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

for coord_system, check rank and name

methods are cleaner
added length check to decide if it is the same region

rather than CREATE TABLE SELECT.  This way we retain the primary key
etc.

for method transcript_display_xref_sources, updated the ignore setup to be consistent with refactoring of DisplayXrefs.pm