GitLab

like "aspergillus_fumigatusa1163_core_5_58_1a"
(containing integers as part of the second part
of their names).

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)