* dev:
  transcript table in patch database now contains data genome_container test module updated to reflect the change

genome_container test module updated to reflect the change

* dev:
  there can be several statistics for prediction_count

Introducing a new version of our GTF dumper. Now supports
gene and transcript features, seleno markup, ccds xrefs and
a new readme.

* dev:
  corrected argument for structural_variation count

* dev:
  canonical_annotation has been retired, removing leftover variables

This is more of a SQL provider independent way of doing the deletes
but MySQL’s IN subselect statement performance is less than fantastic.
We need to avoid these like the plague.

[ENSCORESW-822]. BiotypeManager decommissioned in favour of Biotype manager directly talking to the production db.

* dev:
  annual copyright update for 2014
  update contact details

Having to fix the problems with OperonTranscriptAdaptor and OperonAdaptor. We must have the columns for dates in the bind variables not in the explicit binds

Merge branch 'experimental/db-portability/master' of https://github.com/Anacode/ensembl into Anacode-experimental/db-portability/master

an empty additional suffix for backup as otherwise the $file
command was being mistaken for part of the sed replace

New test for valid foreign keys in InnoDB applications. foreign_keys.sql cleaned. Tabs assassinated.