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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo 80d9b7011c Complete rewrite of low-level machinery of LIBS, not hooked up 
-- AlignmentStateMachine does what SAMRecordAlignmentState should really do.  It's correct in that it's more accurate than the LIB_position tests themselves.  This is a non-broken, correct implementation.  Needs cleanup, contracts, etc.
-- This version is like 6x slower than the original implementation (according to the google caliper benchmark here).  Obvious optimizations for future commit
 		2013-01-11 15:17:16 -05:00
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commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk LIBS can now (optionally) track the unique reads it uses from the underlying read iterator 2013-01-11 15:17:16 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils Complete rewrite of low-level machinery of LIBS, not hooked up 2013-01-11 15:17:16 -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