Mark DePristo 84160bd83f Reorganization of Sample ... -- Moved Gender and Afflication to separate public enums -- PedReader 90% implemented -- Improve interface cleanup to XReadLines and UserException		2011-09-30 15:50:54 -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	Bugfix for file that must not exist on disk	2011-08-29 17:00:10 -04:00
gatk	Reorganization of Sample	2011-09-30 15:50:54 -04:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Renamed ReadBackedPileup getXSampleName() functions to getXSample	2011-09-30 10:02:57 -04:00
BaseTest.java	TestDataProvider now can be named	2011-09-22 17:04:32 -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	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00