6ad5a3c086
removed color-space support
...
which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
91debf412b
move smem iterators to bwamem.{c,h}
2013-01-31 13:59:48 -05:00
292f9061ab
r132: optionally copy FASTA/Q comment to SAM
2012-10-26 12:54:32 -04:00
3abfd0743a
r131: r128 plus remote changes
2012-06-28 14:52:18 -04:00
f44edd4fc9
r128: more conservative chaining filter
2012-06-28 14:51:02 -04:00
09ee115dcc
r126: release bwa-0.6.2
2012-06-19 13:29:44 -04:00
29ed2d8287
rename the "api" branch as "master"
2012-06-19 13:13:29 -04:00
d97ff6bf72
r124: updated version number
2012-04-17 20:45:07 -04:00
790df95e1a
updated revision number
2012-04-02 11:43:32 -04:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
91a4a0c8ea
Release bwa-0.6.1
2011-11-28 09:52:07 -05:00
bf65b6463a
fastmap: optionally output the original query seq
2011-11-24 19:44:21 -05:00
b5170e0efa
output the NM tag
2011-11-24 11:51:38 -05:00
196b50dde3
optionally mark multi-part hits as secondary
2011-11-23 23:39:59 -05:00
182cb2e89c
use standard SW when no SSE2
2011-11-19 19:38:21 -05:00
dc4008936c
avoid duplicated XA tags
2011-11-19 14:52:47 -05:00
8f89f55484
fixed a segfault when there are too few good bases.
2011-11-17 22:13:38 -05:00
770a5f2ae0
Release BWA-0.6.0
2011-11-12 20:04:39 -05:00
7544aca718
updated revision number
2011-11-12 16:56:21 -05:00
8060693411
multithreading works again
2011-11-12 16:50:58 -05:00
fa8cfe5567
bugfix: wrong mapping quality
2011-11-12 12:12:45 -05:00
b42910ada6
proper mate information
2011-11-12 00:49:21 -05:00
e06685db45
bwa-sw PE seems working (SAM is incorrect)
2011-11-07 00:51:43 -05:00
673ae4aaf8
throw an error if insufficient memory during index
2011-10-31 13:26:24 -04:00
02946df28a
fixed a off-by-1 bug
2011-10-27 13:55:48 -04:00
7babb54e4c
drop smem based mapping algorithm
...
While we can compute smems very efficiently, there is still a long way to get
the alignment. On simulated data, this smem-based algorithm is 4X faster than
bwasw and twice as fast as bowtie2, but the accuracy is far lower than bwasw
and even lower than bowtie2 in the high-mapQ range. I am kind of sure that if
we continue to increase the mapping accuracy, the speed will approach to bwasw,
if not slower.
Smem-based mapping algorithm is still interesting, but given that I am short of
time, I will not explore it further.
2011-10-27 10:56:09 -04:00
7664795ffb
fixed a minor issue about +/-1
2011-10-25 13:00:41 -04:00
7168f5c10a
updated revision number
2011-10-25 12:50:19 -04:00
22c2252e15
added bidirectional bwt; seems buggy
2011-10-25 00:22:28 -04:00
7b4266a6e5
bugfix: integer overflow and strand error in sampe
2011-10-24 17:07:12 -04:00
b59fd2bf47
fixed an integer overflow
2011-10-24 14:39:57 -04:00
8f3c780552
fixed a potential int overflow
2011-10-24 14:22:39 -04:00
1f970b4557
updated revision number
2011-10-24 14:14:42 -04:00
26b77eabef
updated version number
2011-10-21 12:32:00 -04:00
46123639cf
removed reverse pac; bwa is not working right now
2011-10-20 12:09:35 -04:00
d70754e234
update revision number
2011-10-14 10:32:31 -04:00
72563c38f3
automatically choose the algorithm for BWT
2011-06-09 17:33:25 -04:00
a74523a68d
increase maximum barcode length limit to 63bp
2011-06-09 17:17:13 -04:00
243e735431
applied patches from Alec Wysoker
2011-05-04 09:46:50 -04:00
87664941b0
Release bwa-0.5.9 (r16)
2011-01-24 22:00:24 -05:00
7fd8948689
Added recommendation for PacBio reads
2011-01-22 13:20:11 -05:00
1d7d8be9e8
Put BC: to both ends
2011-01-18 20:16:57 -05:00
51d354cd28
Added barcode support
2011-01-15 15:35:39 -05:00
10721ca602
Added an option to accept Illumina 1.3+ fastq
2011-01-15 14:07:08 -05:00
f335b33624
fixed a bug in bwase: no RG for unmapped read pairs
2011-01-15 10:32:45 -05:00
5e30884730
Update to the latest modfication 0.5.9rc1-2. Update ChangeLog
2011-01-13 20:54:10 -05:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Heng Li
Heng Li