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• 3c28777e7e Release minimap2-2.31 (r1302) master v2.31 Heng Li 2026-05-19 18:39:04 -04:00
• d8371a403b removed duplicate check in sim2bed Heng Li 2026-04-25 00:35:59 -04:00
• e5066c7976 added sim2bed to convert simulated read names to BED Heng Li 2026-04-25 00:22:26 -04:00
• f8381755f1 r1299: fix wrong subchain selection Heng Li 2026-04-24 16:17:45 -04:00
• 80d92c686f r1298: fixed out-of-bound local alignment Heng Li 2026-04-24 13:25:19 -04:00
• 37a650f58c output simulated identity with badread Heng Li 2026-04-14 12:49:35 -04:00
• 4ca5a951ca command line help Heng Li 2026-04-13 23:52:07 -04:00
• dd5b2c04b8 Merge remote-tracking branch 'remotes/origin/master' Heng Li 2026-04-13 23:43:43 -04:00
• ca6f4dc5e2 convert badread output to evaluation format Heng Li 2026-04-13 23:43:11 -04:00
• de3c6ec646 Fix use-after-free in mappy (#1345) blawrence-ont 2026-02-13 17:14:56 +00:00
• e2542e6425 Merge remote-tracking branch 'remotes/origin/master' Heng Li 2025-12-12 11:39:33 -05:00
• 9bb4d2bed4 r1290: support ds in Python Heng Li 2025-12-12 11:39:01 -05:00
• 6d49eb690f convert unmapped reads in sam2paf (#1324) Alex Leonard 2025-10-06 01:43:23 +02:00
• bd0cba5012 upgrade arm64-linux to v3 Heng Li 2025-09-09 13:52:16 -04:00
• 370f3f8236 add an alert about phishing Heng Li 2025-09-09 11:23:09 -04:00
• 79c9cc186b Release minimap2-2.30 (r1287) v2.30 Heng Li 2025-06-15 17:54:11 -04:00
• ea4c8935bd added one more example Heng Li 2025-06-03 20:22:14 -04:00
• 3187782b1a r1285: better --spsc support Heng Li 2025-05-26 15:47:14 -04:00
• 005c9a1f6b exoneval may skip terminal exons in aa mode Heng Li 2025-05-17 23:06:41 -04:00
• 1fd85be6e2 Release minimap2-2.29 (r1283) v2.29 Heng Li 2025-04-18 13:41:47 -04:00
• e616b0dacf drafted the release notes Heng Li 2025-04-18 13:17:13 -04:00
• b58b97423a r1281: with --write-junc, ignore aln with low mapQ Heng Li 2025-04-17 21:46:54 -04:00
• df9e650346 r1280: heuristic to avoid aligning full introns Heng Li 2025-04-16 23:38:39 -04:00
• 7a540c37ca r1278: reduced --min-dp-len to 20 for splice:sr Heng Li 2025-04-16 21:55:59 -04:00
• c19e3ccb86 r1277: don't apply rescored filtering with -P Heng Li 2025-04-14 22:26:47 -04:00
• 94d171b01e r1276: skip unnecessary reverse spliced alignment Heng Li 2025-04-14 14:57:23 -04:00
• ff312a2957 documented 2-pass in README Heng Li 2025-04-13 17:14:44 -04:00
• 01ccedd5a0 r1275: renamed --jump-pass1 to --pass1 Heng Li 2025-04-13 17:07:39 -04:00
• 819b3bf017 r1274: a little better pass-1 Heng Li 2025-04-13 13:55:15 -04:00
• e88110463a r1273: reading pass1 junctions works Heng Li 2025-04-13 00:47:28 -04:00
• fb81e150f2 r1272: support pass-1 junction processing Heng Li 2025-04-12 23:15:04 -04:00
• d930ea94ad r1271: code refactoring in prep for 2-pass Heng Li 2025-04-11 17:20:34 -04:00
