Vervet-AGM added to xrefs config

ENSCORESW-1137: regexp now deals with GN that have or have not evidence level tags, and stores only the gene name

useful if wanting to scp an InnoDB database for example

ENSCORESW-1134: HGNC download file does not contain the version CCDS ids, fetch dbprimary_acc to match

required for RefSeqCoordinateParser

some sanity checks to make sure the file contains the data we expect

recovered from cvs commits in 2012, not tested

Change to xref_config.ini for flycatcher

Removed method 'set_source_id_to_external_name' to revert back to the default behaviour which is to report the display db name in the source field of the gene description.

Removed method 'set_source_id_to_external_name' to revert back to the default behaviour which is to report the display db name in the source field of the gene description.

Added ncRNA_EG::EG source to species, Triticum aestivum

changed attributes to use correct casing as per GFF spec

changed attributes to use correct casing as per http://gmod.org/wiki/GFF3. Extended testcase to include transcript to test Parent attribute

fix for _get_by_slice on feature-less slices

ensure that even for slices with no features, the adaptor bind params are left clean and empty once the method completes

update argument description for sub_Slice method