Bio::EnsEMBL::Mapper objects from cigar lines, but does not use
them yet (ranges are not supported and the reply will be in the
"other" coordinate system).  Relies on the availablility of a
<tab>-delimited file where each line has the following format:

QueryID TargetID QueryAlignBegin TargetAlignBegin CigarLine

The cigar line should be on the non-exonerate format
("218MI728M" rather than "M 218 I 1 728 M").  The *Begin values
are in "between"-type coodinates (like what exonerate uses).

It's messy, but it's not done yet...