cf93e5c0a1
more functional minimap2.py; added categories
2017-09-17 17:06:39 -04:00
0b660c70e2
syntax error
2017-09-17 16:02:06 -04:00
5715c423ff
exposed timer and verbose-level to mappy
2017-09-17 15:21:36 -04:00
c8a019fae8
exposed fasta/q reader to mappy
2017-09-17 14:41:59 -04:00
e9c57f6d8b
r402: exposed kseq (for API in mappy later)
2017-09-17 13:09:16 -04:00
3edf2a9130
renamed mm2-lite.py to minimap2.py
2017-09-17 09:41:37 -04:00
89151b2588
added python 3.6 test
2017-09-17 00:55:31 -04:00
cc0a538bd3
try python3 in travis
2017-09-17 00:49:16 -04:00
e9e86f5a48
try python build again
2017-09-17 00:46:39 -04:00
c0779f0359
revert to the old travis
...
can't get cython working...
2017-09-17 00:40:18 -04:00
875ea06302
install cython with travis
2017-09-17 00:37:09 -04:00
2c7007a11b
try again
2017-09-17 00:31:15 -04:00
fc87b767ba
travis for python (test)
2017-09-17 00:28:34 -04:00
dba8b50ee9
change python version to rc1
2017-09-17 00:08:54 -04:00
d5012a1b17
this is embarrassing: rename again to mappy
2017-09-17 00:05:30 -04:00
eaaf53c9b8
bumped version number
...
due to conflict with PyPI (already uploaded)
2017-09-16 23:51:49 -04:00
ef46a8aed4
remaining minimap2=>mmappy in doc
2017-09-16 23:49:02 -04:00
28fd3d63fd
renamed module name from minimap2 to mmappy
...
minimap2 clashed with minimap2 from conda
2017-09-16 23:29:41 -04:00
06b79c4a52
Merge branch 'master' of github.com:lh3/minimap2
2017-09-16 22:53:34 -04:00
8cdaae0935
fixed a few typos
...
eh... a missing fix
2017-09-16 22:53:24 -04:00
38aa9aa9a7
eh... a missing fix
2017-09-16 22:52:52 -04:00
f8cb865ec5
fixed a few typos
2017-09-16 22:52:26 -04:00
1d90742b35
fixed hyperlink
2017-09-16 22:46:30 -04:00
5103cea7d3
load python README.rst into setup.py
2017-09-16 22:43:52 -04:00
7da9a08a6f
reformat
2017-09-16 22:36:19 -04:00
ddc2c6f279
change to rst for PyPI
2017-09-16 22:29:52 -04:00
7e98b18ba2
for python3 compatibility
2017-09-16 20:37:49 -04:00
3544c60c71
allow to test if index is present
2017-09-16 20:09:17 -04:00
6b66ec6167
minor
2017-09-16 19:55:33 -04:00
cb7fb77bb9
python documentation
2017-09-16 19:50:52 -04:00
322e5a16e5
minor tweaks to python
2017-09-16 18:11:43 -04:00
10bd4079d1
fixed a bug on rev strand; added example
2017-09-16 17:51:13 -04:00
b22703a354
improvement to the python binding
2017-09-16 11:14:01 -04:00
7e34bea7ab
minor
2017-09-16 09:30:00 -04:00
c07f9f9a49
r372: default mm_verbose to 1, and change in main
2017-09-16 09:14:34 -04:00
446bde214d
first python version
2017-09-16 08:44:47 -04:00
5966e5d6e4
make reader_open() work even if idxopt is NULL
2017-09-15 11:29:49 -04:00
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
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
Heng Li