Geraldine Van der Auwera d70bf64737 Created new DeprecatedToolChecks class ... --Based on existing code in GenomeAnalysisEngine --Hashmaps hold mapping of deprecated tool name to version number and recommended replacement (if any) --Using FastUtils for maps; specifically Object2ObjectMap but there could be a better type for Strings... --Added user exception for deprecated annotations --Added deprecation check to AnnotationInterfaceManager.validateAnnotations --Run when annotations are initialized --Made annotation sets instead of lists		2013-03-20 06:46:02 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Created new DeprecatedToolChecks class	2013-03-20 06:46:02 -04:00
test	AssessNA12878 bugfixes	2013-03-18 15:48:08 -04:00