no clone coordinate system in mouse exists in the new assembly, don't project to clone for mouse either

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.

Fixed an inappropriate method of getting species aliases and changed a couple of lines to be more direct.

Using the "best" HTTP client available i.e. avoid making people install LWP if they are on a late enough version of Perl. HTTP::Tiny is very nice

Asking if a dereferenced array ref is undefined is not testing what you think it is and is deprecated in Perl 5.16.0. You are seeing if the first element was defined when in actual fact you needed to assert if the array reference was undefined and act accordingly.

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

New test case for applying the current release's patches. This downloads the last release of the core schema, finds all patches relevant to this release and patches the DB accordingly. The code requires access to CVSWEB and so supports proxies but can also skip the tests if the schema cannot be found. Failure of this test is not an issue for external users & so should not be punished as such

First draft of revised projections. Exclusions in place for inappropriate mammalian traits on birds and reptiles. Also platypus.

Awaiting GOA full blacklist of undesirable projections.

translated sequence, not transcript sequence.

phase change was removed because it meant that an exon whose sequence
and position had not changed would become a candidate for similarity
mapping.  This caused lots of criss-crossing stable ID history entries
between genes/transcripts/translations in some gene families.