xhmm genotype wrapper

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala

+package nl.lumc.sasc.biopet.extensions.xhmm
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.Reference
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
+
+/**
+  * Created by Sander Bollen on 23-11-16.
+  */
+class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
+
+  @Input
+  var inputMatrix: File = _
+
+  @Input
+  var inputXcnv: File = _
+
+  @Output
+  var outputVcf: File = _
+
+  @Input
+  var r: File = _
+
+  @Argument
+  var discoverParamsFile: File =  config("discover_params", namespace = "xhmm")
+
+  def cmdLine = {
+    executable + required("--genotype") +
+      required("-p", discoverParamsFile) +
+      required("-r", inputMatrix) +
+      required("-R", r) +
+      required("-g", inputXcnv) +
+      required("-F", referenceFasta()) +
+      required("-v", outputVcf)
+  }
+
+
+
+}