bthomas b4f6f54502 Reorganizing the way interval arguments are processed ... Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java: -- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments -- initializeIntervals modified -- some helper functions deprecated for cleanliness Includes new set of unit tests, GenomeAnalysisEngineTest.java New restrictions: -- all interval arguments are now checked to be on the reference contig -- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-01 12:47:48 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Reorganizing the way interval arguments are processed	2010-04-01 12:47:48 +00:00
test/org/broadinstitute/sting	Reorganizing the way interval arguments are processed	2010-04-01 12:47:48 +00:00