Adding vt decompose extension

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala

+package nl.lumc.sasc.biopet.extensions.vt
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{Reference, Version}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+/**
+  * Created by pjvanthof on 20/11/15.
+  */
+class VtDecompose(val root: Configurable) extends Vt with Version with Reference {
+  def versionRegex = """decompose (.*)""".r
+  override def versionExitcode = List(0, 1)
+  def versionCommand = executable + " decompose"
+
+  @Input(required = true)
+  var inputVcf: File = _
+
+  @Output(required = true)
+  var outputVcf: File = _
+
+  var intervalsFile: Option[File] = config("intervals_file")
+
+  val smartDecompose: Boolean = config("smart_decompose", default = false)
+
+  def cmdLine = required(executable) + required("decompose") +
+    required("-o", outputVcf) +
+    optional("-I", intervalsFile) +
+    conditional(smartDecompose, "-s") +
+    required(inputVcf)
+}
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