98f8966750
r329: ditch stdaln.{c,h}; no changes to bwa-mem
...
stdaln.{c,h} was written ten years ago. Its local and SW extension code are
actually buggy (though that rarely happens and usually does not affect the
results too much). ksw.{c,h} is more concise, potentially faster, less buggy,
and richer in features.
2013-03-05 12:00:24 -05:00
bb37e14d02
replace aln_global in bwase.c
2013-03-05 10:38:47 -05:00
cda85be059
fixed a couple bugs identified by gcc
...
Recent gcc is better.
2013-02-23 17:15:07 -05:00
ee4540c394
support read group in bwa-mem
2013-02-23 16:41:44 -05:00
cfa7165036
cleanup index loading code
2013-02-23 16:10:48 -05:00
904c3205c0
removed a few unused variables
...
These variables have been assigned but never actually used. Reported by
gcc-4.7. Lower version cannot give such warnings.
2013-02-23 13:26:50 -05:00
f122fad562
minor code clean up
...
bwtio.c is merged to bwt.c
2013-02-22 17:09:40 -05:00
6ad5a3c086
removed color-space support
...
which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
1cef219667
compute CIGAR; rev seq not working
2012-04-07 22:00:03 -04:00
66154ff5d2
towards refined gapped; unfinished
2012-04-07 01:25:39 -04:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
a471f1918b
bugfix: long-existing out-of-boundary bug
2012-03-19 13:45:09 -04:00
dc4008936c
avoid duplicated XA tags
2011-11-19 14:52:47 -05:00
7664795ffb
fixed a minor issue about +/-1
2011-10-25 13:00:41 -04:00
aabb807734
concatenate for-rev sequences in the end
2011-10-25 11:22:08 -04:00
7b4266a6e5
bugfix: integer overflow and strand error in sampe
2011-10-24 17:07:12 -04:00
1cb409aaf2
use forward-only pac to reduce memory
2011-10-21 12:03:14 -04:00
ec307a10e6
PE seems working; more testing needed
2011-10-20 17:45:41 -04:00
243e735431
applied patches from Alec Wysoker
2011-05-04 09:46:50 -04:00
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