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7 Commits (b3d0a13b3206d2c01cce43628ebbd5d531cf0152)

Author SHA1 Message Date
Rob Davies cca27c1ef5 Merge branch 'master' into master_fixes 
Conflicts:
	bwamem.c
	bwamem_pair.c
	example.c
 2013-03-13 12:12:28 +00:00
Heng Li 8f0d439913 prepare to replace the SAM printing code 
This move is dangerous as SAM printing is very complex, but it will benefit in
the long run. The planned change will reduce the redundancy, improves clarity
and most importantly makes it much easier to output multiple primary hits in an
optional tag.
 2013-03-11 21:25:17 -04:00
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 99907c98fb separated and improved SAM printing code 
This is for the PE mode. The routines may also be useful for bwa-sw, but
probably I won't change the old code.
 2013-02-11 15:29:03 -05:00
Heng Li 1fd51fc3f7 code backup 2013-02-07 14:36:18 -05:00
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 007c3eb75d Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00