Mark DePristo 1c03ebc82d Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP ... -- Reuse infrastructure for RODs for reads to implement general IntervalReferenceOrderedView so that both TraverseReads and TraverseActiveRegions can use the same underlying infrastructure -- TraverseActiveRegions now provides a meaningful RefMetaDataTracker to ActiveRegionWalker.map -- Cleanup misc. code as it came up -- Resolves GSA-808: Write general utility code to do rsID allele matching, hook up to UG and HC		2013-06-10 16:20:31 -04:00
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R	Updating gsalib for R-3.0 compatibility	2013-05-18 12:43:38 -04:00
c	…
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
keys	…
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	…
scala	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
testdata	Somehow the index of exampleDBSNP.vcf was missing	2013-05-28 15:29:43 -04:00