populate xref description with ensembl object description if the xref description is empty and copy_description_from_object parameter is true

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.

store description instead of accession in the label field http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-180

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

Allowing backups to go to a directory other than our current working directory. Can cause some issues with disk quotas

does not store density feature with value of 0

updated the $option in repeat coverage case . Repeat coverage script now use "-pattern" to find a database instead of -d.