code: def _parse_nucmer_coords_file(coords_file, ref_name):
          '''Input is coords file made by self._run_nucmer. Reference should have one sequence only.
             ref_name is name fo the reference sequence, to sanity check the coords file.
             Returns dictionary. Key = assembly contig name. Value = list of nucmer hits to that contig'''
          file_reader = pymummer.coords_file.reader(coords_file)
          nucmer_hits = {}
          for hit in file_reader:
              assert hit.ref_name == ref_name
              contig = hit.qry_name
              if contig not in nucmer_hits:
                  nucmer_hits[contig] = []
              nucmer_hits[contig].append(copy.copy(hit))
  
          return nucmer_hitf _parse_nucmer_coords_file(coords_file, ref_name):
          '''Input is coords file made by self._run_nucmer. Reference should have one sequence only.
             ref_name is name fo the reference sequence, to sanity check the coords file.
             Returns dictionary. Key = assembly contig name. Value = list of nucmer hits to that contig'''
          file_reader = pymummer.coords_file.reader(coords_file)
          nucmer_hits = {}
          for hit in file_reader:
              assert hit.ref_name == ref_name
              contig = hit.qry_name
              if contig not in nucmer_hits:
                  nucmer_hits[contig] = []
              nucmer_hits[contig].append(copy.copy(hit))
  
          return nucmer_hits
docs: Input is coords file made by self._run_nucmer. Reference should have one sequence only.
             ref_name is name fo the reference sequence, to sanity check the coords file.
             Returns dictionary. Key = assembly contig name. Value = list of nucmer hits to that contig