aaron 898f65547e Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-11 02:07:20 +00:00
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dataSources	Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code.	2009-05-05 18:17:07 +00:00
executive	Add tag to ignore node class.	2009-04-30 20:27:34 +00:00
iterators	Changes to the interface to the simple data source rippled out to a bunch of files.	2009-04-30 20:35:56 +00:00
traversals	Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.	2009-05-08 21:27:54 +00:00
GATKArgumentCollectionTest.java	Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now.	2009-05-11 02:07:20 +00:00
GenomeAnalysisTKTest.java	Cut the test time down	2009-05-05 22:05:51 +00:00
OutputTrackerTest.java	N-way parallelism. Works for small test cases. Untested for large test cases.	2009-05-01 19:34:09 +00:00