25366c7220
Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual). Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments.
2013-03-05 20:48:16 +00:00
98f8966750
r329: ditch stdaln.{c,h}; no changes to bwa-mem
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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
8a078cc16d
Merge branch 'master' into master_fixes
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Conflicts:
bntseq.c
bwamem.c
2013-03-05 10:21:07 +00:00
35fb7f9fdf
r315: move kopen.o out of libbwa.a
2013-03-01 11:47:51 -05:00
6beab5f765
Merge branch 'master' into master_fixes
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Merge changes to commit c5434ac
2013-03-01 10:22:49 +00:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
df7c3f0000
r308: added a new API to convert region to CIGAR
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and an example program demonstrating how to do single-end alignment in <50
lines of C code.
2013-02-27 22:28:29 -05:00
64d92d26df
more documentation in ksw.h
2013-02-27 21:40:46 -05:00
570e082b38
change CC back to gcc
2013-02-24 23:45:40 -05:00
6e7903e9f3
added kopen support
2013-02-23 17:09:23 -05:00
e613195e17
moved some common code to bwa.{c,h}
2013-02-23 15:30:46 -05:00
6230f86799
merged bwtmisc.c to bwtindex.c
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bwtmisc.c implements routines related to indexing
2013-02-22 17:23:34 -05:00
f122fad562
minor code clean up
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bwtio.c is merged to bwt.c
2013-02-22 17:09:40 -05:00
df1ff2b36e
better and proper way to infer orinentation
2013-02-14 12:59:32 -05:00
2fc469d0c9
code backup
2013-02-12 12:09:36 -05:00
95d18449b3
merge bseq.{h,c} to utils.{h,c}
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I do not like many small files.
2013-02-12 10:36:15 -05:00
6ad5a3c086
removed color-space support
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which has been broken since 0.6.x
2013-02-12 10:21:17 -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
59eaf650ac
code backup
2013-02-11 10:59:38 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
91debf412b
move smem iterators to bwamem.{c,h}
2013-01-31 13:59:48 -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
1cef219667
compute CIGAR; rev seq not working
2012-04-07 22:00:03 -04:00
a1abfe9977
API: aln seems working
2012-04-07 00:23:01 -04:00
182cb2e89c
use standard SW when no SSE2
2011-11-19 19:38:21 -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
f56edd07dd
forward-backward search seems working
2011-10-25 12:31:36 -04:00
22c2252e15
added bidirectional bwt; seems buggy
2011-10-25 00:22:28 -04:00
b96f180a15
move bwt_gen/* to the root directory
2011-10-20 11:56:24 -04:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Jon Sorenson
Heng Li
Rob Davies
Heng Li