code: def _get_extra_args(extra_args, arg_keys):
      
      # XXX back compatible hack -- should have a way to specify these.
      single_keys = set(["sam_ref", "config"])
      out = []
      for i, arg_key in enumerate(arg_keys):
          vals = [xs[i] for xs in extra_args]
          if arg_key in single_keys:
              out.append(vals[-1])
          else:
              out.append(vals)
      return out
docs: Retrieve extra arguments to pass along to combine function.
  
      Special cases like reference files and configuration information
      are passed as single items, the rest as lists mapping to each data
      item combined.