hanna 608a66e6ab TbyLocibyRef previously didn't seem to support traversals with no interval specified. Put in a temporary fix until the threaded approach is in place. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@363 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-10 22:14:06 +00:00
..
dataSources	Should've been calling queryOverlapping in locus mode.	2009-04-10 20:22:04 +00:00
executive	Cleanup, and support either by-interval traversals or full traversals in data source-backed code.	2009-04-10 22:09:01 +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	New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java	2009-04-09 22:04:59 +00:00
traversals	TbyLocibyRef previously didn't seem to support traversals with no interval specified. Put in a temporary fix until the threaded approach is in place.	2009-04-10 22:14:06 +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	New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java	2009-04-09 22:04:59 +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