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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src/org/broadinstitute/sting	Make command-line arguments available in walker constructor, provide back door from	2009-03-26 20:45:27 +00:00
test/org/broadinstitute/sting/utils/cmdLine	added our first junit test, for the argument parser	2009-03-24 21:14:30 +00:00