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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providers	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
reads	Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage	2013-05-29 12:07:12 -04:00
reference	Remove auto-creation of fai/dict files for fasta references	2013-04-02 18:34:08 -04:00
rmd	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00