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
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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
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
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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
Heng Li
ba60aac6f6
r1191: fixed wrong reverse() and revcomp()
...
due to k8 incompatibility. Resolves #1161
2024-03-11 22:09:01 -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
0efc886012
r1189: fixed an out-of-memory issue
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Resolves #1166
2024-03-11 10:14:20 -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
a12673611f
Merge remote-tracking branch 'origin/master'
2024-03-10 13:49:30 -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
bc588c0eeb
r1182: improved paftools.js compatibility
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Older k8/v8 can't use large memory. The previous change read large FASTA as
strings and might have problems. The new change tests k8 version.
2023-10-30 16:37:29 -04:00
Heng Li
ab717023b6
reverted to the previous paftools.js
2023-10-30 16:24:18 -04:00
Heng Li
9506e7ac3f
r1180: paftools.js call compatibility with k8-1.0
2023-10-28 15:54:37 -04:00
Heng Li
ce03fbc275
Merge remote-tracking branch 'remotes/origin/master'
2023-10-24 09:53:51 -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
f8d46a7a30
Revert #868 and use the old setup.py
2023-04-29 11:48:41 -04:00
Heng Li
4483f89ee5
Release minimap2-2.25 (r1173)
2023-04-25 12:44:52 -04:00
Heng Li
f1b3c7ad06
added -ldl for asan on some linux
2023-04-25 11:14:15 -04:00
Heng Li
180faa3594
r1171: add operator priority explicit with ()
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I can never remember the operator priority of & and &&
2023-04-21 11:09:07 -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
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
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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
Heng Li
01b98e8e52
r1155: fixed a bug on parsing --rmq
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resolves #1010
2023-01-17 09:09:25 -05:00
Heng Li
16b8d50199
removed debugging code
2023-01-06 11:16:09 -05:00
Heng Li
226fd6114c
fixed a wrong comment. Resolves #997
2022-11-30 09:22:39 -05:00
Heng Li
822ccd1733
r1152: evaluate base Sn and Sp
2022-11-01 21:58:45 -04:00
Heng Li
f67849c9af
r1151: added exoneval
2022-11-01 21:10:35 -04:00
Heng Li
b0b199f503
r1150: the prev impl counted one less submer
2022-10-21 21:00:22 -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