Add "_synonym" to database name for cross reference lines that are generated from external_synonyms (previously they were indistinguishable).

Note that Uniprot, EMBL etc are still "merged" so that Uniprot/SWISSPROT and Uniprot/TREMBL become Uniprot.

Also fixed bug that was causing EntrezGene to be changed to ENSEMBLGene

Always de-reference the value got from get_mapping_path().
Found by Magali.

distribution.

database in GFF format (STDOUT).

Added code to delete names/GO terms if the -delete_only option is specified. Added code to check whether
-registryconf is submitted as a string from the submit_projections.pl script or as a file on the command
line.

translation ID, and ALWAYS update it to the correct translation ID
later, after storing the translation.

Avoids problems (the canonical_translation_id being duplicated) when
transferring transcripts with translations from another database.

Amonida found this.

  Fix store() so that the canonical_translation_id in the transcript
  table is updated if the translation gets a new dbID when it is stored.