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Author SHA1 Message Date
Heng Li
ca6f4dc5e2 convert badread output to evaluation format 2026-04-13 23:43:11 -04:00
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) v2.30 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) v2.29 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 
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
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
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