kiran 758f8aa89b Experimental refactoring. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@674 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-12 19:46:34 +00:00
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gatk	Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete.	2009-05-12 18:52:42 +00:00
playground	Experimental refactoring.	2009-05-12 19:46:34 +00:00
utils	added method indelPileup. Generates a pileup of indel alleles given reads and ofsets (as from a locus walker).	2009-05-12 15:08:24 +00:00