10 Commits (8a0338c7b7cbdd9ab91e120489dc7be47c8d2d0e)

Author	SHA1	Message	Date
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
Mark DePristo	f0d798d47c	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
Mark DePristo	38a2518668	Merge branch 'master' into rodRefactor	2011-07-27 15:34:54 -04:00
Mark DePristo	097828a466	ParsingEngine now maintains the list of rodBindings ... No longer try to reparser objects to find the right fields Direct support in RodBinding for getTags()	2011-07-27 11:36:53 -04:00
Mark DePristo	38969b9783	Prototype of RODBinding @Arguments instead of -B syntax ... Initial version of RodBinding class. Flow from walker Rodbinding @Arguments -> RMDTriplet (old system) -> GATK engine (standard). Will need refactoring.	2011-07-26 11:09:06 -04:00
Matt Hanna	8014fad6ff	Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-25 13:20:44 -04:00
Matt Hanna	2ac490dbdf	Fix improper detection of command-line arguments with missing values.	2011-07-25 13:20:00 -04:00
Mark DePristo	6fa17d86ae	Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator	2011-07-21 00:18:07 -04:00
Mark DePristo	9992c373be	Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.	2011-07-17 20:29:58 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00