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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo 9e23c592e6 ReadBackedPileup cleanup 
-- Only ReadBackedPileupImpl (concrete class) and ReadBackedPileup (interface) live, moved all functionality of AbstractReadBackedPileup into the impl
-- ReadBackedPileupImpl was literally a shell class after we removed extended events.  A few bits of code cleanup and we reduced a bunch of class complexity in the gatk
-- ReadBackedPileups no longer accept pre-cached values (size, nMapQ reads, etc) but now lazy load these values as needed
-- Created optimized calculation routines to iterator over all of the reads in the pileup in whatever order is most efficient as well.
-- New LIBS no longer calculates size, n mapq, and n deletion reads while making pileups.
-- Added commons-collections for IteratorChain
 		2013-01-11 15:17:18 -05:00
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commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk Split original and optimized ART into largely independent pieces 2013-01-11 15:17:18 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils ReadBackedPileup cleanup 2013-01-11 15:17:18 -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