Mark DePristo e36994e36b Refactored a FeatureManager class from RMDTrackBuilder ... New class handles (vastly more cleanly) the db of tribble codecs, features, and names for use throughout the GATK. Added SelfScopingFeatureCodec interface that allows a FeatureCodec to examine a file and determine if the file can be parsed. This is the first step towards allowing the GATK to dynamically determine the type of a RodBinding.		2011-08-08 14:04:46 -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	Adding missing import	2011-08-04 21:57:00 -04:00
gatk	Refactored a FeatureManager class from RMDTrackBuilder	2011-08-08 14:04:46 -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	Bug fix: call RodBinding.resetNameCounter() in new ParsingEngine() so that we don't magically misnumber arguments in the integration tests where the GATK is only instantiated once.	2011-08-04 12:06:10 -04:00
BaseTest.java	Added b37dbSNP129, needed for Queue	2011-08-07 11:26:07 -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