Fix args

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
 import org.broadinstitute.gatk.queue.QScript
 
 /// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
@@ -47,7 +47,6 @@ class Breakdancer(val root: Configurable) extends QScript with BiopetQScript wit
   }
 
   override def init(): Unit = {
-    
   }
 
   def biopetScript() {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala

@@ -51,8 +51,8 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio
   var x: Option[Int] = config("x", default = 1000)
   var b: Option[Int] = config("b", default = 100)
   var t: Boolean = config("t", default = false)
-  var d: String = config("d")
-  var g: String = config("g")
+  var d: Option[String] = config("d")
+  var g: Option[String] = config("g")
   var l: Boolean = config("l", default = false)
   var a: Boolean = config("a", default = false)
   var h: Boolean = config("h", default = false)