9dbf152e31
added the pipeline script
2014-11-03 15:16:14 -05:00
40c4a6ffe1
better CLI; more comments
2014-11-03 12:09:29 -05:00
4bc01e90c8
not used any more
2014-11-03 11:51:25 -05:00
b7d0a2d537
first HLA typing script
2014-11-03 11:47:23 -05:00
9bf898fa10
r963: expose mask_level
2014-10-30 11:33:43 -04:00
6b4e6bf7dd
Merge branch 'dev'
2014-10-28 13:47:02 -04:00
6db2fd98aa
r960: merge changes from the master branch
2014-10-28 13:46:40 -04:00
9867634f72
r960: XA tags occasionally missing for PE
2014-10-28 13:43:26 -04:00
6f39715e6e
keep mate positions
2014-10-28 13:03:33 -04:00
5c87869d91
keep RG
2014-10-27 10:45:07 -04:00
dbe74ca9b8
Merge branch 'dev'
2014-10-25 23:10:25 -04:00
0f8a164bd3
bugfix: .ctw not generated properly
2014-10-25 23:08:29 -04:00
2bfcc421d9
bugfix: alignments not outputted
2014-10-25 22:13:31 -04:00
7327f8fa10
output all overlapping HLA hits
...
A contig longer than HLA genes may not get hits to HLA and thus won't be used
in typing.
2014-10-25 12:00:15 -04:00
33938e1ed0
save reads mapped to each HLA gene
...
for downstream typing
2014-10-24 16:54:48 -04:00
ba3ab0ca98
removed hla typing - not good enough
2014-10-24 14:52:16 -04:00
7a8019e6ee
removed debugging code
2014-10-24 14:51:05 -04:00
7c362bef69
added another paper
2014-10-23 15:15:20 -04:00
3a1da27c1c
added Bai et al. Seems good, too.
2014-10-23 15:08:18 -04:00
d61a1226a8
highlight Liu et al. It seems good.
2014-10-23 14:52:48 -04:00
b45442fbc1
Merge branch 'dev'
2014-10-23 14:43:06 -04:00
f005ea4bf3
coarse HLA typing and doc
2014-10-23 14:42:45 -04:00
af606fc31a
Merge branch 'dev'
2014-10-22 16:17:36 -04:00
3d129be642
r943: change the default -y to 20, but ...
...
for GRCh38 ALT, this is not enough. We need -y at least 40 to get high accuracy
because a locus at chr19 has 35 copies.
2014-10-22 12:42:58 -04:00
4177d6c2c7
r942: ignore ALT hits when counting n_sub for ...
...
non-ALT hits. Counting leads to underestimated mapQ.
2014-10-22 10:24:16 -04:00
60b728487a
r941: set a min length for 3rd-round seeding
2014-10-21 13:15:42 -04:00
282130a64e
r940: fixed a bug - missing primary hit
2014-10-21 12:57:49 -04:00
5e00d08346
r939: fixed a memory leak (issue #35 )
2014-10-21 09:26:19 -04:00
574098d034
updated directory name
2014-10-21 00:57:06 -04:00
acf4922fe4
Merge branch 'dev'
2014-10-21 00:55:19 -04:00
4260699a09
updated ALT readme due to recent changes
2014-10-21 00:55:00 -04:00
e3adc4275b
Merge branch 'dev'
2014-10-21 00:23:39 -04:00
76a15ea91b
r933: with bwa-postalt ready, drop option -g
2014-10-21 00:23:14 -04:00
2bfa3c767b
CLI help
2014-10-21 00:22:59 -04:00
497913d404
working largely as expected
2014-10-21 00:16:41 -04:00
a6b5a30dab
r930: use 3rd round seeding by default
...
This strategy is similar to the seeding heuristic used by LAST. When it is used
alone, it is not as accurate as the current seeding strategy at least for short
reads. However, it may do a better job for a long contig mapped to multiple ALT
contigs. This seeding strategy is also relatively cheap to perform.
2014-10-20 17:34:15 -04:00
038af2a551
r929: added simplified LAST-like seeding
2014-10-20 17:00:31 -04:00
25d45512d9
code backup
2014-10-20 14:17:56 -04:00
6f41a27e27
towards adding "-r" to postprocessing
2014-10-19 20:53:47 -04:00
3370ae9e35
r926: prepare to move -g to bwa-postalt.js
2014-10-19 20:43:53 -04:00
6e13694721
removed coverity
2014-10-17 21:46:11 -04:00
e65dc133f4
updated Travis CI link
2014-10-17 21:34:43 -04:00
f968b4b73d
added drone build
2014-10-17 21:28:44 -04:00
059c8eb899
for coverity
2014-10-17 21:03:11 -04:00
c4ac1bee88
added Travis CI integration
2014-10-17 17:02:26 -04:00
fa50c1b77f
Merge branch 'dev'
2014-10-17 16:39:24 -04:00
1b2eb4c9ab
added travis CI
2014-10-17 16:39:14 -04:00
d0a796b644
moved bwashm.o to AOBJS
2014-10-17 16:23:35 -04:00
c8ae5029b3
minor change to example
2014-10-17 16:19:21 -04:00
a06646493b
r915: fixed broken example.c
2014-10-17 16:17:28 -04:00
Heng Li