kshakir 80259b9e20 Changed fullCallingPipeline to output all contigs in the refence if scattering. ... When the cleaner interval scatter count is set to one explicitly setting the intrevals to Nil. TODO: Need to add an option that lets the user choose from the command line to scatter all contigs or just those in the intervals list. For now can get relatively the same behavior by setting the interval scatter count equal to the number of contigs+1, assuming the random contigs come at the end of the sequence dictionary. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4565 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-24 03:01:06 +00:00
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qscript	Changed fullCallingPipeline to output all contigs in the refence if scattering.	2010-10-24 03:01:06 +00:00
src	Changed fullCallingPipeline to output all contigs in the refence if scattering.	2010-10-24 03:01:06 +00:00
test/org/broadinstitute/sting/queue	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.	2010-10-22 22:22:30 +00:00