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03d6894517 backup Heng Li 2017-09-20 11:47:46 -04:00
645db3350e Merge branch 'master' into sr Heng Li 2017-09-20 11:15:14 -04:00
75e6bbc9f6 r421: removed the MM_F_SPLICE_BOTH mode Heng Li 2017-09-20 11:11:53 -04:00
7a9b4db874 replaced --approx-ext with --sr Heng Li 2017-09-20 10:51:18 -04:00
4979e66ff0 Merge branch 'master' into sr Heng Li 2017-09-20 10:20:31 -04:00
a686461e83 added github downloads counts Heng Li 2017-09-20 10:11:58 -04:00
fd14618e61 no effective changes Heng Li 2017-09-20 10:11:05 -04:00
5caadc28b4 Merge branch 'master' into sr Heng Li 2017-09-19 22:31:14 -04:00
56014ba3db avoid assertion failure given 0-length reads Heng Li 2017-09-19 22:30:32 -04:00
b99c22840f r414: avoid assertion failure for 0-length reads Heng Li 2017-09-19 22:21:27 -04:00
c04420698e fixed an uninitialized value Heng Li 2017-09-19 16:21:21 -04:00
fb1bcc0084 early exploration Heng Li 2017-09-19 16:18:28 -04:00
11081c6c27 r411: refactored kalloc for clarity Heng Li 2017-09-18 19:49:15 -04:00
60485790b4 updated version number in README Heng Li 2017-09-17 20:25:54 -04:00
ea5a0cd17d Release minimap2-2.2 (r409) v2.2 Heng Li 2017-09-17 20:08:47 -04:00
ffff953e2c added python version badge Heng Li 2017-09-17 17:15:55 -04:00
48705e9bfa don't build for python-3.0 (unavailable in travis) Heng Li 2017-09-17 17:07:42 -04:00
cf93e5c0a1 more functional minimap2.py; added categories Heng Li 2017-09-17 17:06:39 -04:00
0b660c70e2 syntax error Heng Li 2017-09-17 16:02:06 -04:00
5715c423ff exposed timer and verbose-level to mappy Heng Li 2017-09-17 15:21:36 -04:00
c8a019fae8 exposed fasta/q reader to mappy Heng Li 2017-09-17 14:41:59 -04:00
e9c57f6d8b r402: exposed kseq (for API in mappy later) Heng Li 2017-09-17 13:09:16 -04:00
3edf2a9130 renamed mm2-lite.py to minimap2.py Heng Li 2017-09-17 09:41:37 -04:00
89151b2588 added python 3.6 test Heng Li 2017-09-17 00:55:31 -04:00
cc0a538bd3 try python3 in travis Heng Li 2017-09-17 00:49:16 -04:00
e9e86f5a48 try python build again Heng Li 2017-09-17 00:46:39 -04:00
c0779f0359 revert to the old travis Heng Li 2017-09-17 00:40:18 -04:00
875ea06302 install cython with travis Heng Li 2017-09-17 00:37:09 -04:00
2c7007a11b try again Heng Li 2017-09-17 00:31:15 -04:00
fc87b767ba travis for python (test) Heng Li 2017-09-17 00:28:34 -04:00
dba8b50ee9 change python version to rc1 Heng Li 2017-09-17 00:08:54 -04:00
d5012a1b17 this is embarrassing: rename again to mappy Heng Li 2017-09-17 00:05:30 -04:00
eaaf53c9b8 bumped version number Heng Li 2017-09-16 23:51:49 -04:00
ef46a8aed4 remaining minimap2=>mmappy in doc Heng Li 2017-09-16 23:49:02 -04:00
28fd3d63fd renamed module name from minimap2 to mmappy Heng Li 2017-09-16 23:29:41 -04:00
06b79c4a52 Merge branch 'master' of github.com:lh3/minimap2 Heng Li 2017-09-16 22:53:34 -04:00
8cdaae0935 fixed a few typos Heng Li 2017-09-16 22:52:26 -04:00
38aa9aa9a7 eh... a missing fix Heng Li 2017-09-16 22:52:52 -04:00
f8cb865ec5 fixed a few typos Heng Li 2017-09-16 22:52:26 -04:00
1d90742b35 fixed hyperlink Heng Li 2017-09-16 22:46:30 -04:00
5103cea7d3 load python README.rst into setup.py Heng Li 2017-09-16 22:43:52 -04:00
7da9a08a6f reformat Heng Li 2017-09-16 22:36:19 -04:00
ddc2c6f279 change to rst for PyPI Heng Li 2017-09-16 22:29:52 -04:00
7e98b18ba2 for python3 compatibility Heng Li 2017-09-16 20:37:49 -04:00
3544c60c71 allow to test if index is present Heng Li 2017-09-16 20:09:17 -04:00
6b66ec6167 minor Heng Li 2017-09-16 19:55:33 -04:00
cb7fb77bb9 python documentation Heng Li 2017-09-16 19:50:52 -04:00
322e5a16e5 minor tweaks to python Heng Li 2017-09-16 18:11:43 -04:00
10bd4079d1 fixed a bug on rev strand; added example Heng Li 2017-09-16 17:51:13 -04:00
b22703a354 improvement to the python binding Heng Li 2017-09-16 11:14:01 -04:00
7e34bea7ab minor Heng Li 2017-09-16 09:30:00 -04:00
