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157 Commits

Author SHA1 Message Date
Heng Li
3c28777e7e Release minimap2-2.31 (r1302) 2026-05-19 18:39:04 -04:00
Heng Li
79c9cc186b Release minimap2-2.30 (r1287) 2025-06-15 17:54:11 -04:00
Heng Li
3187782b1a r1285: better --spsc support 2025-05-26 15:47:14 -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
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
01ccedd5a0 r1275: renamed --jump-pass1 to --pass1 
Also documented 2-pass
 2025-04-13 17:07:39 -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
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
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
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
d4a396c5c3 r1239: resovled #963 2025-03-31 23:15:34 -04:00
Heng Li
f536b69b81 r1237: documented -x splice:sr 2025-03-30 21:47:47 -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
Marcus Fedarko
69e3629916 Mention in man page that CIGAR strings in SA tags are approximate (#1213) 
* Mention approx CIGAR strings in man page #724

* Fix FAQ typo
 2024-05-22 15:58:33 -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
b6762503a9 Release minimap2-2.27 (r1193) 2024-03-12 13:20:07 -04:00
Heng Li
8140259974 r1183: added lr:hq; fixed transition 
* Added the lr:hq preset suggested by Nanopore developers (#1127)
 * Fixed transition scoring. It did not work with presets.
 * Cleaned up preset documentation
 2024-03-10 13:47:34 -04:00
Heng Li
98a3aa1b39 document --secondary-seq in manpage 
Resolve #1122
 2023-10-24 09:52:39 -04:00
Heng Li
e28a55be86 Release minimap2-2.26 (r1175) 2023-04-29 12:21:09 -04:00
Heng Li
4483f89ee5 Release minimap2-2.25 (r1173) 2023-04-25 12:44:52 -04:00
Heng Li
a026c69b89 r1163: increased the default -I to 8G 
To reduce accidental errors when mapping against diploid human assemblies.
 2023-04-07 01:22:22 -04:00
Heng Li
c2f07ff2ac r1149: implemented random open syncmer 
On the mm2-update dataset, -j8 leads to sparser k-mer selection at higher
accuracy. The speed becomes a little slower. There seems a benefit but not a
big one.
 2022-10-21 19:07:28 -04:00
Heng Li
cefd0d9f6c removed -b0 (a typo) 2022-10-21 17:37:04 -04:00
Heng Li
767556b6f0 clarify multi-part index in option -I (#301) 2022-06-13 15:50:15 -04:00
Heng Li
fe35e679e9 Release minimap2-2.24 (r1122) 2021-12-26 15:14:54 -05:00
Heng Li
3bde3450a0 r1121: updated obsolete settings in manpage 
Resolve #851
 2021-12-26 14:33:14 -05:00
Heng Li
d3a89d34d4 r1118: use -r1k,100k for asm* modes 2021-12-23 20:43:54 -05:00
Heng Li
c8f0a35c40 r1117: added --no-hash-name for deterministic 2021-11-24 16:49:48 -05:00
Heng Li
d0cff3eb36 Release minimap2-2.23 (r1111) 2021-11-18 17:11:48 -05:00
Heng Li
05a8a45d44 r1105: avoid long running time occasionally (#771) 
Caused by highly repetitive minimizers on a query sequence. The solution is to
filter out these query minimizers.
 2021-08-15 19:43:01 -04:00
Heng Li
7358a1ead1 Release minimap2-2.22 (r1101) 2021-08-07 11:30:31 -04:00
Heng Li
8a6edab847 dev-r1078: decoupling ranking penalty 2021-07-18 16:22:48 -04:00
Heng Li
581f2d7123 Release minimap2-2.21 (r1071) 2021-07-06 13:18:55 -04:00
Heng Li
15471bd629 Release minimap2-2.20 (r1061) 2021-05-27 15:26:04 -04:00
Heng Li
ca19463268 r1060: safer ways to use -rNUM1,NUM2 2021-05-27 10:55:13 -04:00
Heng Li
9febf532c1 Release minimap2-2.19 (r1057) 2021-05-26 21:23:42 -04:00
Heng Li
ef09ccf104 Release minimap2-2.19 (r1055) 2021-05-26 21:01:03 -04:00
Heng Li
41d7ccb191 r1052: default -g to 5k 2021-05-24 16:46:16 -04:00
Heng Li
6c96078ed0 r1034: changed multiple defaults; updated manpage 2021-05-03 22:51:34 -04:00
Heng Li
0f5608c4a4 r1028: backport minigraph -U 2021-05-01 15:41:39 -04:00
Heng Li
e8823a3709 r1027: renamed hifi to map-hifi; changed default 2021-05-01 15:22:51 -04:00
Heng Li
b6ff332de1 Release minimap2-2.18 (r1015) 2021-04-09 13:33:34 -04:00
Heng Li
1c4b7e8a48 explained --junc-bed in README 2021-03-06 19:44:24 -05:00
Heng Li
f995f55610 added --mask-len for #659 2020-08-21 11:12:50 -04:00