ebanks 337b54136f 2 fixes. For Mark: when insertions can be partially left-aligned, we were reading off the wrong bases. For GS post: the stored VariantContext.REFERENCE_BASE_FOR_INDEL_KEY needs to be updated when left-aligning because it can change. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5375 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-04 21:00:08 +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	2 fixes. For Mark: when insertions can be partially left-aligned, we were reading off the wrong bases. For GS post: the stored VariantContext.REFERENCE_BASE_FOR_INDEL_KEY needs to be updated when left-aligning because it can change.	2011-03-04 21:00:08 +00:00
test	A change to the definition of CpG sites (is now, from 5' to 3' a CG dinucleotide in the reference, and the CpG site is at the C, rather than either at the C or a G).	2011-03-04 15:36:07 +00:00