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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo fee9b367e4 VariantContext genotypes are now stored as GenotypeMap objects 
-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples
-- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type.
-- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous.  Now everything uses GenotypeMap with a specific ordering of samples (by name)
-- Integrationtests updated and all pass
 		2011-11-11 15:00:35 -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 VariantContext genotypes are now stored as GenotypeMap objects 2011-11-11 15:00:35 -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jna Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE 2011-09-23 21:03:22 -04:00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 VariantContext genotypes are now stored as GenotypeMap objects 2011-11-11 15:00:35 -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 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