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Author SHA1 Message Date
Heng Li 3c28777e7e Release minimap2-2.31 (r1302) 2026-05-19 18:39:04 -04:00
Heng Li d8371a403b removed duplicate check in sim2bed 2026-04-25 00:35:59 -04:00
Heng LiandClaude Opus 4.5 e5066c7976 added sim2bed to convert simulated read names to BED 
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2026-04-25 00:22:26 -04:00
Heng Liandgemini-cli f8381755f1 r1299: fix wrong subchain selection 
This and the last bug were both reported by Jeremy Wang.

Co-authored-by: gemini-cli <gemini-cli@users.noreply.github.com>
 2026-04-24 16:17:45 -04:00
Heng Li 80d92c686f r1298: fixed out-of-bound local alignment 
I believe this would not lead to memory violation; it may occasionally include
a few base beyond the intended alignment start/end.
 2026-04-24 13:25:19 -04:00
Heng Li 37a650f58c output simulated identity with badread 2026-04-14 12:49:35 -04:00
Heng Li 4ca5a951ca command line help 2026-04-13 23:52:07 -04:00
Heng Li dd5b2c04b8 Merge remote-tracking branch 'remotes/origin/master' 2026-04-13 23:43:43 -04:00
Heng Li ca6f4dc5e2 convert badread output to evaluation format 2026-04-13 23:43:11 -04:00
Heng Li e2542e6425 Merge remote-tracking branch 'remotes/origin/master' 2025-12-12 11:39:33 -05:00
Heng Li 9bb4d2bed4 r1290: support ds in Python 2025-12-12 11:39:01 -05:00
Heng Li bd0cba5012 upgrade arm64-linux to v3 2025-09-09 13:52:16 -04:00
Heng Li 370f3f8236 add an alert about phishing 2025-09-09 11:23:09 -04:00
Heng Li 79c9cc186b Release minimap2-2.30 (r1287) 2025-06-15 17:54:11 -04:00
Heng Li ea4c8935bd added one more example 
This shows STAR doesn't try to match the GTR..YAG consensus.
 2025-06-03 20:22:14 -04:00
Heng Li 3187782b1a r1285: better --spsc support 2025-05-26 15:47:14 -04:00
Heng Li 005c9a1f6b exoneval may skip terminal exons in aa mode 2025-05-17 23:06:41 -04:00
Heng Li 1fd85be6e2 Release minimap2-2.29 (r1283) 2025-04-18 13:41:47 -04:00
Heng Li e616b0dacf drafted the release notes 2025-04-18 13:17:13 -04:00
Heng Li b58b97423a r1281: with --write-junc, ignore aln with low mapQ 2025-04-17 21:46:54 -04:00
Heng Li df9e650346 r1280: heuristic to avoid aligning full introns 
This speeds up alignment a lot
 2025-04-16 23:38:39 -04:00
Heng Li 7a540c37ca r1278: reduced --min-dp-len to 20 for splice:sr 
30% reduced time at 0.01% more junction errors
 2025-04-16 21:55:59 -04:00
Heng Li c19e3ccb86 r1277: don't apply rescored filtering with -P 
Since v2.19-ish, minimap2 rescores base alignment based on the best alignment
of a read. This heuristic sometimes improve the mapping accuracy of the best
alignment but may too aggressively filter weaker hits.

Resolve #969
 2025-04-14 22:26:47 -04:00
Heng Li 94d171b01e r1276: skip unnecessary reverse spliced alignment 
for short-read RNA-seq only
 2025-04-14 14:57:23 -04:00
Heng Li ff312a2957 documented 2-pass in README 2025-04-13 17:14:44 -04:00
Heng Li 01ccedd5a0 r1275: renamed --jump-pass1 to --pass1 
Also documented 2-pass
 2025-04-13 17:07:39 -04:00
Heng Li 819b3bf017 r1274: a little better pass-1 
Also fixed a bug in jump
 2025-04-13 13:55:15 -04:00
Heng Li e88110463a r1273: reading pass1 junctions works 
but we need extra logic when using them. Tomorrow.
