4cb5110d03
Merge branch 'master' into master_fixes
2013-04-22 09:51:07 +01:00
3f8caef33c
r381: fixed a bug when upper bound < max read len
2013-04-19 17:44:35 -04:00
be11e27e12
r378: bugfix - wrong CIGAR
...
This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
2013-04-19 12:00:37 -04:00
aabd990e8f
Merge branch 'master' into master_fixes
...
Conflicts:
Makefile
bwape.c
bwase.c
bwtsw2_aux.c
stdaln.c
2013-03-08 16:46:45 +00:00
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
3d33ab063e
Merge branch 'master' into master_fixes
...
Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
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
2fc469d0c9
code backup
2013-02-12 12:09:36 -05:00
6ad5a3c086
removed color-space support
...
which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
e5ab59db53
Multiple changes:
...
1. Removed bwa.{h,c}. I am not going to finish them anyway.
2. Updated to the latest khash.h, which should be faster.
3. Define 64-bit vector and 128-bit integer/vector in utils.h.
2013-02-12 09:50:28 -05:00
b081ac9b8b
Use wrapper functions to catch system errors
...
Use the wrapper functions in utils.c plus a few extra bits of error
checking code to catch system errors and exit non-zero when they occur.
2012-12-16 10:34:57 +00:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
64e353ce49
bugfix: bwa-sw PE segfault in rare case
2011-11-28 09:12:21 -05:00
dc4008936c
avoid duplicated XA tags
2011-11-19 14:52:47 -05:00
56a18659b6
crash under non-typical setting (by John Marshall)
2011-11-12 16:53:53 -05:00
7b4266a6e5
bugfix: integer overflow and strand error in sampe
2011-10-24 17:07:12 -04:00
ec307a10e6
PE seems working; more testing needed
2011-10-20 17:45:41 -04:00
d6155ecf90
fixed a couple of gcc warnings
2011-10-19 17:45:27 -04:00
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
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
Rob Davies
Heng Li
Heng Li