nupdate paper). This score however is not calculated when there is only one hit.\nAs a result, the ms:i tag varies depends on other sequences in the reference\ngenome, which is confusing. This change lets minimap2 to output the unadjusted\nscore at ms:i. At present, the adjusted score is not outputted.\n\nResolves #1146","shortMessageHtmlLink":"r1190: output unadjusted dp_max to ms:i"}},{"before":"940388f8e48e2f0dae63ca23d2faea4b431fd61e","after":"0efc88601259c57830ec66ac43cae8b24dcc5a33","ref":"refs/heads/master","pushedAt":"2024-03-11T14:15:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1189: fixed an out-of-memory issue\n\nResolves #1166","shortMessageHtmlLink":"r1189: fixed an out-of-memory issue"}},{"before":"a12673611f9a5863f1f498099158b931de84ec8e","after":"940388f8e48e2f0dae63ca23d2faea4b431fd61e","ref":"refs/heads/master","pushedAt":"2024-03-10T19:24:08.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1188: added --ds to output tag ds\n\nAdapted from minigraph","shortMessageHtmlLink":"r1188: added --ds to output tag ds"}},{"before":"f3e59fc2a09e89fdb2c166b6d02281e98288c326","after":"a12673611f9a5863f1f498099158b931de84ec8e","ref":"refs/heads/master","pushedAt":"2024-03-10T17:49:43.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/master'","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/master'"}},{"before":"fc2e1607d73ea4870e6f396697c79051aff23eed","after":"f3e59fc2a09e89fdb2c166b6d02281e98288c326","ref":"refs/heads/master","pushedAt":"2024-01-24T17:32:06.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Avoid NULL pointer dereference (#1154)\n\nIf the allocated region is 0 bytes then it's unsafe to dereference it.\r\n\r\nFixes #1147.","shortMessageHtmlLink":"Avoid NULL pointer dereference (#1154)"}},{"before":"bc588c0eeb26426d0d90a93fb0877358a389c515","after":"fc2e1607d73ea4870e6f396697c79051aff23eed","ref":"refs/heads/master","pushedAt":"2024-01-03T14:06:08.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Update paftools.js (#1145)\n\nIn mapeval \"-Q INT\" reports wrong alignments with mapQ>=INT, not with mapQ>INT","shortMessageHtmlLink":"Update paftools.js (#1145)"}},{"before":"9506e7ac3f139a1537dcff9e0f9cf12ad79c8021","after":"bc588c0eeb26426d0d90a93fb0877358a389c515","ref":"refs/heads/master","pushedAt":"2023-10-30T20:39:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1182: improved paftools.js compatibility\n\nOlder k8/v8 can't use large memory. The previous change read large FASTA as\nstrings and might have problems. The new change tests k8 version.","shortMessageHtmlLink":"r1182: improved paftools.js compatibility"}},{"before":"ce03fbc275e40e256e495500ef673f2d1368cdf8","after":"9506e7ac3f139a1537dcff9e0f9cf12ad79c8021","ref":"refs/heads/master","pushedAt":"2023-10-28T19:54:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"r1180: paftools.js call compatibility with k8-1.0","shortMessageHtmlLink":"r1180: paftools.js call compatibility with k8-1.0"}},{"before":"ae05f8485fab6d629be58993663db1f4eb97e779","after":"ce03fbc275e40e256e495500ef673f2d1368cdf8","ref":"refs/heads/master","pushedAt":"2023-10-24T13:53:55.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'remotes/origin/master'","shortMessageHtmlLink":"Merge remote-tracking branch 'remotes/origin/master'"}},{"before":"ace990c381c647d6cf8fae7a4941a7b56fb67ae7","after":"ae05f8485fab6d629be58993663db1f4eb97e779","ref":"refs/heads/master","pushedAt":"2023-10-24T13:23:06.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Add bw_long option to mappy's Aligner class (#1124)\n\nThe Minimap2 behavior was found to handle sequences with large\r\ndeletions differently when upgraded from v2.17 to v2.26, causing\r\npotential issues in projects mapping extensive deletions of ~1200 base\r\npairs. The originally suggested solution of setting `-r 500,500` was\r\nobserved to be partially non-applicable since the Python Wrapper,\r\n`mappy`, only allowed manipulation of parameter `bw`.\r\n\r\nIn response to issue #1111, where this was originally reported,\r\nthis commit introduces a modification in the Python wrapper,\r\n`mappy`. Until now, `mappy` only allowed manipulation of the `bw`\r\nparameter, preventing the suggested fix of setting `-r 500,500`.\r\n\r\nThis commit introduces a modification in the Python wrapper to include\r\nthe `bw_long` option in the `Aligner` class. Consequently, both\r\nparameters `bw` and `bw_long` can be manipulated, thereby allowing the\r\ndesired Minimap2 behavior encountered in version 2.17. As a result,\r\nthis patch ensures consistent handling of sequences containing large\r\ndeletions irrespective of the version upgrade.\"\r\n\r\nCloses #1111","shortMessageHtmlLink":"Add bw_long option to mappy's Aligner class (#1124)"}},{"before":"e28a55be86b298708a2a67c924d665a00b8d829c","after":"ace990c381c647d6cf8fae7a4941a7b56fb67ae7","ref":"refs/heads/master","pushedAt":"2023-06-04T15:06:15.422Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Illumina Complete Long Read presets (#1069)\n\n* Implements a transition-aware alignment scoring scheme and configuration presets for ICLR\r\n\r\n* Fix to enable use of general scoring matrix in ksw as suggested by lh3\r\n\r\n---------\r\n\r\nCo-authored-by: koadman <>","shortMessageHtmlLink":"Illumina Complete Long Read presets (#1069)"}},{"before":"f8d46a7a3019d69696beeee3ea9587a0c4b2ba93","after":"e28a55be86b298708a2a67c924d665a00b8d829c","ref":"refs/heads/master","pushedAt":"2023-04-29T16:21:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Release minimap2-2.26 (r1175)","shortMessageHtmlLink":"Release minimap2-2.26 (r1175)"}},{"before":"4483f89ee5c0e5972820a2b981ffcb88cc3eff6f","after":"f8d46a7a3019d69696beeee3ea9587a0c4b2ba93","ref":"refs/heads/master","pushedAt":"2023-04-29T15:49:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Revert #868 and use the old setup.py","shortMessageHtmlLink":"Revert #868 and use the old setup.py"}},{"before":"f1b3c7ad0686862d051a38837a263bc63ee6c74c","after":"4483f89ee5c0e5972820a2b981ffcb88cc3eff6f","ref":"refs/heads/master","pushedAt":"2023-04-25T16:45:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lh3","name":"Heng Li","path":"/lh3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/480346?s=80&v=4"},"commit":{"message":"Release minimap2-2.25 (r1173)","shortMessageHtmlLink":"Release minimap2-2.25 (r1173)"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEUVPEJQA","startCursor":null,"endCursor":null}},"title":"Activity ยท lh3/minimap2"}