code: def _remove_haplotype_chroms(in_file, data):
      
      larger_chroms = set(_get_larger_chroms(dd.get_ref_file(data)))
      out_file = os.path.join(_sv_workdir(data), "%s-chromfilter%s" % utils.splitext_plus(os.path.basename(in_file)))
      if not utils.file_exists(out_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:
                      for line in in_handle:
                          if ((line.find("chromosome") >= 0 and line.find("start") >= 0)
                                or line.split()[0] in larger_chroms):
                              out_handle.write(line)
      return out_file
docs: Remove shorter haplotype chromosomes from cns/cnr files for plotting.