Added musa acuminata, solanum tuberosum species; added two new sources, phytozome_gmax and pgsc; added UniParc source to plants genomes

Added PhytozomeGmax_GENE and PGSC_GENE to the list of external_db entries to set the gene display ids and descriptions

Enforced strict matching in fetch_by_region synonym lookup. Returns undef, rather than giving the user what might be the correct answer, and emits a warning. Only allowed to auto-select coordinate system when it is not known.

Fixed regression problem in fetch_by_region, where a valid synonym with an invalid coordinate system caused a never-ending loop. Added a coordinate system check to ensure the synonym query is on the correct coordinate system.

[ENSCORESW-264] Can now handle odd sequence region names involving . - _ now. The supercontig names seemed to be a good source of these

Added a space after some commenting characters (ie --) where it is missing, otherwise mysql complains

  there's no need to start the index at '1'.
* Don't check the assembly_exception table if this is the first set of
  patches to be added.

[ENSCORESW-217] & [ENSCORESW-263]. Added automatic generation of the primary assembly file and cleaned up the readme slightly pending full re-design.

Added a 'flag' at Genebuilder request to allow them to switch off collection of NMD choices. They want to investigate these cases. Hacky job for a hacky script.

[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 ...