chartl 52a474b27d Fixed an issue with VCF combine in sites like the following: ... Broad: Filtered BC: No call These were being treated the same as Broad: Call BC: No call Added some verbosity to separate them. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3686 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-30 16:49:31 +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	Fixed an issue with VCF combine in sites like the following:	2010-06-30 16:49:31 +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