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
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This reduces the peak memory.
2024-03-20 15:53:12 -04:00
Heng Li
89d4d219cd
r1206: enabled RMQ for lr:hqae
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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
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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
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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
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 )
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* 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
fc24c8a348
r1169: improved kexpand compatibility
2023-04-21 10:53:23 -04:00
Heng Li
c41518ae85
r1166: sync kalloc with miniwfa and miniprot
2023-04-19 21:38:47 -04:00
Chris Seymour
819d843e3c
make mm_tbuf_t public
2023-04-19 21:32:23 -04:00
Heng Li
5e7242303c
r1164: changed the syntax of -J
2023-04-07 22:54:33 -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
ea2042a577
r1162: fixed a typo; also increased splice pen
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Now slightly better on ISO-seq
2023-04-07 01:19:18 -04:00
Heng Li
1834b1fd42
r1161: merged the simple and complex models
2023-04-06 23:42:50 -04:00
Heng Li
7ced0f16a0
r1160: splice model code cleanup
2023-04-06 23:32:06 -04:00
Heng Li
35732f3025
Merge branch 'master' into splice-model
2023-04-06 21:09:18 -04:00
Chris Seymour
6ce0dd8b70
move MM_VERSION define to minimap.h
2023-03-17 20:58:43 +01:00
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
6c2cbf7903
miniprot-like splice model
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slightly worse on iso-seq and slightly better on direct-RNA
2022-10-06 09:10:17 -04:00
Heng Li
c8f0a35c40
r1117: added --no-hash-name for deterministic
2021-11-24 16:49:48 -05:00
Heng Li
39bdd45875
r1108: fixed missing inversions for #816 and #806
2021-10-04 16:34:30 -04:00
Heng Li
aefa2c0d86
added --chain-skip-scale
2021-10-01 16:58:03 -04:00
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
7e33fde82b
dev-r1087: added --cap-kalloc
2021-07-19 21:20:04 -04:00
Heng Li
161ae7ff73
dev-r1079: per-read error rate
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more tuning needed
2021-07-18 20:38:53 -04:00
Heng Li
8a6edab847
dev-r1078: decoupling ranking penalty
2021-07-18 16:22:48 -04:00
Heng Li