Mark DePristo 03741fb640 Merge branch 'master' into rodRefactor ... Conflicts: public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java		2011-08-02 14:21:58 -04:00
..
arguments	Updating tools to use the RodBinding<T> syntax	2011-08-02 14:05:51 -04:00
datasources	Continuing refactoring of RefMetaDataTracker.	2011-07-28 17:48:28 -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	Merge branch 'master' into rodRefactor	2011-08-02 14:21:58 -04:00
report	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
traversals	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
walkers	Merge branch 'master' into rodRefactor	2011-08-02 14:21:58 -04:00
GenomeAnalysisEngineUnitTest.java	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
WalkerManagerUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00