Mark DePristo 7b07c4e04e RefMetaDataTracker now has get() methods accepting RodBindings ... RodBinding no longer duplicates the get() methods in RMDT. This is just an object now that connects the command line system to the RMDT. Updated programs to use new style Added UnitTests for the RodBinding accessors.		2011-07-30 15:34:11 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
gatk	RefMetaDataTracker now has get() methods accepting RodBindings	2011-07-30 15:34:11 -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	Moved all of the distributed GATK code to archive.	2011-07-22 09:20:32 -04:00
BaseTest.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -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