4cb5110d03
Merge branch 'master' into master_fixes
2013-04-22 09:51:07 +01:00
f6ae0d4d0f
r382: similar treatment in bwa-sw (see r381)
2013-04-19 17:52:06 -04:00
8a078cc16d
Merge branch 'master' into master_fixes
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Conflicts:
bntseq.c
bwamem.c
2013-03-05 10:21:07 +00:00
1a451df800
prepare to ditch stdaln.{h,c}
2013-03-04 10:32:33 -05:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
557daabf38
bugfix: bug in the new ksw.c
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On my test data, one alignment is different, caused by polyA
2013-02-12 17:48:46 -05:00
28a7d501f2
updated to the latest ksw; NOT TESTED YET!!!
2013-02-12 16:35:05 -05:00
e5ab59db53
Multiple changes:
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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
4431e359e2
analyze isize distribution
2013-02-11 12:15:12 -05:00
b081ac9b8b
Use wrapper functions to catch system errors
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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
cd818687ac
r115: added -I and -S to bwasw
2012-04-17 20:43:43 -04:00
64e353ce49
bugfix: bwa-sw PE segfault in rare case
2011-11-28 09:12:21 -05:00
182cb2e89c
use standard SW when no SSE2
2011-11-19 19:38:21 -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
c8c79ef024
mate rescue seems working (not MT)
2011-11-06 16:20:40 -05:00
17eaac5a21
compute insert size distribution
2011-11-05 23:17:52 -04:00
Rob Davies
Heng Li
Heng Li