Heng Li
80d92c686f
r1298: fixed out-of-bound local alignment
...
I believe this would not lead to memory violation; it may occasionally include
a few base beyond the intended alignment start/end.
2026-04-24 13:25:19 -04:00
Heng Li
37a650f58c
output simulated identity with badread
2026-04-14 12:49:35 -04:00
Heng Li
4ca5a951ca
command line help
2026-04-13 23:52:07 -04:00
Heng Li
dd5b2c04b8
Merge remote-tracking branch 'remotes/origin/master'
2026-04-13 23:43:43 -04:00
Heng Li
ca6f4dc5e2
convert badread output to evaluation format
2026-04-13 23:43:11 -04:00
blawrence-ont
de3c6ec646
Fix use-after-free in mappy ( #1345 )
...
mm_map_aux() takes in |b._b| which can end up reallocating |km| at the
end of mm_map_frag_core(). Since the address of |km| is cached before
those calls it ends up pointing to freed memory.
This can result in a crash as seen in #1183 , however it also happens to
Just Work most of the time since the new allocation often lands at the
same address as the old one. Preloading ASAN or a similar replacement
allocator that doesn't have that behaviour results in a reliable crash.
2026-02-13 12:14:56 -05:00
Heng Li
e2542e6425
Merge remote-tracking branch 'remotes/origin/master'
2025-12-12 11:39:33 -05:00
Heng Li
9bb4d2bed4
r1290: support ds in Python
2025-12-12 11:39:01 -05:00
Alex Leonard
6d49eb690f
convert unmapped reads in sam2paf ( #1324 )
2025-10-05 19:43:23 -04:00
Heng Li
bd0cba5012
upgrade arm64-linux to v3
2025-09-09 13:52:16 -04:00
Heng Li
370f3f8236
add an alert about phishing
2025-09-09 11:23:09 -04:00
Heng Li
79c9cc186b
Release minimap2-2.30 (r1287)
2025-06-15 17:54:11 -04:00
Heng Li
ea4c8935bd
added one more example
...
This shows STAR doesn't try to match the GTR..YAG consensus.
2025-06-03 20:22:14 -04:00
Heng Li
3187782b1a
r1285: better --spsc support
2025-05-26 15:47:14 -04:00
Heng Li
005c9a1f6b
exoneval may skip terminal exons in aa mode
2025-05-17 23:06:41 -04:00
Heng Li
1fd85be6e2
Release minimap2-2.29 (r1283)
2025-04-18 13:41:47 -04:00
Heng Li
e616b0dacf
drafted the release notes
2025-04-18 13:17:13 -04:00
Heng Li
b58b97423a
r1281: with --write-junc, ignore aln with low mapQ
2025-04-17 21:46:54 -04:00
Heng Li
df9e650346
r1280: heuristic to avoid aligning full introns
...
This speeds up alignment a lot
2025-04-16 23:38:39 -04:00
Heng Li
7a540c37ca
r1278: reduced --min-dp-len to 20 for splice:sr
...
30% reduced time at 0.01% more junction errors
2025-04-16 21:55:59 -04:00
Heng Li
c19e3ccb86
r1277: don't apply rescored filtering with -P
...
Since v2.19-ish, minimap2 rescores base alignment based on the best alignment
of a read. This heuristic sometimes improve the mapping accuracy of the best
alignment but may too aggressively filter weaker hits.
Resolve #969
2025-04-14 22:26:47 -04:00
Heng Li
94d171b01e
r1276: skip unnecessary reverse spliced alignment
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for short-read RNA-seq only
2025-04-14 14:57:23 -04:00
Heng Li
ff312a2957
documented 2-pass in README
2025-04-13 17:14:44 -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
819b3bf017
r1274: a little better pass-1
...
Also fixed a bug in jump
2025-04-13 13:55:15 -04:00
Heng Li
e88110463a
r1273: reading pass1 junctions works
...
but we need extra logic when using them. Tomorrow.
2025-04-13 00:47:28 -04:00
Heng Li
fb81e150f2
r1272: support pass-1 junction processing
...
NOT tested yet
2025-04-12 23:15:04 -04:00
Heng Li
d930ea94ad
r1271: code refactoring in prep for 2-pass
2025-04-11 17:20:34 -04:00
Heng Li
a832a42f6f
r1270: fixed ts tag for PE reads
...
this also fixed the wrong --write-junc
2025-04-11 01:08:16 -04:00
Heng Li
a5411fc3c0
r1269: added --write-junc
...
in preparation for 2-pass
2025-04-11 01:00:15 -04:00
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
...
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
