Merge branch 'fix-haplotypercaller' into 'develop'

fixed a config value



See merge request !417

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 = "")
@@ -522,12 +522,4 @@ object HaplotypeCaller {
     hc.out = outputFile
     hc
   }
-
-  def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
-    val hc = apply(root, List(inputFile), outputFile)
-    hc.emitRefConfidence = "GVCF"
-    hc.variant_index_type = Some("LINEAR")
-    hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
-    hc
-  }
 }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala

@@ -34,9 +34,16 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
 
   def getGvcfs = gVcfFiles
 
+  override def fixedValues = Map("haplotypecaller" -> Map("emitRefConfidence" -> "GVCF"))
+
+  override def defaults = Map("haplotypecaller" -> Map(
+    "variant_index_type" -> "LINEAR",
+    "variant_index_parameter" -> 128000)
+  )
+
   def biopetScript() {
     val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
-      val hc = gatk.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
+      val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))
       add(hc)
       sample -> hc.out
     }