Retain the backslash on escaped single quotes when generating a hash from a flattened string.

[ENSCORESW-1688] Add connection FAQ to docs, to illustrate best practices when long-running connections drop.

the check is redundant in the context of the fetch_by_location calling
method, since it already performs the same check.

Stop fetch_all_Transcripts returning an empty list when there aren't any transcripts. The old behaviour was to return undef

store ontology term synonym xref separately from name

- Shortcut to only checkout the bioperl release we want and not pull the whole git tree

added support for ensembl-metadata

Update schema_patcher.pl

Funcgen has renamed its sql file from 'efg.sql' to 'table.sql', therefore schema_patcher.pl has to be modified to reflect this change.

Correct serializer behaviour, if an attribute for column 9 of the GFF…

Patch for release 85 adding a confident_relationship flag to the clos…

Correct serializer behaviour, if an attribute for column 9 of the GFF serializer (the misc, everything column) contains an empty array in the feature structure, skip printing the attribute rather than attribute=ARRAY(0xABCD)

Configuration to allow alignments to be exported to GFF

Allow feature boundaries to be retrieved for DNA and protein alignments (this bit of code only appears to be called when handling circular chromosomes)