delangel 2ac938fe4e 1) ... Minor fixes to avoid crashes vs CG indel files: - Add count for complex events, not just insertions and deletions - Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions. 2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-30 21:08:25 +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)	2010-11-30 21:08:25 +00:00
test	The dev team has decided to change the filter that is added to records that are set to monomorphic by Beagle. It no longer lists the reference allele. Added those filters to the header of the output VCF file. Finally, we no longer use R2=NaN values coming from Beagle.	2010-11-30 17:19:54 +00:00