kshakir 6d59dd3455 Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass. ... Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass. QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]]. Added an QCommandPlugin.initScript utility method for handling specialized script types.		2012-11-14 10:33:20 -05:00
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qscript/org/broadinstitute/sting/queue/qscripts	Only run UG in the bundle for chr20	2012-10-30 15:09:46 -04:00
src/org/broadinstitute/sting/queue	Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.	2012-11-14 10:33:20 -05:00
test/org/broadinstitute/sting/queue	updating pipeline test md5s	2012-10-29 18:53:27 -04:00