depristo 919a86e876 Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@179 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-24 22:32:45 +00:00
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gatk	Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited...	2009-03-24 22:32:45 +00:00
playground	Fixed a bug wherein the loop variable for the second end of the pair was actually looping over the entire raw read (first and second ends combined).	2009-03-24 21:59:25 +00:00
utils	added some cleanup of code, and new junit targets to the build file	2009-03-24 21:16:12 +00:00