fix some more

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

@@ -11,6 +11,6 @@ abstract class Xhmm extends BiopetCommandLineFunction with Version {
 
   executable = config("exe", namespace = "xhmm", default = "xhmm")
 
-  def versionCommand = executable + required("--version")
+  def versionCommand = executable + " --version"
   def versionRegex = """xhmm (.*)""".r
 }

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala

@@ -94,6 +94,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
     val genotype = new XhmmGenotype(this)
     genotype.inputXcnv = discover.outputXcnv
     genotype.inputMatrix = secondMatrix.outputMatrix
+    genotype.r = thirdMatrix.outputMatrix
     genotype.outputVcf = new File(xhmmDir, "xhmm.vcf")
     add(genotype)