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