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
1b44275802
Merge branch 'master' into sr
2017-09-13 11:10:23 -04:00
2f2b11624a
reverted to the Travis badge as it is faster
2017-09-13 10:50:03 -04:00
cb57bd6146
updated badges
2017-09-13 10:46:25 -04:00
885db1233d
updated badges
...
for fun
2017-09-13 10:29:41 -04:00
2bf2f137dd
added a license badge
2017-09-13 10:03:15 -04:00
8706f6bdf8
Merge branch 'master' into sr
2017-09-12 22:37:46 -04:00
2028e8c266
show bioconda version
2017-09-12 16:21:49 -04:00
0cc8d277ba
changed to the "install with conda" badge
2017-09-12 16:20:01 -04:00
14f0cce4e2
malformatted conda badge
2017-09-12 16:17:07 -04:00
8ddbf7169f
added bioconda download link
2017-09-12 16:16:26 -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()
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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
59c822b722
removed some commented code
...
which *might* return at some time later
2017-09-09 08:38:39 -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
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old code does not check AVX2
2017-09-05 13:10:30 -04:00
46e8b6a4f9
r338: portable CPU dispatch, which is the default
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working with gcc, icc, clang and msvc.
2017-09-03 20:29:24 -04:00
3c997ca016
r337: support CPU dispatch for gcc-4.8+
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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
f4a71d447f
Merge branch 'master' of github.com:lh3/minimap2
2017-09-03 11:07:32 -04:00
6db9b7579c
Better MSVC support
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* get rid of alloca()
* no variable-sized arrays
2017-09-03 11:05:55 -04:00
f50b9a14a7
last commit can't be compiled
2017-09-02 21:07:19 -04:00
33423e1568
get rid of the last var-sized array in ksort
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for MSVC
2017-09-02 21:05:03 -04:00
aeb6b5eeb1
fixed an issue due to the 64-bit assumption
2017-09-02 19:29:52 -04:00
3d3fde8224
replaced remaining alloca()
2017-09-02 18:50:42 -04:00
6f4cbf4f12
ok, %zu is a C99 feature...
2017-09-02 18:48:14 -04:00
2a5d5b6f12
print size_t with %zu instead of %lu
2017-09-02 18:37:48 -04:00
3d48516885
reduced a heap allocation
...
which *might* be frequent for short reads
2017-09-02 18:32:45 -04:00
00416c76d1
for MinGW32 compatibility
...
get rid of alloca()
2017-09-02 18:23:29 -04:00
2b8681ead7
fixed memory leak in example
2017-09-02 17:55:25 -04:00
0a3ebdc916
for better windows compatibility
2017-09-02 17:52:33 -04:00
b97620afed
moved gettimeofday() to misc.c
2017-09-02 17:40:10 -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
40665d1083
Merge pull request #23 from simonrharris/segfaultfix
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Fixed segfault caused when reading from index file
2017-09-02 00:46:55 +08:00
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
Heng Li
Simon Harris
Stefan von Deylen