hanna f18ac069e2 A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup. ... Provides a cleaner interface with extended events inheriting all of the basic RBP functionality. Implementation is still slightly messy, but should allow users to provide separate implementations of methods for sample split pileups and unsplit pileups for efficiency's sake. Methods not covered by unit/integration tests have not been sufficiently tested yet. Unit tests will follow this week. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3597 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-20 04:42:26 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
test/org/broadinstitute/sting	GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.	2010-06-19 21:36:41 +00:00