code: def _remap_cortex_out(cortex_out, region, out_file):
      
      def _remap_vcf_line(line, contig, start):
          parts = line.split("\t")
          if parts[0] == "" or parts[1] == "":
              return None
          parts[0] = contig
          try:
              parts[1] = str(int(parts[1]) + start)
          except ValueError:
              raise ValueError("Problem in {0} with \n{1}".format(
                      cortex_out, parts))
          return "\t".join(parts)
      def _not_filtered(line):
          parts = line.split("\t")
          return parts[6] == "PASS"
      contig, start, _ = region
      start = int(start)
      with open(cortex_out) as in_handle:
          with open(out_file, "w") as out_handle:
              for line in in_handle:
                  if line.startswith("##fileDate"):
                      pass
                  elif line.startswith("#"):
                      out_handle.write(line)
                  elif _not_filtered(line):
                      update_line = _remap_vcf_line(line, contig, start)
                      if update_line:
                          out_handle.write(update_line)
docs: Remap coordinates in local cortex variant calls to the original global region.