gatk-3.8

Author	SHA1	Message	Date
hanna	3b79f9eddc	Support 'N's and other mismatch characters in the reference. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1721 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-24 21:41:30 +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