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
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()
...
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
...
old code does not check AVX2
2017-09-05 13:10:30 -04:00
46e8b6a4f9
r338: portable CPU dispatch, which is the default
...
working with gcc, icc, clang and msvc.
2017-09-03 20:29:24 -04:00
3c997ca016
r337: support CPU dispatch for gcc-4.8+
...
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
Heng Li