• a832a42f6f r1270: fixed ts tag for PE reads Heng Li 2025-04-11 01:08:16 -04:00
• a5411fc3c0 r1269: added --write-junc Heng Li 2025-04-11 01:00:15 -04:00
• bd03d975fc r1268: avoid extra small introns Heng Li 2025-04-07 23:32:56 -04:00
• 9c3c4b1ce8 r1267: penalize introns without signals Heng Li 2025-04-07 09:51:33 -04:00
• 3542a3d153 r1266: fine tune mapq for short RNA-seq reads Heng Li 2025-04-07 00:57:39 -04:00
• 75619c7b51 r1265: prefer spliced alignment Heng Li 2025-04-07 00:31:04 -04:00
• fbb9c0fcba r1264: added --jump-min-match, default to 3 Heng Li 2025-04-06 23:18:55 -04:00
• af094640e5 r1263: ~5-10% performance improvement Heng Li 2025-04-06 20:48:55 -04:00
• d43f356ef9 fixed minor grammar issues Heng Li 2025-04-06 18:35:46 -04:00
• 38acd6617f r1261: code clean up; renamed --jump-bed to -j Heng Li 2025-04-06 18:32:58 -04:00
• 3d351267a0 document --jump-bed Heng Li 2025-04-06 17:43:11 -04:00
• 54a4718c9b r1259: --jump-bed now functional Heng Li 2025-04-06 17:12:49 -04:00
• dbc12b2838 r1258: update blen, mlen and dp_max0 Heng Li 2025-04-06 15:26:01 -04:00
• 2ed264db4e r1257: fixed the sorting of BED files Heng Li 2025-04-06 10:53:16 -04:00
• a8094ad859 r1256: working for one example, but still buggy Heng Li 2025-04-06 10:33:57 -04:00
• 1877818239 r1255: moved jump code to a separate file Heng Li 2025-04-06 09:33:51 -04:00
• 9ede5c4255 backup Heng Li 2025-04-06 00:07:15 -04:00
• 405511fe8d Merge branch 'master' into junc-jump Heng Li 2025-04-04 16:37:39 -04:00
• dd90d9dde6 caution that the splice:sr is experimental Heng Li 2025-04-04 16:34:40 -04:00
• a8c567b5e9 r1251: read junctions for jumps Heng Li 2025-04-04 16:23:19 -04:00
• d9d3c0cc3f refactored --junc-bed Heng Li 2025-04-03 21:02:50 -04:00
• cbe8d61ca4 r1249: remove redundant junctions in --junc-bed Heng Li 2025-04-03 20:43:06 -04:00
• 9d06cef13e r1248: support --end-bonus in splice mode Heng Li 2025-04-02 21:39:41 -04:00
• 924fc4d671 minor Heng Li 2025-04-02 13:06:03 -04:00
• fc2d1e95b3 document splice:sr in README Heng Li 2025-04-02 11:24:44 -04:00
• bbf0bb871b r1245: allow shorter hits for splice:sr Heng Li 2025-04-02 00:13:37 -04:00
• 83e9b2e28c r1242: append /[12] to read name in --frag mode Heng Li 2025-04-01 10:48:15 -04:00
• e816fd071c r1241: error out on unintended --score-N Heng Li 2025-04-01 10:12:53 -04:00
• a955b1f31d documented zd; resolve #1108 Heng Li 2025-04-01 09:34:05 -04:00
• eec02c07b1 updated the manpage gh-pages Heng Li 2025-04-01 09:25:01 -04:00
• 54fa925e2e r1240: fixed wrong logging information Heng Li 2025-04-01 09:17:39 -04:00
• d4a396c5c3 r1239: resovled #963 Heng Li 2025-03-31 23:15:34 -04:00
• bdf46f5786 r1238: resolve #589 Heng Li 2025-03-31 23:08:37 -04:00
• f536b69b81 r1237: documented -x splice:sr Heng Li 2025-03-30 21:47:47 -04:00
• 4b8b4418df r1236: support paired-end short-read RNA-seq Heng Li 2025-03-30 19:30:19 -04:00
