Mark DePristo 9b5c79b49d Renamed InferredGeneticContext to CommonInfo ... -- I have no idea why I named this InferredGeneticContext, a totally meaningless term -- Renamed to CommonInfo. -- Made package protected, as no one should use this outside of VariantContext and Genotype -- UGEngine was using IGC constant, but it's now using the public one in VariantContext.		2011-11-14 14:28:52 -05:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	GenotypeMap contains a Map, not extends it	2011-11-14 12:55:03 -05:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00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	Renamed InferredGeneticContext to CommonInfo	2011-11-14 14:28:52 -05:00
BaseTest.java	merge master	2011-10-25 16:08:39 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00