c07f9f9a49 r372: default mm_verbose to 1, and change in main Heng Li 2017-09-16 09:14:34 -04:00
446bde214d first python version Heng Li 2017-09-16 08:44:47 -04:00
5966e5d6e4 make reader_open() work even if idxopt is NULL Heng Li 2017-09-15 11:29:49 -04:00
14b853499f r369: updated example with the latest API Heng Li 2017-09-14 22:44:10 -04:00
75ff7ceec5 r368: API documentation Heng Li 2017-09-14 22:23:04 -04:00
e2823d4aee r367: index reader optionally writes index Heng Li 2017-09-14 21:18:13 -04:00
eb00521d9b redesigned indexing and option APIs Heng Li 2017-09-14 17:02:01 -04:00
0f7455cefa r365: documented the "sr" preset Heng Li 2017-09-14 12:57:21 -04:00
4d3768bf26 r364: improved the mapq heuristics Heng Li 2017-09-14 12:37:03 -04:00
47e9d76ca1 further mapq tuning Heng Li 2017-09-14 10:46:14 -04:00
f4a8766283 r362: fixed overestimated chaining score Heng Li 2017-09-14 10:15:22 -04:00
6a82a21dee r361: improved mapq for short reads Heng Li 2017-09-13 15:32:39 -04:00
3c91d652dd r360: allow to set integer max occ Heng Li 2017-09-13 11:37:00 -04:00
1b44275802 Merge branch 'master' into sr Heng Li 2017-09-13 11:10:23 -04:00
2f2b11624a reverted to the Travis badge as it is faster Heng Li 2017-09-13 10:50:03 -04:00
cb57bd6146 updated badges Heng Li 2017-09-13 10:46:25 -04:00
885db1233d updated badges Heng Li 2017-09-13 10:29:41 -04:00
2bf2f137dd added a license badge Heng Li 2017-09-13 10:03:15 -04:00
8706f6bdf8 Merge branch 'master' into sr Heng Li 2017-09-12 22:37:46 -04:00
2028e8c266 show bioconda version Heng Li 2017-09-12 16:21:49 -04:00
0cc8d277ba changed to the "install with conda" badge Heng Li 2017-09-12 16:20:01 -04:00
14f0cce4e2 malformatted conda badge Heng Li 2017-09-12 16:17:07 -04:00
8ddbf7169f added bioconda download link Heng Li 2017-09-12 16:16:26 -04:00
d7f2ac1d4f better parameters for short reads Heng Li 2017-09-12 16:11:23 -04:00
eea9e851d8 Merge branch 'dev' into short Heng Li 2017-09-11 09:32:28 -04:00
c7c3585531 r347: merged mm_map_frag() into mm_map() Heng Li 2017-09-10 15:02:55 -04:00
87a278d06a Merge branch 'dev' into short Heng Li 2017-09-09 08:49:58 -04:00
59c822b722 removed some commented code Heng Li 2017-09-09 08:38:39 -04:00
f422175e4e r344: avoid unnecessary refName retrieval Heng Li 2017-09-08 22:44:14 -04:00
709b6ec1f1 increase seed occurrences Heng Li 2017-09-08 22:42:39 -04:00
0031158936 Merge branch 'master' into short Heng Li 2017-09-07 11:41:32 -04:00
ef3f7ea2f2 Release minimap2-2.1.1 (r341) v2.1.1 Heng Li 2017-09-06 13:46:51 -04:00
8b9f2aaf04 r339: improved SIMD detection Heng Li 2017-09-05 13:10:30 -04:00
46e8b6a4f9 r338: portable CPU dispatch, which is the default Heng Li 2017-09-03 20:29:24 -04:00
3c997ca016 r337: support CPU dispatch for gcc-4.8+ Heng Li 2017-09-03 14:29:49 -04:00
f9ccc522cd Merge branch 'master' into short Heng Li 2017-09-03 11:58:15 -04:00
101b8bb97d r335: report an error if query can't be opened Heng Li 2017-09-03 11:54:38 -04:00
f4a71d447f Merge branch 'master' of github.com:lh3/minimap2 Heng Li 2017-09-03 11:07:32 -04:00
6db9b7579c Better MSVC support Heng Li 2017-09-02 18:23:29 -04:00
f50b9a14a7 last commit can't be compiled Heng Li 2017-09-02 21:07:19 -04:00
33423e1568 get rid of the last var-sized array in ksort Heng Li 2017-09-02 21:05:03 -04:00
aeb6b5eeb1 fixed an issue due to the 64-bit assumption Heng Li 2017-09-02 19:29:52 -04:00
3d3fde8224 replaced remaining alloca() Heng Li 2017-09-02 18:50:42 -04:00
6f4cbf4f12 ok, %zu is a C99 feature... Heng Li 2017-09-02 18:48:14 -04:00
2a5d5b6f12 print size_t with %zu instead of %lu Heng Li 2017-09-02 18:37:48 -04:00
3d48516885 reduced a heap allocation Heng Li 2017-09-02 18:32:45 -04:00
00416c76d1 for MinGW32 compatibility Heng Li 2017-09-02 18:23:29 -04:00
2b8681ead7 fixed memory leak in example Heng Li 2017-09-02 17:55:25 -04:00
0a3ebdc916 for better windows compatibility Heng Li 2017-09-02 17:52:33 -04:00

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