depristo e3956148ac removing unused fastqtobam ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4985 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-13 14:29:32 +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	removing unused fastqtobam	2011-01-13 14:29:32 +00:00
test	Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.	2011-01-13 14:12:30 +00:00