gatk-3.8

Author	SHA1	Message	Date
hanna	4fbb6d05d0	Refactoring. Push the revisions to the common aligner interface down into the aligner base classes. Hack the managed implementation to support the new interface. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-20 17:08:09 +00:00
hanna	38a030f2ba	Finishing off data transfer conduits for single alignment generator. Misc bug fixes elsewhere. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2101 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-20 15:21:59 +00:00
hanna	a95302fe98	Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still needs to plumbed through and it may leak memory. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-19 21:20:03 +00:00
hanna	ce5034dc5d	Finally reinstate the iterator-style interface. Get rid of some scaffolding code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2052 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-16 02:34:19 +00:00
hanna	15c14add4d	Repackage the aligner for better partitioning. The C aligner, for example, is now partitioned from the Java aligner, and both are partitioned from the more general- purpose BWT reader. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-13 22:55:27 +00:00