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

[ENSCORESW-395]. Addition of -eg and -ue options to get people to ping different database servers for ensembl genomes and useast respectively. Also allow users to specify the species used.

first, test all the cases and add seq_region_mapping entries when necessary
then, update the mapping_set table
prevents us from skipping a species where a previous run might have failed

[ENSCORESW-448]. new overlap algorithm and better test cases. supports overlaps when you do not want to normalise WRT the backing slice

[ENSCORESW-445]. Fixes an issue with transformed and transfered transcripts. Attribute arrays are shallowed copied so attributes meant for the transformed object go back into the parent object. This causes more issues when you start to do multiple transformations from the same transcript. Regression test case added

There are some circumstances where exon coordinate recalculation is not the right thing to do and the user has them correctly set out (ori spanning transcription models). Rather than tie this directly into the coordinate recalculations we are allowing skipping this procedure. It is up to the user to do the right thing if using this module. It also does not alter any existing functionality