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Author SHA1 Message Date
Heng Li
c07f9f9a49 r372: default mm_verbose to 1, and change in main 2017-09-16 09:14:34 -04:00
Heng Li
446bde214d first python version 2017-09-16 08:44:47 -04:00
Heng Li
5966e5d6e4 make reader_open() work even if idxopt is NULL 2017-09-15 11:29:49 -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
1b44275802 Merge branch 'master' into sr 2017-09-13 11:10:23 -04:00
Heng Li
2f2b11624a reverted to the Travis badge as it is faster 2017-09-13 10:50:03 -04:00
Heng Li
cb57bd6146 updated badges 2017-09-13 10:46:25 -04:00
Heng Li
885db1233d updated badges 
for fun
 2017-09-13 10:29:41 -04:00
Heng Li
2bf2f137dd added a license badge 2017-09-13 10:03:15 -04:00
Heng Li
8706f6bdf8 Merge branch 'master' into sr 2017-09-12 22:37:46 -04:00
Heng Li
2028e8c266 show bioconda version 2017-09-12 16:21:49 -04:00
Heng Li
0cc8d277ba changed to the "install with conda" badge 2017-09-12 16:20:01 -04:00
Heng Li
14f0cce4e2 malformatted conda badge 2017-09-12 16:17:07 -04:00
Heng Li
8ddbf7169f added bioconda download link 2017-09-12 16:16:26 -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
59c822b722 removed some commented code 
which *might* return at some time later
 2017-09-09 08:38:39 -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) v2.1.1 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
f4a71d447f Merge branch 'master' of github.com:lh3/minimap2 2017-09-03 11:07:32 -04:00
Heng Li
6db9b7579c Better MSVC support 
* get rid of alloca()
* no variable-sized arrays
 2017-09-03 11:05:55 -04:00
Heng Li
f50b9a14a7 last commit can't be compiled 2017-09-02 21:07:19 -04:00
Heng Li
33423e1568 get rid of the last var-sized array in ksort 
for MSVC
 2017-09-02 21:05:03 -04:00
Heng Li
aeb6b5eeb1 fixed an issue due to the 64-bit assumption 2017-09-02 19:29:52 -04:00
Heng Li
3d3fde8224 replaced remaining alloca() 2017-09-02 18:50:42 -04:00
Heng Li
6f4cbf4f12 ok, %zu is a C99 feature... 2017-09-02 18:48:14 -04:00
Heng Li
2a5d5b6f12 print size_t with %zu instead of %lu 2017-09-02 18:37:48 -04:00
Heng Li
3d48516885 reduced a heap allocation 
which *might* be frequent for short reads
 2017-09-02 18:32:45 -04:00
Heng Li
00416c76d1 for MinGW32 compatibility 
get rid of alloca()
 2017-09-02 18:23:29 -04:00
Heng Li
2b8681ead7 fixed memory leak in example 2017-09-02 17:55:25 -04:00
Heng Li
0a3ebdc916 for better windows compatibility 2017-09-02 17:52:33 -04:00
Heng Li
b97620afed moved gettimeofday() to misc.c 2017-09-02 17:40:10 -04:00