David Roazen d647ea4fdc Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache ... non-static to avoid problems when multiple references are used within the same thread (eg., during integration tests). This should kill the intermittent IndelRealignerIntegrationTest failures.		2011-07-01 16:04:30 -04:00
..
commandline	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
datasources/pipeline	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
gatk	The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.	2011-06-30 15:26:09 -04:00
jna	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
utils	Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache	2011-07-01 16:04:30 -04:00
BaseTest.java	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00