Mark DePristo fee8d86f63 VariantEval optimization ... -- Use a LinkedHashMap not a TreeMap so iteration is faster. -- Note that with a lot of stratifications the update0 is taking up a lot of time. For example, with 822 samples and functional class and sample on there are 100K contexts and 30% of the runtime is just in the update0 call		2012-03-22 22:13:24 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	VariantEval optimization	2012-03-22 22:13:24 -04:00
test	Unified, standard IndelSummary metrics for VariantEval	2012-03-22 21:24:37 -04:00