Added vt normalizer extension

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

+/**
+  * Biopet is built on top of GATK Queue for building bioinformatic
+  * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+  * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+  * should also be able to execute Biopet tools and pipelines.
+  *
+  * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+  *
+  * Contact us at: sasc@lumc.nl
+  *
+  * A dual licensing mode is applied. The source code within this project that are
+  * not part of GATK Queue is freely available for non-commercial use under an AGPL
+  * license; For commercial users or users who do not want to follow the AGPL
+  * license, please contact us to obtain a separate license.
+  */
+package nl.lumc.sasc.biopet.extensions.vt
+
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
+
+/**
+  * General bwa extension
+  *
+  * Created by pjvan_thof on 1/16/15.
+  */
+abstract class Vt extends BiopetCommandLineFunction {
+  override def subPath = "vt" :: super.subPath
+  executable = config("exe", default = "vt")
+}

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.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.{Output, Input}
+
+/**
+  * Created by pjvanthof on 20/11/15.
+  */
+class VtNormalize(val root: Configurable) extends Vt with Version with Reference {
+  def versionRegex = """normalize (.*)""".r
+  override def versionExitcode = List(0, 1)
+  def versionCommand = executable + " normalize"
+
+  @Input(required = true)
+  var inputVcf: File = _
+
+  @Output(required = true)
+  var outputVcf: File = _
+
+  var windowSize: Option[Int] = config("windows_size")
+
+  var intervalsFile: Option[File] = config("intervals_file")
+
+  var reference: File = _
+
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    reference = referenceFasta()
+  }
+
+  def cmdLine = required(executable) + required("normalize") +
+    required("-o", outputVcf) +
+    optional("-w", windowSize) +
+    optional("-I", intervalsFile) +
+    required("-r", reference)
+    required(inputVcf)
+}
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