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

  get_production_name()
  get_short_name()
  get_common_name()
  get_scientific_name()

These will return the corresponding meta values (for keys
'species.common_name' etc.) once these have been inserted
in the Core databases (during the release process of 59).

Details:
http://www.ebi.ac.uk/seqdb/confluence/display/EnsGen/Meta+Changes+for+59+and+release+6

into account.

table.