asivache 8ffea42b75 about 10% improvement in SW alignment (and hence IndelRealigner!) speed by using c-style linearized array representation for matrices instead of java 2D arrays... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4751 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-30 00:06:50 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	about 10% improvement in SW alignment (and hence IndelRealigner!) speed by using c-style linearized array representation for matrices instead of java 2D arrays...	2010-11-30 00:06:50 +00:00
test	consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation).	2010-11-30 00:01:56 +00:00