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	14477bb48e	Unidirectional alignments with mismatches now working. Significant refactoring will be required. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1686 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-22 19:05:10 +00:00
hanna	c186a49d55	Time for a reorganization. Repackage generally useful alignment classes lower in the package structure, and create a subpackage for bwa-specific code. Repackage BWA alignment code away from BWT representation. Isolate byte- and word-packing streams in another package that will ultimately be killed off en masse. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1648 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-17 23:28:47 +00:00