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Author SHA1 Message Date
Heng Li c8a019fae8 exposed fasta/q reader to mappy 2017-09-17 14:41:59 -04:00
Heng Li e9c57f6d8b r402: exposed kseq (for API in mappy later) 2017-09-17 13:09:16 -04:00
Heng Li 3edf2a9130 renamed mm2-lite.py to minimap2.py 2017-09-17 09:41:37 -04:00
Heng Li 89151b2588 added python 3.6 test 2017-09-17 00:55:31 -04:00
Heng Li cc0a538bd3 try python3 in travis 2017-09-17 00:49:16 -04:00
Heng Li e9e86f5a48 try python build again 2017-09-17 00:46:39 -04:00
Heng Li c0779f0359 revert to the old travis 
can't get cython working...
 2017-09-17 00:40:18 -04:00
Heng Li 875ea06302 install cython with travis 2017-09-17 00:37:09 -04:00
Heng Li 2c7007a11b try again 2017-09-17 00:31:15 -04:00
Heng Li fc87b767ba travis for python (test) 2017-09-17 00:28:34 -04:00
Heng Li dba8b50ee9 change python version to rc1 2017-09-17 00:08:54 -04:00
Heng Li d5012a1b17 this is embarrassing: rename again to mappy 2017-09-17 00:05:30 -04:00
Heng Li eaaf53c9b8 bumped version number 
due to conflict with PyPI (already uploaded)
 2017-09-16 23:51:49 -04:00
Heng Li ef46a8aed4 remaining minimap2=>mmappy in doc 2017-09-16 23:49:02 -04:00
Heng Li 28fd3d63fd renamed module name from minimap2 to mmappy 
minimap2 clashed with minimap2 from conda
 2017-09-16 23:29:41 -04:00
Heng Li 06b79c4a52 Merge branch 'master' of github.com:lh3/minimap2 2017-09-16 22:53:34 -04:00
Heng Li 8cdaae0935 fixed a few typos 
eh... a missing fix
 2017-09-16 22:53:24 -04:00
Heng Li 38aa9aa9a7 eh... a missing fix 2017-09-16 22:52:52 -04:00
Heng Li f8cb865ec5 fixed a few typos 2017-09-16 22:52:26 -04:00
Heng Li 1d90742b35 fixed hyperlink 2017-09-16 22:46:30 -04:00
Heng Li 5103cea7d3 load python README.rst into setup.py 2017-09-16 22:43:52 -04:00
Heng Li 7da9a08a6f reformat 2017-09-16 22:36:19 -04:00
Heng Li ddc2c6f279 change to rst for PyPI 2017-09-16 22:29:52 -04:00
Heng Li 7e98b18ba2 for python3 compatibility 2017-09-16 20:37:49 -04:00
Heng Li 3544c60c71 allow to test if index is present 2017-09-16 20:09:17 -04:00
Heng Li 6b66ec6167 minor 2017-09-16 19:55:33 -04:00
Heng Li cb7fb77bb9 python documentation 2017-09-16 19:50:52 -04:00
Heng Li 322e5a16e5 minor tweaks to python 2017-09-16 18:11:43 -04:00
Heng Li 10bd4079d1 fixed a bug on rev strand; added example 2017-09-16 17:51:13 -04:00
Heng Li b22703a354 improvement to the python binding 2017-09-16 11:14:01 -04:00
Heng Li 7e34bea7ab minor 2017-09-16 09:30:00 -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 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) 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
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
Heng Li 40665d1083 Merge pull request #23 from simonrharris/segfaultfix 
Fixed segfault caused when reading from index file
 2017-09-02 00:46:55 +08:00
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
Heng Li c4080aaf7e Merge branch 'master' into short 2017-08-28 07:02:22 +08:00
Heng Li 2641613686 various minor improvements 2017-08-25 17:56:16 +08:00
Heng Li 5f96d851a8 added spliced alignment example 2017-08-25 14:11:54 +08:00
Heng Li bf8246f872 Release minimap2-2.1-r311 2017-08-25 13:35:55 +08:00
Heng Li 5cbd776651 test data for spliced alignment 2017-08-25 13:17:56 +08:00
Heng Li 0fe1a224ab r309: improved SAM header output 2017-08-25 10:35:58 +08:00
Heng Li 240f6caaff backup manuscript 2017-08-24 22:05:14 +08:00
Heng Li b8bdac7e64 backup 2017-08-22 17:45:01 +08:00
Heng Li 19e4b2aab0 backup 2017-08-20 22:10:03 +08:00
Heng Li ce859dbe1c evaluate introns 
this simplies the metrics
 2017-08-20 21:54:59 +08:00
Heng Li a4c41f64a5 the final version 
to be replaced by intron-eval
 2017-08-20 21:54:35 +08:00
Heng Li 5ed2faf270 minor tuning to the matching rules 2017-08-19 16:21:49 +08:00
Heng Li 8058c85b72 moved appendix to methods; detailed splice aln 2017-08-18 23:33:57 +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