diff --git a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
index 41b9f9769..ced1ffa7a 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
@@ -85,18 +85,18 @@ trait QFunction {
   def failOutputs = statusPaths.map(path => new File(path + ".fail"))
 
   /** The complete list of fields on this CommandLineFunction. */
-  def functionFields = QFunction.classFields(this.getClass).functionFields
+  def functionFields = QFunction.classFields(this.functionFieldClass).functionFields
   /** The @Input fields on this CommandLineFunction. */
-  def inputFields = QFunction.classFields(this.getClass).inputFields
+  def inputFields = QFunction.classFields(this.functionFieldClass).inputFields
   /** The @Output fields on this CommandLineFunction. */
-  def outputFields = QFunction.classFields(this.getClass).outputFields
+  def outputFields = QFunction.classFields(this.functionFieldClass).outputFields
   /** The @Argument fields on this CommandLineFunction. */
-  def argumentFields = QFunction.classFields(this.getClass).argumentFields
+  def argumentFields = QFunction.classFields(this.functionFieldClass).argumentFields
   
   /**
-   * Called at most once, returns the list of fields for this function.
+   * Returns the class that should be used for looking up fields.
    */
-  protected def initFunctionFields = ParsingEngine.extractArgumentSources(this.getClass).toList
+  protected def functionFieldClass = this.getClass
 
   /**
    * Returns the input files for this function.
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
index 85ea2606e..11ccff984 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
@@ -33,7 +33,7 @@ class CloneFunction extends CommandLineFunction {
 
   override def dotString = originalFunction.dotString
   override def description = originalFunction.description
-  override protected def initFunctionFields = originalFunction.functionFields
+  override protected def functionFieldClass = originalFunction.getClass
   override def useStatusOutput(file: File) =
     file != jobOutputFile && file != jobErrorFile && originalFunction.useStatusOutput(file)