If PASS is not pulled out into a local variable then passed into DBI we will attempt to connect to a database (DBI->trace() confirms the passing of a password). Perl is very odd

Counting features over HAPs/Patches/PARs was not working. Fixed by adding a SQL based filtering stage. The normal code will not use this as it is quite nasty

data should rely on protein evidence levels provided by Uniprot

[ENSCORESW-315]. Fixing a bug where the bind params need to be reused on subsequent queries. MySQL/DBI/DBD::mysql is really bad at warning us when we submit a query with a single ? and no bind parameters (it compensates). Wish it didn't

[ENSCORESW-314]. Synonym lookup bug fixed. Passed coord system id into the lookup rather than the actual coord system name. Bad bad bad

added a quick_check to enable quick heuristic check to allow rapid processing of genomes where there are no alternative transcripts

Ordering only by the session's created date failed to realise we could have more than one entry for the same stable id. Ordering now by the score as a way of getting rid of this ambiguity. Issue was picked up by Rhoda running the code on an older MySQL version which consistently exhibited different behaviour to later MySQL versions