6 Commits (c83f9432ebb8455661d56092775a68cabb93baec)

Author	SHA1	Message	Date
Mark DePristo	c83f9432eb	Cleaned up RefMetaDataTracker ... Renamed many functions to more clearly state what they are actually doing Removed unnecessary / unused functionality, reducing interface complexity Updated all uses of this code in GATK Added generic, type-safe accessors to RefMetaDataTracker such as public <T> List<T> getValues(final String name, Class<T> clazz) Added standard refMetaDataTracker accessors to RodBinding, so you can do everything you can for generic rods with the tracker directly with with the RodBinding	2011-07-27 23:25:52 -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	9dfb57168a	RodBinding source is no longer assumed to be a file	2011-07-26 13:59:44 -04:00
Mark DePristo	d0badd5bd6	RodBinding subclassed to VariantContextRodBinding for easy access to VariantContext providing RODs	2011-07-26 13:54:55 -04:00
Mark DePristo	7ab8b53339	Support for List<RodBinding> argument type	2011-07-26 11:37:31 -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