Switch to using $subsequence_slice than $self for the start and end values. If we don't then we will try to retrieve all repeat features for an entire chromosome.

Simplification of the AUTOLOAD since there were blocks of code which could never be called. Removed these unused blocks.

Escape _ in the input parameters as otherwise we spend a lot of time doing very expensive LIKE operations

(rather than 'not_biotypes'), for cleaner looking configuration.

canonical human-readable names of the hosts.

Reformat.

use alt_allele data from vega to populate core as gene names may not be up to date in core when alt_alleles.pl is run

  If the configuration parameter 'not_biotypes' is present, exclude all
  genes whose biotype is listed (but include all other genes).

  If the configuration parameter 'biotypes' is present, include all
  genes whose biotype is listed (as usual).

  It is an error to define both options in the configuration.