Fixing output files of sambamba markdup

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala

@@ -40,6 +40,13 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
   override def defaultThreads = 4
   override def defaultCoreMemory = 4.0
 
+  @Output
+  private var indexOutput: File = _
+
+  override def beforeGraph(): Unit = {
+    indexOutput = new File(output + ".bai")
+  }
+
   /** Returns command to execute */
   def cmdLine: String = required(executable) +
     required("markdup") +