Mark DePristo 0d593cff70 Refactor rsID and overlap detection in VariantOverlapAnnotator utility class ... -- Variants will be considered matching if they have the same reference allele and at least 1 common alternative allele. This matching algorithm determines how rsID are added back into the VariantContext we want to annotate, and as well determining the overlap FLAG attribute field. -- Updated VariantAnnotator and VariantsToVCF to use this class, removing its old stale implementation -- Added unit tests for this VariantOverlapAnnotator class -- Removed GATKVCFUtils.rsIDOfFirstRealVariant as this is now better to use VariantOverlapAnnotator -- Now requires strict allele matching, without any option to just use site annotation.		2013-06-10 15:51:13 -04:00
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src	Refactor rsID and overlap detection in VariantOverlapAnnotator utility class	2013-06-10 15:51:13 -04:00
test	This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK.	2013-06-10 10:44:42 -04:00