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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PileupElementUnitTest.java	Near final cleanup of PileupElement	2013-01-11 15:17:17 -05:00
ReadBackedPileupUnitTest.java	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00