[ENSCORESW-262]. Customised the Exon summary as hash, gene and transcript summaries have been improved. Biotype mapper can ask objects for their SO term and knows Variation objects are already annotated with a code. BioType mapper caches SO retrieval so it is a massive speed increase for large result sets.

[ENSCORESW-261]. Edits to allow for easier regulation adaptor creation. Grab the species name from the DB if it wasn't given to the adaptor and make sure we avoid returning the coord system core adaptor if the group was funcgen

will get unique regions with variation_feature, stops it from counting snps twice on chromosome Y

Pushing pig specific hacks for the naming of transcripts and the overwriting of xref pipeline assigned values (in a similar way we do for zfish)

Fix for parsing files from Ken @ CSHL. ORIGIN was used in another context apart from notifying the start of the sequence in a genbank a.thaliana file

for gene display xref, ignore gene xrefs where uniprot_genename is dependent on a low-evidence uniprot entry

do not use uniprot_genename as display xref if the master xref it is dependent on is of low evidence

The old way was possibly the WORST way to blank a LRU cache by replacing it for a bare hash. Possible memory leak fixed ...

rather than return all toplevel slices, returns all slices with genes
does not affect much species with a reduced number of toplevel slices but increases things considerably for large number of toplevel slices

Adding patch from James Allen where a copy/paste bug has meant the incorrect setting of end_Exon to be on the $translation and not alternative $translation

also supports trinomial species names

Imports recombination maps.

when counting features, do not use strict lower/higher