 2025-04-13 00:47:28 -04:00
Heng Li fb81e150f2 r1272: support pass-1 junction processing 
NOT tested yet
 2025-04-12 23:15:04 -04:00
Heng Li d930ea94ad r1271: code refactoring in prep for 2-pass 2025-04-11 17:20:34 -04:00
Heng Li a832a42f6f r1270: fixed ts tag for PE reads 
this also fixed the wrong --write-junc
 2025-04-11 01:08:16 -04:00
Heng Li a5411fc3c0 r1269: added --write-junc 
in preparation for 2-pass
 2025-04-11 01:00:15 -04:00
Heng Li bd03d975fc r1268: avoid extra small introns 2025-04-07 23:32:56 -04:00
Heng Li 9c3c4b1ce8 r1267: penalize introns without signals 2025-04-07 09:51:33 -04:00
Heng Li 3542a3d153 r1266: fine tune mapq for short RNA-seq reads 2025-04-07 00:57:39 -04:00
Heng Li 75619c7b51 r1265: prefer spliced alignment 
mapq needs to be elevated
 2025-04-07 00:31:04 -04:00
Heng Li fbb9c0fcba r1264: added --jump-min-match, default to 3 
To match STAR
 2025-04-06 23:18:55 -04:00
Heng Li af094640e5 r1263: ~5-10% performance improvement 
Via larger batches and more short-read heuristics. Identical alignment on 2
million reads. Short DNA-seq read alignment may be improved in corner cases.
 2025-04-06 20:48:55 -04:00
Heng Li d43f356ef9 fixed minor grammar issues 2025-04-06 18:35:46 -04:00
Heng Li 38acd6617f r1261: code clean up; renamed --jump-bed to -j 
Also added --pairing to replace --no-pairing and --pe-ind-chain
 2025-04-06 18:32:58 -04:00
Heng Li 3d351267a0 document --jump-bed 2025-04-06 17:43:11 -04:00
Heng Li 54a4718c9b r1259: --jump-bed now functional 2025-04-06 17:12:49 -04:00
Heng Li dbc12b2838 r1258: update blen, mlen and dp_max0 2025-04-06 15:26:01 -04:00
Heng Li 2ed264db4e r1257: fixed the sorting of BED files 2025-04-06 10:53:16 -04:00
Heng Li a8094ad859 r1256: working for one example, but still buggy 2025-04-06 10:33:57 -04:00
Heng Li 1877818239 r1255: moved jump code to a separate file 2025-04-06 09:33:51 -04:00
Heng Li 9ede5c4255 backup 2025-04-06 00:07:15 -04:00
Heng Li 405511fe8d Merge branch 'master' into junc-jump 2025-04-04 16:37:39 -04:00
Heng Li dd90d9dde6 caution that the splice:sr is experimental 2025-04-04 16:34:40 -04:00
Heng Li a8c567b5e9 r1251: read junctions for jumps 2025-04-04 16:23:19 -04:00
Heng Li d9d3c0cc3f refactored --junc-bed 2025-04-03 21:02:50 -04:00
Heng Li cbe8d61ca4 r1249: remove redundant junctions in --junc-bed 2025-04-03 20:43:06 -04:00
Heng Li 9d06cef13e r1248: support --end-bonus in splice mode 
but this is not enabled by default for now
 2025-04-02 21:39:41 -04:00
Heng Li 924fc4d671 minor 2025-04-02 13:06:03 -04:00
Heng Li fc2d1e95b3 document splice:sr in README 2025-04-02 11:24:44 -04:00
Heng Li bbf0bb871b r1245: allow shorter hits for splice:sr 2025-04-02 00:13:37 -04:00
Heng Li 83e9b2e28c r1242: append /[12] to read name in --frag mode 
Resolve #1079
 2025-04-01 10:48:15 -04:00
Heng Li e816fd071c r1241: error out on unintended --score-N 
Resolve #1226
 2025-04-01 10:12:53 -04:00
Heng Li a955b1f31d documented zd; resolve #1108 2025-04-01 09:34:05 -04:00
Heng Li 54fa925e2e r1240: fixed wrong logging information 
resolve #1192
 2025-04-01 09:17:39 -04:00
Heng Li d4a396c5c3 r1239: resovled #963 2025-03-31 23:15:34 -04:00
Heng Li bdf46f5786 r1238: resolve #589 2025-03-31 23:08:37 -04:00
Heng Li f536b69b81 r1237: documented -x splice:sr 2025-03-30 21:47:47 -04:00
Heng Li 4b8b4418df r1236: support paired-end short-read RNA-seq 2025-03-30 19:30:19 -04:00
Heng Li ce30004e02 r1235: allow --splice and --frag at the same time 
This seems to largely work, though the accuracy is reduced and no pairs are
proper. More investigation needed for practical uses.
