14b853499f
r369: updated example with the latest API
2017-09-14 22:44:10 -04:00
75ff7ceec5
r368: API documentation
2017-09-14 22:23:04 -04:00
e2823d4aee
r367: index reader optionally writes index
2017-09-14 21:18:13 -04:00
eb00521d9b
redesigned indexing and option APIs
2017-09-14 17:02:01 -04:00
0f7455cefa
r365: documented the "sr" preset
2017-09-14 12:57:21 -04:00
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
47e9d76ca1
further mapq tuning
2017-09-14 10:46:14 -04:00
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
6a82a21dee
r361: improved mapq for short reads
2017-09-13 15:32:39 -04:00
3c91d652dd
r360: allow to set integer max occ
2017-09-13 11:37:00 -04:00
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
eea9e851d8
Merge branch 'dev' into short
2017-09-11 09:32:28 -04:00
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
87a278d06a
Merge branch 'dev' into short
2017-09-09 08:49:58 -04:00
f422175e4e
r344: avoid unnecessary refName retrieval
2017-09-08 22:44:14 -04:00
709b6ec1f1
increase seed occurrences
2017-09-08 22:42:39 -04:00
0031158936
Merge branch 'master' into short
2017-09-07 11:41:32 -04:00
ef3f7ea2f2
Release minimap2-2.1.1 (r341)
2017-09-06 13:46:51 -04:00
8b9f2aaf04
r339: improved SIMD detection
...
old code does not check AVX2
2017-09-05 13:10:30 -04:00
46e8b6a4f9
r338: portable CPU dispatch, which is the default
...
working with gcc, icc, clang and msvc.
2017-09-03 20:29:24 -04:00
3c997ca016
r337: support CPU dispatch for gcc-4.8+
...
using __builtin_cpu_supports()
2017-09-03 14:29:49 -04:00
f9ccc522cd
Merge branch 'master' into short
2017-09-03 11:58:15 -04:00
101b8bb97d
r335: report an error if query can't be opened
2017-09-03 11:54:38 -04:00
0a3ebdc916
for better windows compatibility
2017-09-02 17:52:33 -04:00
743d26eab0
Merge pull request #20 from nanoporetech/msvc14
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ONT source code changes to compile with MSVC 14
2017-09-02 14:35:02 -07:00
62535ecd7f
Merge branch 'dev'
2017-09-01 10:06:21 -07:00
4db1c0295c
Fixed segfault caused when reading from index file
2017-09-01 15:48:59 +01:00
d4074874ee
r316: get rid of a harmless gcc warning
2017-09-01 20:25:27 +08:00
eccdb3a1ca
r315: added getopt from musl
2017-09-01 20:20:34 +08:00
a3c3db6b9b
ONT source code changes to compile with MSVC 14
2017-08-30 16:25:20 +01:00
c4080aaf7e
Merge branch 'master' into short
2017-08-28 07:02:22 +08:00
bf8246f872
Release minimap2-2.1-r311
2017-08-25 13:35:55 +08:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
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
64c1389e1a
Merge branch 'master' into splice
2017-08-17 23:39:27 +08:00
81cff97208
r299: support -h: output to stdout; return 0
2017-08-17 23:38:31 +08:00
bbb37d95f2
support inserting RG lines
2017-08-17 23:34:09 +08:00
2cde8d257c
r297: bidirectional RNA alignment
2017-08-17 06:02:44 -04:00
b5f5929bf9
r296: expose splicing related options to CLI
2017-08-13 21:37:51 -04:00
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
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
53b3265d84
r290: in techrep, explain spliced alignment
2017-08-12 15:40:49 -04:00
a23df2dc91
r289: changed CLI help only
2017-08-12 12:40:07 -04:00
5a74088b74
r288: changed max intron length to 200k
2017-08-12 12:39:21 -04:00
d240318741
r287: refined CLI options and manpage
2017-08-12 12:26:04 -04:00
0f4c823b0c
r286: ignore introns when computing max seg score
2017-08-12 10:58:16 -04:00
a99358bc3d
r282: reduced intron cost; added eval script
2017-08-11 00:06:01 -04:00
163fa36ee6
r281: don't open long gaps on query
2017-08-10 15:04:59 -04:00
c59b0781bc
r280: output introns as "N" in the cdna mode
2017-08-09 11:45:02 -04:00
7429b12164
Merge branch 'master' into cdna
2017-08-08 22:00:24 -04:00
Heng Li
Simon Harris
Stefan von Deylen