Mark DePristo fa454c88bb UnitTests for VariantContext for chrCount, getSampleNames, Order function ... -- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2. -- Naming changes for getSamplesNameInOrder()		2011-11-17 20:37:22 -05:00
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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	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Continuing bugfixes to get new VC working	2011-11-16 10:39:17 -05:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00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	UnitTests for VariantContext for chrCount, getSampleNames, Order function	2011-11-17 20:37:22 -05:00
BaseTest.java	merge master	2011-10-25 16:08:39 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	…
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00