kshakir 2fd816ac5f Updated ordering of integration tests. GVC > VR > AVC ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4669 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-14 06:33:28 +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	Temp bug fix for indel genotyper: if there are two or more variant contexts at a site, just choose the first one containing an indel and genotype that. There might be cases where IGv2 emits 2 indel variant contexts in at the same ref location which made us fail there. A better solution will be to form underlying haplotypes supported by reads and compute likelihoods of that.	2010-11-14 00:21:54 +00:00
test	Updated ordering of integration tests. GVC > VR > AVC	2010-11-14 06:33:28 +00:00