GitLab

Added add_direct_xref() - will be needed for future parsers that create direct_xrefs (e.g. CCDSParser).

Made add_xref return xref_id of last-inserted xref so that it can be passed to add_direct_xref.

LocusLink will from March 2005  no longer be given and will now have a GeneID instead of a LocusID. So at the moment both will be stored if available.

Allow to create objects with undefined or unmapped exons (for keeping track of unmapped exons in AlignSlices)

Now adds version number to label to be consistent with RefSeqParser. Thanks to Abel for pointing this out!

Added dumping of "orphan" xrefs that aren't associated with primary_xrefs or dependent_xrefs - this is currently just Interpro xrefs, but we dump them all just in case.

Now dumps GO linkage types to go_xref and uploads this if required, allowing display of GO xrefs & related information on website, assuming ensembl_go database is present and configured.

Transcripts.

query and target (respectively) covered by the feature

BUG FIX: Bio::EnsEMBL::Mapper->_is_sorted() method was storing a reference to the object itself instead of the assigned value producing a circular reference and, therefore, a potential memory leak.

external_db_name "flybase_transcript" changed to "flybase_transcript_id"
to keep consistency between other flybase(FBxx) identifiers

Removed binary constraint from xref.dbprimary_acc (was only used for drosophila, and is no longer required. Was causing problems for Mart)