-my ( $run_time_beg, $run_time_end, $options, $in, $out, $tmp_dir, $bed_file, $tag_file, $fh_in, $fh_out,
- $cols, $record, $bed_entry, $file_hash, $chr, $strand );
+my ( $options, $in, $out, $tmp_dir, $fh_in, $fh_out, $cols, $record, $bed_entry, %fh_hash, %file_hash, $file, $strand, $id, $tag_file, $bed_file );