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27 Commits (9228e48efdf00f4b1d1b76815406e98d74f12319)

Author SHA1 Message Date
Rob Davies 9228e48efd Merge branch 'master' into master_fixes 
Conflicts:
	Makefile
 2013-03-11 13:50:49 +00:00
Heng Li 740d2c1314 Match to 'N' costs -1, instead of 0. 
This is to prevent alignment through 'N'.
 2013-03-09 18:03:57 -05:00
Rob Davies 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
Heng Li 3e3236dfc4 r337: mem - always read even number of reads 
In the old code, we may read odd number of reads from an interleaved fastq.
 2013-03-07 11:00:15 -05:00
Heng Li 07921659cf move mem_fill_scmat() to bwa.{h,c} 2013-03-05 09:38:12 -05:00
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 f3cff1c609 r311: even tighter bw for CIGAR 2013-02-27 23:59:50 -05:00
Heng Li 292e92b602 r303: bugfix - wrong band width when CIGAR 2013-02-27 15:39:15 -05:00
Heng Li 98787f0ae0 r295: generate NM 2013-02-26 13:36:01 -05:00
Heng Li e70c7c2a71 r284: amend cross-reference hit 
I really hate this: complex and twisted logic for a nasty scenario that almost
never happens to short reads - but it may become serious when the reference
genome consists of many contigs.

On toy examples, the code seems to work. Don't know if it really works...
 2013-02-26 00:03:49 -05:00
Heng Li 61dd3bf13a r283: prepare for fixing cross-ref aln 2013-02-25 22:49:15 -05:00
Heng Li b4c38bcc1c append fasta/q comment 2013-02-23 16:57:34 -05:00
Heng Li 33236de32e a bit more error message 2013-02-23 16:44:02 -05:00
Heng Li ee4540c394 support read group in bwa-mem 2013-02-23 16:41:44 -05:00
Heng Li cfa7165036 cleanup index loading code 2013-02-23 16:10:48 -05:00
Heng Li 67543f19a1 code refactoring 2013-02-23 15:55:55 -05:00
Heng Li e613195e17 moved some common code to bwa.{c,h} 2013-02-23 15:30:46 -05:00
Heng Li 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
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 9c486fa41e updated APIs abit 2012-04-08 00:55:52 -04:00
Heng Li 3b5a9e5595 simplified bwa_se() interface 2012-04-08 00:12:34 -04:00
Heng Li ca93a71e6e complete single-end alignment 2012-04-08 00:02:06 -04:00
Heng Li 080726cb47 preliminary doc 2012-04-07 22:50:07 -04:00
Heng Li 1cef219667 compute CIGAR; rev seq not working 2012-04-07 22:00:03 -04:00
Heng Li 66154ff5d2 towards refined gapped; unfinished 2012-04-07 01:25:39 -04:00
Heng Li a1abfe9977 API: aln seems working 2012-04-07 00:23:01 -04:00