VEGA haplotype slices are non-reference now:

1. add predicate for haplotype slices;
2. workaround for issue with API where haplotype slices are non-reference
    but have no assembly exceptions;
3. fix map_assembly.pl so that it doesn't assume non-reference is a patch.

The other half of this commit is in ensembl-otter git.

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.

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

translated sequence, not transcript sequence.