Heng Li
fbb9c0fcba
r1264: added --jump-min-match, default to 3
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To match STAR
2025-04-06 23:18:55 -04:00
Heng Li
af094640e5
r1263: ~5-10% performance improvement
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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
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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
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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
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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 )
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* 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
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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
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* 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
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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
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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
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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
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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 )
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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
Heng Li
9dceae59a0
r972: renamed --alt-diff to --alt-drop
2020-01-21 10:33:39 -05:00
Heng Li
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
Heng Li
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
Heng Li
e026e18439
added the description of "SA" tag. Closes #438
2019-07-01 09:18:33 -04:00
Heng Li
7bc87b4175
Release minimap2-2.17 (r941)
2019-05-04 23:49:17 -04:00
Heng Li
6762368cf0
r940: added the splice:hq preset
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for high-quality CCS/mRNA splice alignment
2019-05-04 14:00:31 -04:00
Heng Li
c2aec88b84
r938: added --sam-hit-only; resolved #377
2019-04-30 22:40:36 -04:00
Heng Li