ebanks 4ff8b8fc0e 1. Fixing a bug that Mark found where indel-containing clipped reads would get an original cigar tag even when they didn't actually get modified. ... 2. Added some useful logging messages. 3. Added a oneoffs walker to calculate the number of realigned reads and intervals containing them. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3860 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-23 14:24:01 +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	1. Fixing a bug that Mark found where indel-containing clipped reads would get an original cigar tag even when they didn't actually get modified.	2010-07-23 14:24:01 +00:00
test	Improvements to variant combine. Now calculates AC/AN/AF correctly by calling into the VariantAnnotator engine. Automatically removes annotations that are inconsistent across incoming VCs (in simpleMerge). TODO bug fix for Guillermo/Eric.	2010-07-23 13:33:11 +00:00