Add CombineVariants

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala

+package nl.lumc.sasc.biopet.extensions.gatk
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvan_thof on 2/26/15.
+ */
+class CombineVariants(val root: Configurable) extends Gatk {
+  val analysisType = "CombineVariants"
+
+  @Input(required = true)
+  var inputFiles: List[File] = Nil
+
+  @Output(required = true)
+  var outputFile: File = null
+
+  var setKey: String = null
+  var rodPriorityList: List[String] = Nil
+  var minimumN: Int = config("minimumN", default = 1)
+  var genotypeMergeOptions: String = config("genotypeMergeOptions")
+
+  var inputMap: Map[File, String] = Map()
+
+  def addInput(file:File, name:String): Unit = {
+    inputFiles :+= file
+    inputMap += file -> name
+  }
+
+  override def beforeGraph: Unit = {
+    genotypeMergeOptions match {
+      case null | "UNIQUIFY" | "PRIORITIZE" | "UNSORTED" | "REQUIRE_UNIQUE" =>
+      case _ => throw new IllegalArgumentException("Wrong option for genotypeMergeOptions")
+    }
+  }
+
+  override def commandLine = super.commandLine +
+    (for (file <- inputFiles) yield {
+      inputMap.get(file) match {
+        case Some(name) => required("--variant:" + name, file)
+        case _ => required("--variant", file)
+      }}).mkString +
+    required(outputFile) +
+    optional("--setKey", setKey) +
+    (if (rodPriorityList.isEmpty) "" else optional("--rod_priority_list", rodPriorityList.mkString(","))) +
+    optional("-genotypeMergeOptions", genotypeMergeOptions)
+}