Fixed compile errors

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -5,46 +5,6 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-//import java.io.File
-//
-//import nl.lumc.sasc.biopet.utils.config.Configurable
-//import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
-//
-//class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
-//
-//  @Gather(enabled = false)
-//  @Output(required = false)
-//  protected var vcfIndex: File = _
-//
-//  if (config.contains("scattercount")) scatterCount = config("scattercount")
-//  if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
-//  sample_ploidy = config("ploidy")
-//  if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
-//
-//  stand_call_conf = config("stand_call_conf", default = 5)
-//  stand_emit_conf = config("stand_emit_conf", default = 0)
-//
-//  if (config.contains("output_mode")) {
-//    import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
-//    config("output_mode").asString match {
-//      case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
-//      case "EMIT_ALL_SITES"           => output_mode = EMIT_ALL_SITES
-//      case "EMIT_VARIANTS_ONLY"       => output_mode = EMIT_VARIANTS_ONLY
-//      case e                          => logger.warn("output mode '" + e + "' does not exist")
-//    }
-//  }
-//
-//  override val defaultThreads = 1
-//
-//  override def freezeFieldValues() {
-//    super.freezeFieldValues()
-//
-//    genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
-//    nct = Some(getThreads)
-//    memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
-//  }
-//}
-
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -180,7 +140,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
 
   /** The minimum phred-scaled confidence threshold at which variants should be called */
   @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false, exclusiveOf = "", validation = "")
-  var standard_min_confidence_threshold_for_calling: Option[Double] = config("standard_min_confidence_threshold_for_calling")
+  var standard_min_confidence_threshold_for_calling: Option[Double] = config("stand_call_conf")
 
   /** Format string for standard_min_confidence_threshold_for_calling */
   @Argument(fullName = "standard_min_confidence_threshold_for_callingFormat", shortName = "", doc = "Format string for standard_min_confidence_threshold_for_calling", required = false, exclusiveOf = "", validation = "")
@@ -188,7 +148,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
 
   /** The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold) */
   @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", required = false, exclusiveOf = "", validation = "")
-  var standard_min_confidence_threshold_for_emitting: Option[Double] = config("standard_min_confidence_threshold_for_emitting")
+  var standard_min_confidence_threshold_for_emitting: Option[Double] = config("stand_emit_conf")
 
   /** Format string for standard_min_confidence_threshold_for_emitting */
   @Argument(fullName = "standard_min_confidence_threshold_for_emittingFormat", shortName = "", doc = "Format string for standard_min_confidence_threshold_for_emitting", required = false, exclusiveOf = "", validation = "")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -5,12 +5,10 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import java.io.File
-
 import nl.lumc.sasc.biopet.utils.VcfUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
-import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
 
 //class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
 //}
@@ -80,7 +78,7 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
 
   /** Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context */
   @Argument(fullName = "sample", shortName = "sn", doc = "Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context", required = false, exclusiveOf = "", validation = "")
-  var sample: List[String] = config("sample", default = Nil, freeVar = false
+  var sample: List[String] = config("sample", default = Nil, freeVar = false)
 
   /** Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets */
   @Argument(fullName = "known_names", shortName = "knownName", doc = "Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required = false, exclusiveOf = "", validation = "")

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala

@@ -17,7 +17,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
   def biopetScript() {
     val ug = broad.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
     ug.alleles = config("input_alleles")
-    ug.genotyping_mode = "GENOTYPE_GIVEN_ALLELES"
+    ug.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
     add(ug)
   }
 }

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -38,7 +38,8 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
 
   override def defaults = Map(
     "haplotypecaller" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0),
-    "genotypegvcfs" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0)
+    "genotypegvcfs" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0),
+    "unifiedgenotyper" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0)
   )
 
   /** Method to make the variantcalling namespace of shiva */