Added index as output file

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

@@ -52,6 +52,14 @@ class MarkDuplicates(val root: Configurable) extends Picard {
   @Argument(doc = "OPTICAL_DUPLICATE_PIXEL_DISTANCE", required = false)
   var opticalDuplicatePixelDistance: Option[Int] = config("opticalDuplicatePixelDistance")
 
+  @Output(doc = "Bam Index", required = true)
+  private var outputIndex: File = _
+  
+  override def afterGraph {
+    super.afterGraph
+    if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
+  }
+  
   override def commandLine = super.commandLine +
     repeat("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala

@@ -16,6 +16,14 @@ class SortSam(val root: Configurable) extends Picard {
   @Argument(doc = "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} ", required = true)
   var sortOrder: String = _
 
+  @Output(doc = "Bam Index", required = true)
+  private var outputIndex: File = _
+  
+  override def afterGraph {
+    super.afterGraph
+    if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
+  }
+  
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +