Mark DePristo d9cdc5d006 Optimization: track alleles in the PerReadAlleleLikelihoodMap with a HashSet ... -- The previous version of PerReadAlleleLikelihoodMap only stored the alleles in an ArrayList, and used ArrayList.contains() to determine if an allele was already present in the map. This is very slow with many alleles. Now keeps both the ArrayList (for get() performance) and a Set of alleles for contains().		2013-05-21 16:18:56 -04:00
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src	Optimization: track alleles in the PerReadAlleleLikelihoodMap with a HashSet	2013-05-21 16:18:56 -04:00
test	Fixes to get accurate read counts for Read traversals	2013-05-21 15:24:07 -04:00