Eric Banks bdb1da30fd Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.		2011-08-10 22:43:08 -04:00
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arguments	Updating tools to use the RodBinding<T> syntax	2011-08-02 14:05:51 -04:00
datasources	Continuing progress towards RodBinding 1.0	2011-08-03 17:19:28 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
refdata	Refactored a FeatureManager class from RMDTrackBuilder	2011-08-08 14:04:46 -04:00
report	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
traversals	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
walkers	Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.	2011-08-10 22:43:08 -04:00
EngineFeaturesIntegrationTest.java	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
GenomeAnalysisEngineUnitTest.java	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00