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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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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
..
datasources Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP 2013-06-10 16:20:31 -04:00
downsampling Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage 2013-05-29 12:07:12 -04:00
executive Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters 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
iterators Refactor LIBS into utils.locusiterator before refactoring 2013-01-11 15:17:16 -05:00
refdata Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
samples Trivial update to ceutrio.ped file to make it really the CEU trio sample names 2013-05-14 17:08:13 -04:00
traversals Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP 2013-06-10 16:20:31 -04:00
walkers Fixes to get accurate read counts for Read traversals 2013-05-21 15:24:07 -04:00
CommandLineGATKUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java 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
GenomeAnalysisEngineUnitTest.java Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine. 2013-03-06 12:38:59 -05:00
MaxRuntimeIntegrationTest.java Subshard timeouts in the GATK 2013-05-15 07:00:39 -04:00
ReadMetricsUnitTest.java Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP 2013-06-10 16:20:31 -04:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00