chartl 2c8d7b0c44 Forgot the onTraversalDone. That was dumb. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2692 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-26 21:02:46 +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	Forgot the onTraversalDone. That was dumb.	2010-01-26 21:02:46 +00:00
test/org/broadinstitute/sting	Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number.	2010-01-26 18:47:40 +00:00