GitLab

Enforced strict matching in fetch_by_region synonym lookup. Returns undef, rather than giving the user what might be the correct answer, and emits a warning. Only allowed to auto-select coordinate system when it is not known.

Fixed regression problem in fetch_by_region, where a valid synonym with an invalid coordinate system caused a never-ending loop. Added a coordinate system check to ensure the synonym query is on the correct coordinate system.

[ENSCORESW-264] Can now handle odd sequence region names involving . - _ now. The supercontig names seemed to be a good source of these

The old way was possibly the WORST way to blank a LRU cache by replacing it for a bare hash. Possible memory leak fixed ...

Adding patch from James Allen where a copy/paste bug has meant the incorrect setting of end_Exon to be on the $translation and not alternative $translation

We can now set a reconnection timeout outside of the normal realms of MySQL disconnect/reconnect. This means we have something closer to a pooled connection which stays active for as long as people need it & dies off at the required rate

Changing the AssemblyInfo adaptor name to Assembly due to concerns raised by other members in the Ensembl team. Info is too vague & therefore redundant

ENSCORESW-152. Committing the low cardinality and low row count caching framework into the core API. Implement the correct method from BaseAdaptor to have your values cached in local memory

Additional patch to bring in version into the unique key for xref. Also apply changes to gene and transcript

removed warning in store_alt_alleles when none of the alt_alleles in a set is on reference sequence - this is a valid case and doesn't require a warning

Assignment bug; we did not want the cache assigned to the ID of the seq region but wanted the seq region id into a local variable. Fixed.

Simplification of the select. The query for select used fields which are not part of the unique key. We also get the API to issue a throw the moment we miss the xref id retrieval. This should be an impossible scenario to get into though

Patching issue with there being a difference between NULL and and empty string WRT description and also plugged a gap in the code when we were trying to query using a display_label which the api allows to be NULL but the DB does not

ENSCORESW-165. Committing the second attempt at the IntronSupportingEvidence API for genebuild RNASeq data.

Added efficiency boost to fetch_all_by_external_name and sub-methods. Wildcards now escaped in positions 1 and 3 unless user supplies override flag.

POD updated accordingly.