Added single QScript for for VariantAnnotator, not used in Gatk pipeline

gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala

+package nl.lumc.sasc.biopet.pipelines.gatk.modules
+
+import nl.lumc.sasc.biopet.core._
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+
+class BiopetVariantAnnotator(private var globalConfig: Config) extends QScript with BiopetQScript {
+  qscript =>
+  def this() = this(new Config())
+  
+  @Argument(doc="Config Json file",shortName="config", required=false) var configfiles: List[File] = Nil
+  @Argument(doc="Reference",shortName="R") var referenceFile: File = _
+  @Argument(doc="Variant",shortName="V") var variants: List[File] = Nil
+  @Argument(doc="Output directory", shortName="outputDir", required=false) var outputDir: String = _
+  @Argument(doc="Scattercount",shortName="SC") var scattercount: Int = 0
+  
+  def init {
+    for (file <- configfiles) globalConfig.loadConfigFile(file)
+    config = Config.mergeConfigs(globalConfig.getAsConfig("variantannotator"), globalConfig)
+    if (outputDir == null) outputDir = this.qSettings.runDirectory
+    if (scattercount == 0 && config.contains("scattercount")) scattercount = config.getAsInt("scattercount")
+  }
+  
+  def script {
+    init
+    
+    for (inputFile <- qscript.variants) {
+      val variantAnnotator = new VariantAnnotator with gatkArguments {
+        val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("variantannotator"), qscript.config)
+        this.variant = inputFile
+        if (config.contains("dbsnp")) this.dbsnp = config.getAsString("dbsnp")
+        this.out = swapExt(outputDir, inputFile,".vcf",".annotated.vcf")
+        if (qscript.scattercount > 1) this.scatterCount = qscript.scattercount
+        if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
+      }
+      add(variantAnnotator)
+    }
+    
+  }
+  
+  trait gatkArguments extends CommandLineGATK {
+    this.reference_sequence = referenceFile
+    this.memoryLimit = 2
+    this.jobResourceRequests :+= "h_vmem=4G"
+  }
+}