If an alignment record has = for RNEXT and the XA tag lists an alternative alignment to some other reference for the segment, then xa2multi.pl will copy the = to the RNEXT field of the record generated for the alternative alignment. To make the new record refer to the next segment as listed in the original record, the value in the RNAME field of the original record should be copied instead unless it matches the RNAME of the new record.