Heng Li
3187782b1a
r1285: better --spsc support
2025-05-26 15:47:14 -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
fb81e150f2
r1272: support pass-1 junction processing
...
NOT tested yet
2025-04-12 23:15:04 -04:00
Heng Li
a5411fc3c0
r1269: added --write-junc
...
in preparation for 2-pass
2025-04-11 01:00:15 -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
a8094ad859
r1256: working for one example, but still buggy
2025-04-06 10:33:57 -04:00
Heng Li
f536b69b81
r1237: documented -x splice:sr
2025-03-30 21:47:47 -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
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
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
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
ace990c381
Illumina Complete Long Read presets ( #1069 )
...
* 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
4483f89ee5
Release minimap2-2.25 (r1173)
2023-04-25 12:44:52 -04:00
Mikhail Kolmogorov
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
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
1834b1fd42
r1161: merged the simple and complex models
2023-04-06 23:42:50 -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
01b98e8e52
r1155: fixed a bug on parsing --rmq
...
resolves #1010
2023-01-17 09:09:25 -05:00
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
6c2cbf7903
miniprot-like splice model
...
slightly worse on iso-seq and slightly better on direct-RNA
2022-10-06 09:10:17 -04:00
Heng Li
fe35e679e9
Release minimap2-2.24 (r1122)
2021-12-26 15:14:54 -05:00
Heng Li
36942ff711
r1119: fixed a typo in the new chaining code
...
Not affecting v2.23
2021-12-25 12:46:26 -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
fcaadc22b7
r1116: cut long chains at weak points
2021-11-20 19:07:44 -05:00
Heng Li
db37fc43a7
r1115: prepare for chain breaking
2021-11-20 13:42:44 -05:00
Heng Li
a8f1fa8ea3
r1114: retain more candidate inversion alignments
2021-11-18 21:37:10 -05:00
Heng Li
b276772890
r1112: added --print-chains for debugging
2021-11-18 21:26:41 -05:00
Heng Li
d0cff3eb36
Release minimap2-2.23 (r1111)
2021-11-18 17:11:48 -05:00
Heng Li
ac334639ce
r1110: default --cap-kalloc=1g; test more inv
...
See #816 and #823
2021-10-11 14:45:15 -04:00
Heng Li
546623dcb4
r1109: disable chain_skip_scale by default
...
Enabling the option slows down alignment, possibly because it fragments chains
in difficult regions.
2021-10-04 21:24:35 -04:00
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 )
...
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
32f552957e
Merge remote-tracking branch 'remotes/origin/master'
2021-08-07 10:40:02 -04:00
Heng Li
8a1d52bcbe
r1094: for --split-prefix update max_dp at the end
2021-08-06 21:40:43 -04:00
Heng Li
5180b70ff3
r1090: log wall-clock time for each read
2021-08-04 17:45:09 -04:00
