fixed a config value

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala

@@ -90,7 +90,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
 
   /** Mode for emitting reference confidence scores */
   @Argument(fullName = "emitRefConfidence", shortName = "ERC", doc = "Mode for emitting reference confidence scores", required = false, exclusiveOf = "", validation = "")
-  var emitRefConfidence: String = _
+  var emitRefConfidence: Option[String] = config("emitRefConfidence")
 
   /** File to which assembled haplotypes should be written */
   @Output(fullName = "bamOutput", shortName = "bamout", doc = "File to which assembled haplotypes should be written", required = false, exclusiveOf = "", validation = "")
@@ -525,7 +525,7 @@ object HaplotypeCaller {
 
   def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
     val hc = apply(root, List(inputFile), outputFile)
-    hc.emitRefConfidence = "GVCF"
+    hc.emitRefConfidence = Some("GVCF")
     hc.variant_index_type = Some("LINEAR")
     hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
     hc