hanna 96034aee0e Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered ... that the semantics for which reads are in an extended event pileup are not clear at this point. Eric and I have planned a future clarification for this and the two of us will discuss who will implement this clarification and when it'll happen. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3809 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-16 18:57:58 +00:00
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AbstractReadBackedPileup.java	Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered	2010-07-16 18:57:58 +00:00
ExtendedEventPileupElement.java	Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered	2010-07-16 18:57:58 +00:00
ExtendedPileupElement.java	Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.	2009-11-25 03:51:41 +00:00
MergingPileupElementIterator.java	Misc bug fixes: fix tracking of nInsertions with sample-split pileup constructor. Fix performance	2010-06-20 20:32:27 +00:00
PileupElement.java	Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered	2010-07-16 18:57:58 +00:00
PileupElementFilter.java	An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext.	2010-07-07 01:07:46 +00:00
PileupElementTracker.java	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
ReadBackedExtendedEventPileup.java	An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext.	2010-07-07 01:07:46 +00:00
ReadBackedExtendedEventPileupImpl.java	Redo StratifiedAlignmentContext to use ReadBackedPileup's stratification options.	2010-07-01 02:46:05 +00:00
ReadBackedPileup.java	An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext.	2010-07-07 01:07:46 +00:00
ReadBackedPileupImpl.java	Redo StratifiedAlignmentContext to use ReadBackedPileup's stratification options.	2010-07-01 02:46:05 +00:00