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24 Commits (6beab5f76535fd8d1829ad3463765150a8e27684)

Author SHA1 Message Date
Rob Davies 6beab5f765 Merge branch 'master' into master_fixes 
Merge changes to commit c5434ac (0.7.0 release)

Conflicts:
	Makefile
	bwamem.c
 2013-03-01 10:22:49 +00:00
Rob Davies 3d33ab063e Merge branch 'master' into master_fixes 
Merged to master version b621d3a

Conflicts:
	Makefile
	bntseq.c
	bwa.c
	bwase.c
	bwaseqio.c
	bwtaln.c
	bwtindex.c
	bwtio.c
	bwtmisc.c
	bwtsw2_aux.c
	cs2nt.c
	fastmap.c
	khash.h
	kseq.h
	ksw.c
	kvec.h
	simple_dp.c
	utils.c
	utils.h
 2013-03-01 09:37:46 +00:00
Heng Li 4bb0bdddca r306: introduce clipping penalty 
More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
 2013-02-27 21:13:39 -05:00
Heng Li b621d3ae38 r301: left-align indels 
Don't know why the change is working...
 2013-02-27 00:42:19 -05:00
Heng Li ea8f4f4d34 clean bill from valgrind 2013-02-20 20:26:57 -05:00
Heng Li 557daabf38 bugfix: bug in the new ksw.c 
On my test data, one alignment is different, caused by polyA
 2013-02-12 17:48:46 -05:00
Heng Li 28a7d501f2 updated to the latest ksw; NOT TESTED YET!!! 2013-02-12 16:35:05 -05:00
Heng Li d8e4d57956 Don't use narrow band. 
I may retry this feature if the profilter indicates that this greatly helps.
 2013-02-07 21:22:54 -05:00
Heng Li 14e6a7bdb9 fixed a silly bug in ksw_extend() 
Query return value is assigned to the target variable and vice versa...
 2013-02-05 17:29:03 -05:00
Heng Li 1e16f3e701 calling ksw_global(); ksw_extend() is buggy! 2013-02-05 17:13:12 -05:00
Heng Li 86caae811e added comments 2013-02-05 16:58:35 -05:00
Heng Li 1bc9712cd8 explicitly use bit to keep bt matrix 
This also simplifies backtracking.
 2013-02-05 16:28:15 -05:00
Heng Li 7e1466c885 implemented NW backtrack 2013-02-05 16:05:53 -05:00
Heng Li d91e320972 towards reimplementing banded NW alignment 2013-02-05 12:06:56 -05:00
Heng Li 788e9d1e3d fixed a couple of leaks; buggy atm 2013-02-04 15:40:26 -05:00
Heng Li ba18db1a9f sw extension works for the simplest case 2013-02-04 12:37:38 -05:00
Heng Li f83dea36d8 no effective changes 2013-02-03 18:16:43 -05:00
Heng Li 2093398231 bugfix: the first line is wrong 2013-02-03 17:47:57 -05:00
Heng Li e8a1962efe code backup; it is wrong 2013-02-03 17:25:40 -05:00
Heng Li 92b084e553 reimplemented SW extension; not tested yet 2013-02-02 16:38:21 -05:00
Rob Davies 55f1b36534 New wrapper for gzclose; added err_fflush calls and made it call fsync too. 
Added a new utils.c wrapper err_gzclose and changed gzclose calls to use it.

Put in some more err_fflush calls before files being written are closed.

Made err_fflush call fsync.  This is useful for remote filesystems where
errors may not be reported on fflush or fclose as problems at the server
end may only be detected after they have returned.  If bwa is being used
only to write to local filesystems, calling fsync is not really necessary.
To disable it, comment out #define FSYNC_ON_FLUSH in utils.c.
 2013-01-03 16:57:37 +00:00
Rob Davies 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
Heng Li 182cb2e89c use standard SW when no SSE2 2011-11-19 19:38:21 -05:00
Heng Li c8c79ef024 mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00