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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TraversalEngine.java	Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.	2010-05-26 22:12:25 +00:00
TraversalStatistics.java	Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.	2010-05-26 22:12:25 +00:00
TraverseDuplicates.java	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
TraverseLoci.java	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
TraverseReadPairs.java	For Sarah Calvo: initial implementation of read pair traversal, for BAM files	2010-03-21 23:22:25 +00:00
TraverseReads.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00