hanna c9d5345150 Redo StratifiedAlignmentContext to use ReadBackedPileup's stratification options. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3699 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-01 02:46:05 +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/org	Redo StratifiedAlignmentContext to use ReadBackedPileup's stratification options.	2010-07-01 02:46:05 +00:00
test/org/broadinstitute/sting	Refactored and generalized the database/comp annotations in VariantAnnotator. Now one can provide comp tracks as with VariantEval (e.g. compHapMap, comp1KG_CEU) and the INFO field will be annotated with the track name (without the 'comp') if the variant record overlaps a comp site (e.g. ...;1KG_CEU;...). This means that you can now pass 1kg calls to the Unified Genotyper and automatically have records annotated with their presence in 1kg.	2010-06-30 16:37:31 +00:00