kshakir 4f51a02dea Changed logging level to default at INFO instead of WARN. ... Changes to StingUtils command line for use in Queue, replacing Queue's use of property files. Updates to walkers used in existing QScripts to add @Input/@Output. RMD used in @Required/@Allows now has a new default equal to "any" type. New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions. Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.) Removed dependency on BroadCore by porting LSF job submitter to scala. Ivy now pulls down module dependencies from maven. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-09 16:42:48 +00:00
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edu.mit.broad	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
gov.nist	Adding Jama for Ryan.	2010-04-27 14:30:36 +00:00
net.sf	Rev Picard with new IndexedFastaSequenceFile patch.	2010-07-01 03:05:43 +00:00
org.broad	fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no	2010-07-23 18:39:55 +00:00
org.reflections	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00