GitLab

Simplify cdna_start() and cdna_end() by use of transcript().

Transcript.pm.  Avoids littering the code with calls to weaken().

Scalar::Util::weaken() to avoid memory leak.

* Add a transcript() method to the Translation object to retrieve its
  Transcript.

* Modify seq() in Translation so that it temporarily swaps out the
  canonical translation of the transcript if needed.

replace the Bio::EnsEMBL::Collection modules in release 60.

  The is_current attribute was set to 1 when the transcript had it set
  to 0.  There's a difference between undef and 0...

Bugfix to _list_dbIDs() when it was using the generic bind params method from DBAdaptor however we never went through generic_fetch() so params were never bound.

added support for fetching somatic mutations from a slice, and tidied up the general variation feature fetching code

Pointed out by Andy Yates.

reset staus for genes and transcripts to those from havana if ALL transcripts for a gene and the gene itself have a valid status in havana

change to using registry so that we do not have to specify the release number. That way we do not have to change the config file for every release