Mark DePristo 46e7370128 this.allele, getAlleles(), and getAltAlleles() now return List not set ... -- Changes associated code throughout the codebase -- Updated necessary (but minimal) UnitTests to reflect new behavior -- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC		2011-10-09 11:45:55 -07:00
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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	this.allele, getAlleles(), and getAltAlleles() now return List not set	2011-10-09 11:45:55 -07:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00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	this.allele, getAlleles(), and getAltAlleles() now return List not set	2011-10-09 11:45:55 -07:00
BaseTest.java	Made the BaseTest.testDir absolute	2011-10-06 22:33:21 -04:00
MD5DB.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00