gatk-3.8

Author	SHA1	Message	Date
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
Mark A. DePristo	defa3cfe85	Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.	2011-06-30 14:59:58 -04:00
David Roazen	f18fffd625	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
Eric Banks	33c67a139c	Wrong package; this should have been moved when VC got moved in from Tribble	2011-06-29 14:56:02 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00