has unrelated remark beginning with string "selenocysteine ". Found to be the
case in OTTDART00000030742 for Dec 19th 2011 Havana data-freeze of Zebra fish.

First stage commit only. Partial functionality (detailed below), but works and reduces
chance of missing problems.

1. Made exception data structure richer for check_for_stops to allow a number of different
types of exception to to be expressed.

2. Added a new exception type, that of known TGA-stopping Sec-coding transcript.

3. Added data-structure to add_selcys stop checking to allow specification of known
TGA-stopping Sec-coding transcripts.

Adding in a patch which synchronises the state of default values between core like DBs and their master DBs

Modification to bring the dropping of bak tables back in since they cause a large number of issues with the HCs & are not normally removed before the databases are moved to staging/live. We force table backup to disk now to make sure we do not loose this data

Update to description line parsing by EG's request. Seaprate multiple description lines with ; rather than concatenating them together into an un-fathomable string.

1. Fix check_for_stops to cope with multiple adjacent internal stops without a loss of codon to AA sync.
Found when running add_selcys.pl on zebrafish for Vega 47.

2. Fix to existing conditional in vega Sec QC script which tests for an anacode bug before deciding to complain
about missing Sec markup for selenoproteins that also stop with TGA, so that this conditional actually spots
this case in more proteins and so cries wolf less often.

sql to get xrefs with failed priority produces duplicate xref_ids, added IGNORE to INSERT statement for xref

Adding a check in here to highlight when a regular expression failed to match meaning we've found a corrupted schema patch identifier which should be removed