code: def rna_bases(rna_cov, scaffold, bases, line):
      
      start = int(line[3])
      stop = start + bases - 1
      if scaffold not in rna_cov:
          return rna_cov
      for pos in rna_cov[scaffold][2]:
          ol = get_overlap([start, stop], pos)
          rna_cov[scaffold][0] += ol
      return rna_cov
docs: determine if read overlaps with rna, if so count bases