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gatk-3.8/public/java/test/org/broadinstitute/sting
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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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commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk Retire LegacyLocusIteratorByState 2013-01-11 15:17:18 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils LIBS optimizations and performance tools 2013-01-14 16:30:15 -05:00
AutoFormattingTimeUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
BaseTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MD5DB.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MD5Mismatch.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
WalkerTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00