Renamed 'old' reference to the coord_system variable. coord_system had been renamed to central_coord_system.

[ENSCORESW-490]. Point raised by Dan. Default GFF3 for source is . not ensembl. Using . and supporting basic features

[ENSCORESW-490]. Fixing the GFF serializer which would add an additional ; at times and now supports a custom source field. Gene and transcript now both emit this

before, used to log any similarity event
now, only log similarity event if we have not been able to map a stable id
if we have been able to map it, we trust that mapping and do not want to confuse the user with all the potential alternative mappings we could have used

[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run on the lowest level. Tests are only run when we have the ENV TEST_AUTHOR is set to a true value. Otherwise it does not impact on the current test cases. Also had to fix a number of issues associcated with these flags. Mostly were due to not using warnings or strict. Anything I felt was ok or not my call has been annotated with a no critic flag.

[ENSCORESW-458]. _remap() (only used by KaryotypeAdaptor AFAIK) was not working. Used seq region names for commparisons when fastmap() returns seq region ids. Fixed to using just seq_region_ids. Issues originally raised by Steve S

[ENSCORESW-479]. Making this module better at handling homologue Compara errors and also get it to die when you try to get homologues without a compara adaptor configured

[ENSCORESW-475] fixing the dbentry return to prioritise genes, transcripts and translations found on reference slices

Added a method that lists the species in available databases. Ancestral_ are ignored, and the list is filtered to a group type, defaulting to core dbs. Testcase is less than perfect, because the test db has so few species in it.

Swapped the count_by_slice_constraint constraint triggers, as they were the wrong way round. Test suite was passing by luck. Rewrote adjoining comments.

Inverted the sense of the SQL limit flags. It was re-enabling them every loop, and not disabling them ever. ENSCORESW-459

[ENSCORESW-461]. Improved messaging when db doesn't match. Skip db (do not die) if schema version < oldest option

Added:
- patch_71_72b.sql to Ensembl Production (create meta table)
- patch_71_72c.sql to Ontology (add schema_version)

Updated Ontology patch_71_72b.sql to insert patch meta entry

Modified queries to match Variation schema changes. The sample table was removed, and the information was pushed into population and individual tables.

skip transcripts that have a ribosomal_frameshift as well as those having the specific '_rib_frameshift' attribute

[ENSCORESW-457]. Better documentation for the associated xref tables. Passed onto regulation as well