David Roazen 24b72334b3 UnifiedGenotyper now correctly initializes the VariantAnnotator engine. ... This allows the annotation classes to perform any necessary initialization/validation. For example, it allows the SnpEff annotator to (among other things) validate its rod binding. This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding is present. Added an integration test to cover this case so that it doesn't break again.		2011-10-11 12:02:05 -04:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Bugfix for file that must not exist on disk	2011-08-29 17:00:10 -04:00
gatk	UnifiedGenotyper now correctly initializes the VariantAnnotator engine.	2011-10-11 12:02:05 -04:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Abandoning classfileset/rootfileset approach due to difficulting managing	2011-10-06 12:49:51 -04:00
BaseTest.java	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -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