Merge branch 'feature-fix_logs' into 'develop'

Feature fix logs

Fix for double logs for BiopetQCommandLine

See merge request !42

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

 package nl.lumc.sasc.biopet.core
 
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
 
 trait PipelineCommand extends MainCommand with GatkLogging {
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala

@@ -24,7 +24,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.core.workaround
 
 import java.io.File
 import org.broadinstitute.gatk.utils.commandline._
@@ -32,6 +32,7 @@ import org.broadinstitute.gatk.queue.util._
 import org.broadinstitute.gatk.queue.QCommandPlugin
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.QScriptManager
+import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
 import collection.JavaConversions._
 import org.broadinstitute.gatk.utils.classloader.PluginManager
@@ -43,11 +44,12 @@ import java.net.URL
 import java.util.{ ResourceBundle, Arrays }
 import org.broadinstitute.gatk.utils.text.TextFormattingUtils
 import org.apache.commons.io.FilenameUtils
+import nl.lumc.sasc.biopet.core.BiopetExecutable
 
 /**
  * Entry point of Queue.  Compiles and runs QScripts passed in to the command line.
  */
-object BiopetQCommandLine extends Logging {
+object BiopetQCommandLine extends GatkLogging {
   /**
    * Main.
    * @param argv Arguments.