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
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
gatk	Merge branch 'master' into rodRefactor	2011-08-02 14:21:58 -04:00
jna	Memory limits changed from Int to Double.	2011-07-21 22:57:18 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Updating tools to use the RodBinding<T> syntax	2011-08-02 14:05:51 -04:00
BaseTest.java	Merge branch 'master' into rodRefactor	2011-08-02 14:21:58 -04:00
MD5DB.java	Go for global integrationtest path first, if possible.	2011-07-26 17:35:30 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00