hanna 8a1207e4db Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code. ... Reverts to original TraverseByLociByReference behavior unless a special combination of command-line flags are used. Lightly tested at best, and major flaws include: - MicroManager is not doing MicroScheduling right now; it's driving the traversals. - New database-ish data providers imply by their interface that they're stateless, but they're highly stateful. - Using static objects to circumvent encapsulation. - Code duplication is rampant. - Plus more! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@346 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-09 20:28:17 +00:00
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dataSources	Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code.	2009-04-09 20:28:17 +00:00
executive	Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code.	2009-04-09 20:28:17 +00:00
iterators	Added a bunch of fixes: MSRI wasn't working, sharding had broken edge cases, and SAMBAM DS needed to close the file handles.	2009-04-09 00:20:15 +00:00
refdata	count variant as biallelic if it's just a non-ref homogeneous site!	2009-04-08 01:57:27 +00:00
traversals	Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code.	2009-04-09 20:28:17 +00:00
walkers	Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.	2009-04-03 19:54:54 +00:00
GenomeAnalysisTK.java	Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code.	2009-04-09 20:28:17 +00:00
LocusContext.java	Added ability to downsample to a particular coverage	2009-04-01 20:27:06 +00:00
WalkerManager.java	Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.	2009-03-30 23:20:55 +00:00