Fix some options

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

@@ -9,36 +9,36 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
 
 class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
-  override def afterGraph {
-    super.afterGraph
-
-    min_mapping_quality_score = config("minMappingQualityScore", default = 20)
-    if (config.contains("scattercount")) scatterCount = config("scattercount")
-    if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
-    this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 1)
-    bamOutput = config("bamOutput")
-    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")
-      }
+  min_mapping_quality_score = config("minMappingQualityScore", default = 20)
+  if (config.contains("scattercount")) scatterCount = config("scattercount")
+  if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
+  this.sample_ploidy = config("ploidy")
+  nct = config("threads", default = 1)
+  if (config.contains("bamOutput")) bamOutput = config("bamOutput")
+  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") {
-      dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    } else {
-      dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    }
+  if (config("inputtype", default = "dna").asString == "rna") {
+    dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
+    stand_call_conf = config("stand_call_conf", default = 5)
+    stand_emit_conf = config("stand_emit_conf", default = 0)
+  } else {
+    dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
+    stand_call_conf = config("stand_call_conf", default = 5)
+    stand_emit_conf = config("stand_emit_conf", default = 0)
+  }
+
+  override def afterGraph {
+    super.afterGraph
     if (bamOutput != null && nct.getOrElse(1) > 1) {
       nct = Option(1)
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")