depristo 84dae06d5a Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@576 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-30 22:16:21 +00:00
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TraversalEngine.java	Oops, typo and build problems. FYI, fixing typos is better than packing...	2009-04-25 01:37:17 +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
TraverseByLociByReference.java	Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.	2009-04-24 19:40:21 +00:00
TraverseByLocusWindows.java	Start getting the cleaner working in Walker	2009-04-29 14:59:53 +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	Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator	2009-04-30 22:16:21 +00:00
TraverseLociByReference.java	Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.	2009-04-24 19:40:21 +00:00
TraverseReads.java	Changes to the interface to the simple data source rippled out to a bunch of files.	2009-04-30 20:35:56 +00:00