now works for RGDs format, rather than modified RGD format, also imports RatMap synonyms from RGD file

Bio::Das mumble mumble documentation mumble mumble, grrr.

Fixed "Useless use of a variable in void context" error in Slice

both the graphic and textual displays.  Mapping of the result
ranges into the query coordinates doesn't happen just yet.

performs a query for a disjoint segment if neccesary (a
continous segment on the query sequence that is mapped onto two
separate segements on the target).

Yay!

Doesn't yet map the result though.

them.

I also need to replace all "target" ID strings in the DAS server
replies with the "query" ID string that the user actually asked
for... or come up with another solution which doesn't break
links provided by the DAS server, or confuses the user too much
in other ways.

overridden by command line options or configuration file) and
environment variables removed (since the old valus are now the default
values of exonerate anyway).

Informs user of failed query.

myself (prefer seat-of-the-pants SQL), but someone might find a use
for it.

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...

that could have resulted in errors in other (non-core) DBAdaptors that inherited from DBConnection

-flanking sequence was being partially ignored resulting incorrect snp classification if specified
-internally copied transcripts needed to unset their translations otherwise they could mess up the original transcripts exons
-transcripts fetched from lite did not set the internal translation id

Writing to /dev/tty was bad.
(change doesn't affect -d usage)