Fix scattercounts

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

@@ -8,32 +8,29 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
+  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 def beforeGraph {
     super.beforeGraph
 
     genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
-    if (config.contains("scattercount")) scatterCount = config("scattercount")
-    if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
-    this.sample_ploidy = config("ploidy")
     nct = Some(getThreads(1))
-    memoryLimit = Option(nct.getOrElse(1) * 2)
-    if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
-    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")
-      }
-    }
-
-    if (config("inputtype", default = "dna").asString == "rna") {
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    } else {
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    }
+    memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
   }
 }