Mark DePristo 7eea6b8f92 ReservoirDownsampler optimizations ... -- Add an option to not allocate always ArrayLists of targetSampleSize, but rather the previous size + MARGIN. This helps for LIBS as most of the time we don't need nearly so much space as we allow -- consumeFinalizedItems returns an empty list if the reservior is empty, which it often true for our BAM files with low coverage -- Allow empty sample lists for SamplePartitioner as these are used by the RefTraversals and other non-read based traversals Make the reservoir downsampler use a linked list, rather than a fixed sized array list, in the expectFewOverflows case		2013-01-14 16:30:16 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	ReservoirDownsampler optimizations	2013-01-14 16:30:16 -05:00
test	Refactor PerSampleReadStates into a separate class	2013-01-14 16:30:16 -05:00