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
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R	Moving some of the released R scripts into public from private	2011-06-30 14:55:25 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache	2011-07-01 16:04:30 -04:00
packages	Fixes to the packaging system to work with the new directory structure.	2011-06-30 18:27:17 -04:00
scala	Path-related fixes to the private queue pipeline tests.	2011-07-01 13:41:34 -04:00
testdata	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00