7e0d70bfd3
r445: pair coordinate adjustment working
...
Next: mapq adjustment, which will be tricky...
2017-09-27 15:38:18 -04:00
a349d85280
r444: changed the way orientation is specified
...
The old model doesn't work with RF or RR orientation. The new model only works
with paired-end reads. For >2 segments, only FF is supported.
2017-09-27 12:33:10 -04:00
f611edf6f2
r443: don't filter small cm for split seg
2017-09-26 16:17:58 -04:00
1b1dd0cd57
r442: default max_gap to 200 in the sr mode
2017-09-26 13:31:01 -04:00
92ec8bd859
added the /1 or /2 suffix
2017-09-26 12:04:35 -04:00
55d1e4f638
r440: better chain filtering for PE reads
2017-09-26 11:03:36 -04:00
64c0ad6b35
r439: use splice-like chain gap cost between segs
...
This improves accuracy
2017-09-25 16:04:38 -04:00
9538c985aa
r438: fixed a rare case that leads to missing hits
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It is a bug in chaining.
2017-09-25 14:59:34 -04:00
8f25cfa36e
r437: fixed uninialized memory on rep_len
2017-09-25 14:22:45 -04:00
81008dd371
r436: working on short reads
...
The result is mixed - lots of room for tuning
2017-09-25 14:06:29 -04:00
3bb66e1ed3
multi-seg working on toy examples
2017-09-25 13:42:04 -04:00
a742f10164
get multi-seg code ready; probably not working yet
2017-09-24 15:17:17 -04:00
f0951141a1
allow to read multiple files interleaved
2017-09-24 14:33:05 -04:00
84bbc47152
two arrays should be freed with kfree(0,)
...
though in the current code, they are strictly equivalent.
2017-09-23 10:43:22 -04:00
5400191097
get batch sequence reader ready for paired-end
2017-09-22 09:56:31 -04:00
ef84e8b4e7
Merge branch 'master' into sr
2017-09-20 23:56:06 -04:00
1c948e0d1d
added GMAP iso-seq numbers
2017-09-20 23:54:02 -04:00
997011458c
fixed uninitialized value due to last commit
2017-09-20 15:10:48 -04:00
19d8eca3a1
moved array shrinking into chain_dp()
2017-09-20 14:58:57 -04:00
9943e5fdd0
backup
2017-09-20 14:35:46 -04:00
5b39a1b34b
Merge branch 'master' into sr
2017-09-20 12:24:08 -04:00
e3b5802b2e
r424: reduce memory for long query seqs
2017-09-20 12:22:13 -04:00
03d6894517
backup
2017-09-20 11:47:46 -04:00
645db3350e
Merge branch 'master' into sr
2017-09-20 11:15:14 -04:00
75e6bbc9f6
r421: removed the MM_F_SPLICE_BOTH mode
...
In the default splice mode, minimap2 applies two rounds of spliced alignment:
first assuming GT-AG to be the splice signal across all splicing sites and then
assuming CT-AC to be the signal. This is the idea strategy.
In the MM_F_SPLICE_BOTH mode, minimap2 applies one round of spliced alignment,
assuming GT-AG and CT-AC to be the splice signals AT THE SAME TIME. This will
be faster but less accurate. I don't think anyone would like to run minimap2 in
this mode, so I am removing it for clarity.
2017-09-20 11:11:53 -04:00
7a9b4db874
replaced --approx-ext with --sr
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--sr disables Z-drop and may come with other heurstics
2017-09-20 10:51:18 -04:00
4979e66ff0
Merge branch 'master' into sr
2017-09-20 10:20:31 -04:00
a686461e83
added github downloads counts
2017-09-20 10:11:58 -04:00
fd14618e61
no effective changes
2017-09-20 10:11:05 -04:00
5caadc28b4
Merge branch 'master' into sr
2017-09-19 22:31:14 -04:00
56014ba3db
avoid assertion failure given 0-length reads
2017-09-19 22:30:32 -04:00
b99c22840f
r414: avoid assertion failure for 0-length reads
2017-09-19 22:21:27 -04:00
c04420698e
fixed an uninitialized value
2017-09-19 16:21:21 -04:00
fb1bcc0084
early exploration
2017-09-19 16:18:28 -04:00
11081c6c27
r411: refactored kalloc for clarity
...
The new version is closer to K&R's original implementation.
2017-09-18 19:49:15 -04:00
60485790b4
updated version number in README
2017-09-17 20:25:54 -04:00
ea5a0cd17d
Release minimap2-2.2 (r409)
2017-09-17 20:08:47 -04:00
ffff953e2c
added python version badge
2017-09-17 17:15:55 -04:00
48705e9bfa
don't build for python-3.0 (unavailable in travis)
2017-09-17 17:07:42 -04:00
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
Heng Li