GitLab

Added check to make sure that only the causative allele is evaluated when a variation has more than two alleles

transcript does not have an associated adaptor.

associated with the transcript.

  Args       : None
  Example    :

    my @alt_translations =
      @{ $transcript->get_all_alternative_translations() };

  Description:  Fetches all alternative translations defined for this
                transcript.  The canonical translation is not returned.

  Returntype : Array reference to Bio::EnsEMBL::Translation
  Exceptions : None
  Caller     : General
  Status     : Stable


Added method add_alternative_translation():

  Args       : Bio::EnsEMBL::Translation $translation
  Example    :

    $transcript->add_alternative_translation($translation);

  Description: Adds an alternative translation to this transcript.
  Returntype : None
  Exceptions : None
  Caller     : General
  Status     : Stable

simple sanity check for human and mouse to make sure the core/vega links are up to date with each other

Use registry to get vega and core databases. Plus now only take the core -> vega mapping and not vice versa (to be consistent)

Add PRINTS back as it is needed for the protein alignments but store the source in the  interpro table as this is usefull information, that allows us to ignore PRINTS later.