Mark DePristo 526b524c3c CombineVariants with new RodBinding. Bugfix ... -- CombineVariants now uses the new RodBinding syntax, -V / --variants. Passed all integration tests on first run -- Exposed gapping bug in the List<RodBinding<T>> system now fixed. ParserEngine now has a addRodBinding() that is called by RodBindingArgumentTypeDescriptor when it encounters each RodBinding. This allows the system to work with collection types that are recursively parsed by the system.		2011-08-07 20:16:51 -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	Adding missing import	2011-08-04 21:57:00 -04:00
gatk	CombineVariants with new RodBinding. Bugfix	2011-08-07 20:16:51 -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	Bug fix: call RodBinding.resetNameCounter() in new ParsingEngine() so that we don't magically misnumber arguments in the integration tests where the GATK is only instantiated once.	2011-08-04 12:06:10 -04:00
BaseTest.java	Added b37dbSNP129, needed for Queue	2011-08-07 11:26:07 -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