a blank line was removed in the process

pig (sus_scrofa) is now a merged species, needs to be added to the list of existing three, human, mouse and zebrafish

Added a no_cache override feature plus testcase. Useful in times of memory crisis coupled with annoyingly slow lookups of small data.

[ENSCORESW-271]. Fixed the test being too chatty during cleanup by setting the RUNTESTS_HARNESS_NORESTORE before firing off a thread

[ENSCORESW-270]. Fixed issue with can() call which was returning a boolean flag rather than the coderef can() actually returns. Switched to local variables and the entire thing looks fine now

former script nonsense_transcript_attribs.pl moved to module format to be run as part of the production pipeline
list of populations has been updated after discussion with variation

if there is only one row, result can be retrieved by fetching the first element of the de-referenced array, which is itself an array where each element corresponds to a column

new (resurrected source ncRNA_EG::EG, which replaces RNAMMER, TRNASCAN and RFAM::EG sources); passes as an argument the logic_name instead of a biotype

Introduced a new argument, logic_name, so we can fetch genes by logic_names rather than by biotype, easier for ensemblgenomes to pick up all ncRNA genes, as there are so many biotypes behind them. Goes with new source, nCRNA_EG::EG (resurrected actually). Because this source does not correspond with any external_db ( e.g. RFAM ) , as it was, so I had to add some logic to associate the xref source with an external_db on the fly.

Warn is assembly_exception table is empty.

Revised fetch_all_by_Slice to allow for a proper feature count method that includes overlaps and clones. Response to lack of performance in generic_count for Variation (request from Laurent Gil)

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.