gatk-3.8

Author	SHA1	Message	Date
hanna	c63af32fc7	The BWA/C bindings were triggering the local aligner to repeatedly reload the ref genome. Make sure the reference genome is cached. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-03 00:01:55 +00:00
hanna	1896f334d9	Fixed collection of bugs in reads aligning to multiple locations. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1955 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-02 04:02:09 +00:00
hanna	1f0d852a48	Fix bug where alignments with indels would be busted because bwa reverses the read bases to undo a previous read base reverse that doesn't occur in the libbwa codepath. Also fixed some memory management issues. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a	2009-10-29 21:33:13 +00:00
hanna	f04b80d7db	Fixed epic memory leak. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1934 348d0f76-0448-11de-a6fe-93d51630548a	2009-10-29 16:32:43 +00:00
hanna	c9a3707cfd	Initial version of BWA/C bindings. Still lots of squirrels roaming the code. - Some cigar strings aren't right. - Memory leaks. - BWA codebase changes aren't committed to BWA tree. - Aligner interface butchered to support BWA/C-style alignments. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1928 348d0f76-0448-11de-a6fe-93d51630548a	2009-10-28 21:37:49 +00:00