• ce30004e02 r1235: allow --splice and --frag at the same time Heng Li 2025-03-30 16:32:38 -04:00
• 54f8e5f7d6 r1234: added splice:sr for SE RNA-seq Heng Li 2025-03-30 15:54:12 -04:00
• 2857de7dbd Merge remote-tracking branch 'remotes/origin/master' Heng Li 2025-03-29 22:44:26 -04:00
• e18935fbad r1230: make juncevla work for paired-end SAM Heng Li 2025-03-29 22:43:44 -04:00
• 74ebfb2532 fix error (#1223) Chang Y 2025-03-21 17:21:15 -05:00
• a0cbe2e4d2 Add CI job for Linux & Mac ARM64 too (#1205) Martin Grigorov 2025-03-22 00:19:26 +02:00
• 618d33515e more condition on length differences Heng Li 2024-11-17 19:45:46 -05:00
• a10d4f4496 merge colinear blocks Heng Li 2024-11-17 15:17:13 -05:00
• 1eea2fee11 a new script to cluster similar sequences Heng Li 2024-11-16 16:39:13 -05:00
• 1d346d56bc Merge remote-tracking branch 'remotes/origin/master' Heng Li 2024-11-16 16:36:07 -05:00
• 46750de966 not working well and rarely used in practice Heng Li 2024-11-16 16:35:24 -05:00
• 7d8bbb74a8 Add sc_ambi and max_chain_skip parameters to mappy.pyx (#1240) Leon Rauschning 2024-11-15 21:56:36 +08:00
• c6db201b38 Update README.md (#1245) James Webber 2024-11-15 08:54:25 -05:00
• 358a39850f Allow passing read name to mappy (#1260) Rob Patro 2024-11-15 08:51:10 -05:00
• fcb5d5e6eb r1221: warn about file reading errors Heng Li 2024-10-15 22:44:06 -04:00
• 95807a2224 added "junc_pen" to python accordingly Heng Li 2024-10-13 23:58:33 -04:00
• a4c93e9377 support X and = in mapeval Heng Li 2024-10-12 23:31:17 -04:00
• 7d69334e69 Merge remote-tracking branch 'remotes/origin/master' Heng Li 2024-10-12 23:28:38 -04:00
• 3e1ab2951d document --spsc Heng Li 2024-10-12 23:27:46 -04:00
• 68179ed195 r1215: scoring apparently works Heng Li 2024-10-12 22:29:27 -04:00
• d1f4c8d232 implemented ksw scoring; not tested Heng Li 2024-10-11 23:58:18 -04:00
• 8efe83b744 fill the junction array Heng Li 2024-10-11 23:22:23 -04:00
• 042c8d4d71 added --junc-pen; it does nothing for now Heng Li 2024-10-11 21:27:25 -04:00
• e4e1f7843b backup for spsc Heng Li 2024-10-10 22:43:50 -04:00
• 69e3629916 Mention in man page that CIGAR strings in SA tags are approximate (#1213) Marcus Fedarko 2024-05-22 12:58:33 -07:00
• 0cc3cdca27 ignore filtered SVs in sveval Heng Li 2024-04-07 17:12:31 -04:00
• 8170693de3 Release minimap2-2.28 (r1209) v2.28 Heng Li 2024-03-27 10:57:17 -04:00
• e3d8c708ac r1208: reverted RMQ gap coefficient Heng Li 2024-03-27 08:48:10 -04:00
• 119bdc6029 r1207: reduced cap_kalloc from 1G to 500M Heng Li 2024-03-20 15:53:12 -04:00
• 89d4d219cd r1206: enabled RMQ for lr:hqae Heng Li 2024-03-20 15:29:54 -04:00
• f51ff1abac r1205: updated lr:hqae Heng Li 2024-03-20 14:06:59 -04:00
• 27b254ed6f backup; DON'T USE!!! Heng Li 2024-03-20 10:21:10 -04:00
• c881b14ba5 r1203: added preset lr:hqae Heng Li 2024-03-20 00:25:57 -04:00