code: def subset_to_genome(in_file, out_file, data):
      
      if not utils.file_uptodate(out_file, in_file):
          contigs = set([x.name for x in ref.file_contigs(dd.get_ref_file(data))])
          with utils.open_gzipsafe(in_file) as in_handle:
              with file_transaction(data, out_file) as tx_out_file:
                  with open(tx_out_file, "w") as out_handle:
                      for line in in_handle:
                          parts = line.split()
                          if parts and parts[0] in contigs:
                              out_handle.write(line)
      return out_file
docs: Subset a BED file to only contain contigs present in the reference genome.