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
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Approaching the end for the new RodBinding system	2011-08-02 22:00:06 -04:00
gatk	Approaching the end for the new RodBinding system	2011-08-02 22:00:06 -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	--variants throughout integrationtests	2011-08-02 20:28:47 -04:00
BaseTest.java	Merge branch 'master' into rodRefactor	2011-08-02 14:21:58 -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