code: def _whole_gene_covered_by_nucmer_hits(nucmer_hits, ref_seq, percent_threshold, max_nt_extend):
          '''Returns true iff the reference sequence is covered by nucmer hits.
             nucmer_hits = hits made by self._parse_nucmer_coords_file.
             Counts as covered if (total ref bases covered) / len(ref_seq) >= threshold'''
          coords = AssemblyCompare.nucmer_hits_to_ref_coords(nucmer_hits)
          covered = []
          for coords_list in coords.values():
              covered.extend(coords_list)
          pyfastaq.intervals.merge_overlapping_in_list(covered)
          return (2 * max_nt_extend + pyfastaq.intervals.length_sum_from_list(covered)) / len(ref_seq) >= percent_thresholf _whole_gene_covered_by_nucmer_hits(nucmer_hits, ref_seq, percent_threshold, max_nt_extend):
          '''Returns true iff the reference sequence is covered by nucmer hits.
             nucmer_hits = hits made by self._parse_nucmer_coords_file.
             Counts as covered if (total ref bases covered) / len(ref_seq) >= threshold'''
          coords = AssemblyCompare.nucmer_hits_to_ref_coords(nucmer_hits)
          covered = []
          for coords_list in coords.values():
              covered.extend(coords_list)
          pyfastaq.intervals.merge_overlapping_in_list(covered)
          return (2 * max_nt_extend + pyfastaq.intervals.length_sum_from_list(covered)) / len(ref_seq) >= percent_threshold
docs: Returns true iff the reference sequence is covered by nucmer hits.
             nucmer_hits = hits made by self._parse_nucmer_coords_file.
             Counts as covered if (total ref bases covered) / len(ref_seq) >= threshold