code: def clean_vcf_output(orig_file, clean_fn, config, name="clean"):
      
      base, ext = utils.splitext_plus(orig_file)
      out_file = "{0}-{1}{2}".format(base, name, ext)
      if not utils.file_exists(out_file):
          with open(orig_file) as in_handle:
              with file_transaction(config, out_file) as tx_out_file:
                  with open(tx_out_file, "w") as out_handle:
                      for line in in_handle:
                          update_line = clean_fn(line)
                          if update_line:
                              out_handle.write(update_line)
          move_vcf(orig_file, "{0}.orig".format(orig_file))
          move_vcf(out_file, orig_file)
          with open(out_file, "w") as out_handle:
              out_handle.write("Moved to {0}".format(orig_file))
docs: Provide framework to clean a file in-place, with the specified clean
      function.