gatk-3.8

Author	SHA1	Message	Date
Eric Banks	b20c4d5286	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
Mark DePristo	80924d24de	Single positional arguments are now treated as names unless they actually match a tribble feature	2011-08-08 19:26:27 -04:00
Mark DePristo	8f696c7731	Continuing progress towards RodBinding 1.0 -- Cleaning up old interface to RMDT, docs and contracts added -- Proper type checking for RodBinding for cases where the Tribble type isn't found or is the wrong type	2011-08-03 17:19:28 -04:00
Mark DePristo	b5e843f8f0	Approaching the end for the new RodBinding system -- support for explicit naming of bindings (-X:name,type x) -- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2) -- ParserEngineUnitTest expanded to cover all of the Rodbinding cases -- RodBindingUnitTest tests all of the low-level accessors -- Parsing engine throws UserExceptions when bad bindings are provided on the command line	2011-08-02 22:00:06 -04:00
Mark DePristo	3a27a25cfc	Validates that the tribble binding provides the right object types at startup Tests to ensure this remains working	2011-08-02 20:11:24 -04:00