 2025-03-30 16:32:38 -04:00
Heng Li 54f8e5f7d6 r1234: added splice:sr for SE RNA-seq 2025-03-30 15:54:12 -04:00
Heng Li 2857de7dbd Merge remote-tracking branch 'remotes/origin/master' 2025-03-29 22:44:26 -04:00
Heng Li e18935fbad r1230: make juncevla work for paired-end SAM 2025-03-29 22:43:44 -04:00
Heng Li 618d33515e more condition on length differences 2024-11-17 19:45:46 -05:00
Heng Li a10d4f4496 merge colinear blocks 2024-11-17 15:17:13 -05:00
Heng Li 1eea2fee11 a new script to cluster similar sequences 2024-11-16 16:39:13 -05:00
Heng Li 1d346d56bc Merge remote-tracking branch 'remotes/origin/master' 2024-11-16 16:36:07 -05:00
Heng Li 46750de966 not working well and rarely used in practice 2024-11-16 16:35:24 -05:00
Heng Li fcb5d5e6eb r1221: warn about file reading errors 
Resolves #1229
 2024-10-15 22:44:06 -04:00
Heng Li 95807a2224 added "junc_pen" to python accordingly 2024-10-13 23:58:33 -04:00
Heng Li a4c93e9377 support X and = in mapeval 2024-10-12 23:31:17 -04:00
Heng Li 7d69334e69 Merge remote-tracking branch 'remotes/origin/master' 2024-10-12 23:28:38 -04:00
Heng Li 3e1ab2951d document --spsc 2024-10-12 23:27:46 -04:00
Heng Li 68179ed195 r1215: scoring apparently works 2024-10-12 22:29:27 -04:00
Heng Li d1f4c8d232 implemented ksw scoring; not tested 2024-10-11 23:58:18 -04:00
Heng Li 8efe83b744 fill the junction array 
modifying ksw will be the next
 2024-10-11 23:22:23 -04:00
Heng Li 042c8d4d71 added --junc-pen; it does nothing for now 2024-10-11 21:27:25 -04:00
Heng Li e4e1f7843b backup for spsc 2024-10-10 22:43:50 -04:00
Heng Li 0cc3cdca27 ignore filtered SVs in sveval 2024-04-07 17:12:31 -04:00
Heng Li 8170693de3 Release minimap2-2.28 (r1209) 2024-03-27 10:57:17 -04:00
Heng Li e3d8c708ac r1208: reverted RMQ gap coefficient 
Such that minimap2 can give the same alignment in other modes
 2024-03-27 08:48:10 -04:00
Heng Li 119bdc6029 r1207: reduced cap_kalloc from 1G to 500M 
This reduces the peak memory.
 2024-03-20 15:53:12 -04:00
Heng Li 89d4d219cd r1206: enabled RMQ for lr:hqae 
Also fixed a bug in determining inner_dist for RMQ. It should have no effect on
previous presets.
 2024-03-20 15:29:54 -04:00
Heng Li f51ff1abac r1205: updated lr:hqae 2024-03-20 14:06:59 -04:00
Heng Li 27b254ed6f backup; DON'T USE!!! 2024-03-20 10:21:10 -04:00
Heng Li c881b14ba5 r1203: added preset lr:hqae 2024-03-20 00:25:57 -04:00
Heng Li f18dadb1c4 r1202: halved RMQ gap cost 2024-03-19 23:47:54 -04:00
Heng Li a83b8fe7cc r1201: renamed --dbg-seed-freq to --dbg-seed-occ 2024-03-19 21:53:09 -04:00
Heng Li c22bfe7722 r1200: added --rmq-inner and --dbg-seed-freq 2024-03-19 21:52:07 -04:00
Heng Li 12d441ea22 Merge remote-tracking branch 'origin/master' 2024-03-19 21:47:52 -04:00
Heng Li c7433c2811 r1197: sam2paf to output primary only 2024-03-19 21:47:31 -04:00
Heng Li acab05781e Merge remote-tracking branch 'remotes/origin/master' 2024-03-19 09:56:13 -04:00
Heng Li 98c23bc6d2 r1194: output NM in sam2paf 2024-03-19 09:55:16 -04:00
Heng Li b6762503a9 Release minimap2-2.27 (r1193) 2024-03-12 13:20:07 -04:00
Heng Li 9667468e89 NEWS draft 2024-03-11 22:46:47 -04:00