292e92b602
r303: bugfix - wrong band width when CIGAR
2013-02-27 15:39:15 -05:00
98787f0ae0
r295: generate NM
2013-02-26 13:36:01 -05:00
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
61dd3bf13a
r283: prepare for fixing cross-ref aln
2013-02-25 22:49:15 -05:00
b4c38bcc1c
append fasta/q comment
2013-02-23 16:57:34 -05:00
33236de32e
a bit more error message
2013-02-23 16:44:02 -05:00
ee4540c394
support read group in bwa-mem
2013-02-23 16:41:44 -05:00
cfa7165036
cleanup index loading code
2013-02-23 16:10:48 -05:00
67543f19a1
code refactoring
2013-02-23 15:55:55 -05:00
e613195e17
moved some common code to bwa.{c,h}
2013-02-23 15:30:46 -05:00
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
9c486fa41e
updated APIs abit
2012-04-08 00:55:52 -04:00
3b5a9e5595
simplified bwa_se() interface
2012-04-08 00:12:34 -04:00
ca93a71e6e
complete single-end alignment
2012-04-08 00:02:06 -04:00
080726cb47
preliminary doc
2012-04-07 22:50:07 -04:00
1cef219667
compute CIGAR; rev seq not working
2012-04-07 22:00:03 -04:00
66154ff5d2
towards refined gapped; unfinished
2012-04-07 01:25:39 -04:00
a1abfe9977
API: aln seems working
2012-04-07 00:23:01 -04:00
Heng Li