Mark DePristo 83fcc06e28 LIBS optimizations and performance tools ... -- Made LIBSPerformance a full featured CommandLineProgram, and it can be used to assess the LIBS performance by reading a provided BAM -- ReadStateManager now provides a clean interface to iterate in sample order the per-sample read states, allowing us to avoid many map.get calls -- Moved updateReadStates to ReadStateManager -- Removed the unnecessary wrapping of an iterator in ReadStateManager -- readStatesBySample is now a LinkedHashMap so that iteration occurs in LIBS sample order, allowing us to avoid many unnecessary calls to map.get iterating over samples. Now those are just map native iterations -- Restructured collectPendingReads for simplicity, removing redundant and consolidating common range checks. The new piece is code is much clearer and avoids several unnecessary function calls		2013-01-14 16:30:15 -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	LIBS optimizations and performance tools	2013-01-14 16:30:15 -05:00
test	LIBS optimizations and performance tools	2013-01-14 16:30:15 -05:00