aaron 9f942fdfa0 Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine. ... Also fixed a bug where we'd exception-out if we didn't provide a interval region. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-12 15:33:55 +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	Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine.	2009-05-12 15:33:55 +00:00
test/org/broadinstitute/sting	intervals_file + genome_loc => intervals.	2009-05-12 01:04:18 +00:00