code: def _remove_overlaps(in_file, out_dir, data):
      
      out_file = os.path.join(out_dir, "%s-nooverlaps%s" % utils.splitext_plus(os.path.basename(in_file)))
      if not utils.file_uptodate(out_file, in_file):
          with file_transaction(data, out_file) as tx_out_file:
              with open(in_file) as in_handle:
                  with open(tx_out_file, "w") as out_handle:
                      prev_line = None
                      for line in in_handle:
                          if prev_line:
                              pchrom, pstart, pend = prev_line.split("\t", 4)[:3]
                              cchrom, cstart, cend = line.split("\t", 4)[:3]
                              # Skip if chromosomes match and end overlaps start
                              if pchrom == cchrom and int(pend) > int(cstart):
                                  pass
                              else:
                                  out_handle.write(prev_line)
                          prev_line = line
                      out_handle.write(prev_line)
      return out_file
docs: Remove regions that overlap with next region, these result in issues with PureCN.