delangel a2d6cef181 Weird corner condition fix in indel genotyper: if there are 2 consecutive locations on candidate sites to genotype, we can get both when calling getVariantContexts and if we are triggering on an extended event - this leads to confusion and we can end up picking the wrong one. So, we require start of the vc to be the same as the start of the ref locus to be sure. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4812 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-09 19:34:23 +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	Weird corner condition fix in indel genotyper: if there are 2 consecutive locations on candidate sites to genotype, we can get both when calling getVariantContexts and if we are triggering on an extended event - this leads to confusion and we can end up picking the wrong one. So, we require start of the vc to be the same as the start of the ref locus to be sure.	2010-12-09 19:34:23 +00:00
test	Better testing of BAQ. Now really handles soft clipped reads properly by doing an expensive copy operation :-( will need to be transformed to a ByteBuffer in the near future.	2010-12-08 17:37:00 +00:00