fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-16 05:27:55 +08:00
Code Issues Packages Projects Releases Wiki Activity
396 Commits 9 Branches 35 Tags
c8a019fae8fe83fc2d9a00a6784a44727827bea8
Commit Graph

185 Commits

Author SHA1 Message Date
Heng Li
e9c57f6d8b r402: exposed kseq (for API in mappy later) 2017-09-17 13:09:16 -04:00
Heng Li
c07f9f9a49 r372: default mm_verbose to 1, and change in main 2017-09-16 09:14:34 -04:00
Heng Li
14b853499f r369: updated example with the latest API 2017-09-14 22:44:10 -04:00
Heng Li
75ff7ceec5 r368: API documentation 2017-09-14 22:23:04 -04:00
Heng Li
e2823d4aee r367: index reader optionally writes index 2017-09-14 21:18:13 -04:00
Heng Li
eb00521d9b redesigned indexing and option APIs 2017-09-14 17:02:01 -04:00
Heng Li
0f7455cefa r365: documented the "sr" preset 2017-09-14 12:57:21 -04:00
Heng Li
4d3768bf26 r364: improved the mapq heuristics 
* use repetitive seed lengths, not counts
* compute n_sub to higher accuracy
* use bwa-mem mapq heuristic as a backup

For short single-end reads, minimap2's ROC is not as good as bwa-mem's, but is
close.
 2017-09-14 12:37:03 -04:00
Heng Li
47e9d76ca1 further mapq tuning 2017-09-14 10:46:14 -04:00
Heng Li
f4a8766283 r362: fixed overestimated chaining score 
Caused by ilog2_32(0)=-1. This bug was fixed once and reoccurred as I was
tuning the score function but forgot to apply the fix.
 2017-09-14 10:15:22 -04:00
Heng Li
6a82a21dee r361: improved mapq for short reads 2017-09-13 15:32:39 -04:00
Heng Li
3c91d652dd r360: allow to set integer max occ 2017-09-13 11:37:00 -04:00
Heng Li
d7f2ac1d4f better parameters for short reads 
It turns out the key problem is not the minimizer density. It is the max
occurrence that tends to affect results more, especially sensitivity. There is
still lots of work to do, but for now, it seems a good start.
 2017-09-12 16:11:23 -04:00
Heng Li
eea9e851d8 Merge branch 'dev' into short 2017-09-11 09:32:28 -04:00
Heng Li
c7c3585531 r347: merged mm_map_frag() into mm_map() 
mm_map_frag() was separated due to an earlier design that has been rejected.
 2017-09-10 15:02:55 -04:00
Heng Li
87a278d06a Merge branch 'dev' into short 2017-09-09 08:49:58 -04:00
Heng Li
f422175e4e r344: avoid unnecessary refName retrieval 2017-09-08 22:44:14 -04:00
Heng Li
709b6ec1f1 increase seed occurrences 2017-09-08 22:42:39 -04:00
Heng Li
0031158936 Merge branch 'master' into short 2017-09-07 11:41:32 -04:00
Heng Li
ef3f7ea2f2 Release minimap2-2.1.1 (r341) 2017-09-06 13:46:51 -04:00
Heng Li
8b9f2aaf04 r339: improved SIMD detection 
old code does not check AVX2
 2017-09-05 13:10:30 -04:00
Heng Li
46e8b6a4f9 r338: portable CPU dispatch, which is the default 
working with gcc, icc, clang and msvc.
 2017-09-03 20:29:24 -04:00
Heng Li
3c997ca016 r337: support CPU dispatch for gcc-4.8+ 
using __builtin_cpu_supports()
 2017-09-03 14:29:49 -04:00
Heng Li
f9ccc522cd Merge branch 'master' into short 2017-09-03 11:58:15 -04:00
Heng Li
101b8bb97d r335: report an error if query can't be opened 2017-09-03 11:54:38 -04:00
Heng Li
0a3ebdc916 for better windows compatibility 2017-09-02 17:52:33 -04:00
Heng Li
743d26eab0 Merge pull request #20 from nanoporetech/msvc14 
ONT source code changes to compile with MSVC 14
 2017-09-02 14:35:02 -07:00
Heng Li
62535ecd7f Merge branch 'dev' 2017-09-01 10:06:21 -07:00
Simon Harris
4db1c0295c Fixed segfault caused when reading from index file 2017-09-01 15:48:59 +01:00
Heng Li
d4074874ee r316: get rid of a harmless gcc warning 2017-09-01 20:25:27 +08:00
Heng Li
eccdb3a1ca r315: added getopt from musl 2017-09-01 20:20:34 +08:00
Stefan von Deylen
a3c3db6b9b ONT source code changes to compile with MSVC 14 2017-08-30 16:25:20 +01:00
Heng Li
c4080aaf7e Merge branch 'master' into short 2017-08-28 07:02:22 +08:00
Heng Li
bf8246f872 Release minimap2-2.1-r311 2017-08-25 13:35:55 +08:00
Heng Li
0fe1a224ab r309: improved SAM header output 2017-08-25 10:35:58 +08:00
Heng Li
993a2bb521 r301: separate introns from deletions 
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
 2017-08-18 15:31:15 +08:00
Heng Li
64c1389e1a Merge branch 'master' into splice 2017-08-17 23:39:27 +08:00
Heng Li
81cff97208 r299: support -h: output to stdout; return 0 2017-08-17 23:38:31 +08:00
Heng Li
bbb37d95f2 support inserting RG lines 2017-08-17 23:34:09 +08:00
Heng Li
2cde8d257c r297: bidirectional RNA alignment 2017-08-17 06:02:44 -04:00
Heng Li
b5f5929bf9 r296: expose splicing related options to CLI 2017-08-13 21:37:51 -04:00
Heng Li
28f86688ab r295: gap closure from the middle of non-HPC k 
This WILL slightly affect the result of genomic mapping, but hopefully
in the good direction.
 2017-08-12 23:48:43 -04:00
Heng Li
43506edbc5 backup: preliminary boundary alignment 2017-08-12 23:10:14 -04:00
Heng Li
53b3265d84 r290: in techrep, explain spliced alignment 2017-08-12 15:40:49 -04:00
Heng Li
a23df2dc91 r289: changed CLI help only 2017-08-12 12:40:07 -04:00
Heng Li
5a74088b74 r288: changed max intron length to 200k 2017-08-12 12:39:21 -04:00
Heng Li
d240318741 r287: refined CLI options and manpage 2017-08-12 12:26:04 -04:00
Heng Li
0f4c823b0c r286: ignore introns when computing max seg score 2017-08-12 10:58:16 -04:00
Heng Li
a99358bc3d r282: reduced intron cost; added eval script 2017-08-11 00:06:01 -04:00
Heng Li
163fa36ee6 r281: don't open long gaps on query 2017-08-10 15:04:59 -04:00