hanna 6e394490cb Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@643 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-08 21:27:54 +00:00
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TraversalEngine.java	Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.	2009-05-08 21:27:54 +00:00
TraversalStatistics.java	Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed	2009-04-17 01:27:36 +00:00
TraverseByLoci.java	Interval-based traversals were bleeding file handles. Fixed.	2009-04-26 18:35:54 +00:00
TraverseByLocusWindows.java	Added functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals.	2009-05-08 17:28:16 +00:00
TraverseByReads.java	Enabled ReduceByInterval	2009-04-24 21:39:44 +00:00
TraverseByReference.java	Enabled ReduceByInterval	2009-04-24 21:39:44 +00:00
TraverseDuplicates.java	fixing oddities in duplicates	2009-05-07 18:55:45 +00:00
TraverseLociByReference.java	Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.	2009-05-08 21:27:54 +00:00
TraverseReads.java	Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.	2009-05-08 21:27:54 +00:00