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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engine	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
extensions	Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars.	2012-10-23 14:08:31 -04:00
function	Sending a version of per job status messages.	2012-10-23 15:55:47 -04:00
library	Fix edge case for very small VCFs	2012-01-19 00:51:28 -05:00
util	Merge GATK repo into CMI-GATK	2012-10-23 10:59:11 -04:00
QCommandLine.scala	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
QCommandPlugin.scala	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
QException.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
QScript.scala	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
QScriptManager.scala	Fixed package error and a few deprecated scala warnings.	2012-10-15 15:29:40 -04:00
QSettings.scala	Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems.	2012-10-19 13:20:29 -04:00