hanna 53fe9acf65 Make command-line arguments available in walker constructor, provide back door from ... walker into GATK itself, do some cleanup of output messages, and add some bug fixes. Command-line arguments in walkers are now feature-complete, but still a bit messy. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-26 20:45:27 +00:00
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iterators	Support for dynamically merging data files. Preliminary only -- everything in these systems is still being tested	2009-03-26 14:40:50 +00:00
refdata	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
walkers	Make command-line arguments available in walker constructor, provide back door from	2009-03-26 20:45:27 +00:00
GenomeAnalysisTK.java	Make command-line arguments available in walker constructor, provide back door from	2009-03-26 20:45:27 +00:00
LocusContext.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
TraversalEngine.java	Support for dynamically merging data files. Preliminary only -- everything in these systems is still being tested	2009-03-26 14:40:50 +00:00
WalkerManager.java	Make command-line arguments available in walker constructor, provide back door from	2009-03-26 20:45:27 +00:00