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
a55aac8a43
added section about the completeness of GRCh38
2014-10-17 15:42:17 -04:00
6deafdadca
Merge branch 'dev'
2014-10-17 12:14:40 -04:00
8af17b3478
r912: very minor improvement
2014-10-17 12:14:18 -04:00
c280274331
r911: check before attempting adding
2014-10-17 12:13:09 -04:00
44a185f2c1
Merge branch 'dev'
2014-10-17 09:43:52 -04:00
67c2d69218
made the header smaller
2014-10-16 17:17:02 -04:00
fab1f2b561
README on ALT mapping
2014-10-16 17:15:39 -04:00
76a365a95f
r907: revert to -g.8 by default
2014-10-16 15:56:33 -04:00
d8d8b230d1
r906: don't reduce non-ALT mapQ by default
2014-10-16 15:15:23 -04:00
e318d8e7e5
r905: lower peak RAM for "shm -f"
2014-10-16 11:22:09 -04:00
ad0da1418f
r904: optionally create tmp files for shm staging
2014-10-16 10:52:59 -04:00
97a3102c89
r903: updated revision number
2014-10-16 10:26:25 -04:00
57436ab405
added -lrt on Linux
2014-10-15 23:23:01 -04:00
6804f17d38
replaced Sys V shm with POSIX shm
2014-10-15 23:06:03 -04:00
bfd5e1840f
shm works on small files, but not large ones
...
I don't know why. SHMMAX, SHMALL and SHMMNI are large enough.
2014-10-15 15:44:06 -04:00
6a0952948d
shared memory
2014-10-15 14:44:08 -04:00
c5e859b49f
r898: read the index into a single memory block
...
Prepare for shared memory. Not used now.
2014-10-15 12:27:45 -04:00
c44357926f
updated README, a bit
2014-10-14 23:46:59 -04:00
71277f0fea
r896: more flexible ALT reading
2014-10-14 23:37:24 -04:00
2a18fa114f
r895: increase the default max_XA_hits_alt to 200
...
Because there are >100 HLA haplotypes
2014-10-14 16:58:42 -04:00
Heng Li