hanna 98716138e9 Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions. ... Made fields of command-line argument system non-public by default. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@606 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-06 19:38:05 +00:00
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dataSources	Added TraverseReads test, some bug fixes discovered in the traversal test	2009-05-05 20:36:00 +00:00
executive	Rename some key classes.	2009-05-01 22:01:04 +00:00
iterators	Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing).	2009-05-06 18:40:55 +00:00
refdata	updated interface	2009-04-21 21:07:20 +00:00
traversals	Added TraverseReads test, some bug fixes discovered in the traversal test	2009-05-05 20:36:00 +00:00
walkers	Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x	2009-05-05 22:43:40 +00:00
GenomeAnalysisTK.java	Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions.	2009-05-06 19:38:05 +00:00
LocusContext.java	1. Added a by-interval traversal.	2009-04-24 04:33:35 +00:00
OutputTracker.java	N-way parallelism. Works for small test cases. Untested for large test cases.	2009-05-01 19:34:09 +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