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.