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
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
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
a8c567b5e9
r1251: read junctions for jumps
2025-04-04 16:23:19 -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
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
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
fcb5d5e6eb
r1221: warn about file reading errors
...
Resolves #1229
2024-10-15 22:44:06 -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
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
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
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
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
b6762503a9
Release minimap2-2.27 (r1193)
2024-03-12 13:20:07 -04:00
Heng Li
fcd4df2a73
r1190: output unadjusted dp_max to ms:i
...
This was an oversight affecting v2.22+. The latest minimap2 ranks hits and
estimates mapping quality with an adjusted alignment score (see the minimap2
update paper). This score however is not calculated when there is only one hit.
As a result, the ms:i tag varies depends on other sequences in the reference
genome, which is confusing. This change lets minimap2 to output the unadjusted
score at ms:i. At present, the adjusted score is not outputted.
Resolves #1146
2024-03-11 17:19:13 -04:00
Heng Li
940388f8e4
r1188: added --ds to output tag ds
...
Adapted from minigraph
2024-03-10 15:01:13 -04:00
Heng Li
23d2674c39
r1187: set stage for the ds tag; not added yet
2024-03-10 14:12:56 -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
Aaron Darling and koadman
ace990c381
Illumina Complete Long Read presets ( #1069 )
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* Implements a transition-aware alignment scoring scheme and configuration presets for ICLR
* Fix to enable use of general scoring matrix in ksw as suggested by lh3
---------
Co-authored-by: koadman <>
2023-06-04 11:06:15 -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
180faa3594
r1171: add operator priority explicit with ()
...
I can never remember the operator priority of & and &&
2023-04-21 11:09:07 -04:00
Mikhail Kolmogorov and Heng Li
704fbc6f5c
An option to output SEQ field for secondary alignment ( #687 )
...
* a new option --secondary-seq to output SEQ field for secondary alignments
* comments removed
* Fixed a conflict in #687
---------
Co-authored-by: Heng Li <lh3@me.com >
2023-04-21 11:06:13 -04:00
Heng Li