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The last time we ran patch_test_databases for release 98 it somehow managed
to apply compara's patch_97_98_b without applying patch_97_98_a. I don't
even.

Source: release/98 branch of ols-ensembl-loader and master branches
of all other relevant Ensembl repositories, pulled a few minutes ago.
Compara, Variation and ontology schemas all have already been bumped to
version 98.

ENSCORESW-3132: Limited implementation of Intervals with start > end (i.e. spanning the origin of a circular chromosome)

Deprecated since 2011, non-functional since March 2018. See ENSCORESW-2871.

Note that there is still a reference to GOTermAdaptor in the xref parser
GOSlimParser. However, the parser in question seems to be no longer used
and in any case has not been updated, other than changing the copyright
notices, for years.

See ENSCORESW-3119. If both a versioned and an unversioned database are
present, use the versioned one if the version number matches that of the
software.

Code updated to implement review comments. There is a new package to handle stop codon readthrough in a sequence. Test case has been updated with new regex

The previous test-database update missed some patches for the core and
variation schemas, which is why Travis jobs keep failing these days.

ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

Code updated to implement review comments. There is a new package to handle stop codon readthrough in a sequence. Test case has been updated with new regex

The previous test-database update missed some patches for the core and
variation schemas, which is why Travis jobs keep failing these days.

ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

See ENSCORESW-3054. Only really affects the test suite at this point,
in the code proper the prefix only appears in docstrings.

Apply patch_96_97_{c,d,e}, insert the necessary data into
homo_sapiens/core.

Quote noisy strings properly + avoid double-sigil dereferences.