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a circular slice, so fix the documentation.

Also, format method.

sub check_for_stops can be given a 3rd parameter, an object with the sub _save_log, to save the logs to. This is optional, ommitting it renders the sub functionally equivalent to the previous version

sub check_for_stops can be given a 3rd parameter, an object with the sub _save_log, to save the logs to. This is optional, ommitting it renders the sub functionally equivalent to the previous version

do its thing.

ASMPATCH and ENS stable IDs into account (will need further tweaking).

Relax restriction on format of stable IDs slightly.

Taking out the explicit passing of core DBAdaptors for multi-species funcgen adaptors as it was causing a core & funcgen connection to be held on the target server

make sure the cache stores the same case as the original sequence else it will look wierd (as if softmasked) if you get it again using the cache

method.  This should be the type of the object, if it is known.  Using
this options speeds up searching for the species of the stable ID if we
end up having to do an exhaustive search.

fixed bug where the dbID of an xref that had already been stored was not set in the object when store was called

for origin overlapping genes take into account exons with negative start and with start greater then end

it looks like the features overlapping origin can be attached to a normal slice as well as to an overlapping origin

make sure the sequence is retrieved for both ends of the region overlapping circular chromosome origin