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
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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	Cleaned up RefMetaDataTracker	2011-07-27 23:25:52 -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