Added first go at adding triage stuff i.e. why some refseq and uniprot sequences are not found in ensembl. At the moment if there is no match then this is reported else the actual percentages are given for the closet match with the actual cutoff values used.

Updated to reflect the fact that gene descriptions are now held in the gene table not in a separate gene_description table.

Bug fix: some transcript display_xrefs weren't being assigned correctly if the transcript had more than one associated SwissProt ID and each of the SwissProts was associated with a HUGO ID, e.g. haemoglobin beta/delta chains.

Moved delete_existing to separate metod so it can be called at the start of the process, so generated xref_ids are more sensible.

Fixed bug causing some gene display_xrefs to be incorrectly assigned.

Fixed bug causing query/target identity to not be considered when choosing gene descriptions.

Added "search" for UTR transcripts when generating xref links.

1. Use double-fork (not Open3) to communicate with LSF processes. More reliable and no quoting strangeness.

2. Add option to automatically upload external_db table

3. Bug fix: transcript/gene display_xrefs were not incorporating RefSeq xrefs since the split into RefSeq_peptide and RefSeq_dna had not been taken into account in the display xref calculation.

with the removal of all hugo transcript data (due to mart not allowing both transripts and translations, the script could not find transcript matches, which was presumed, so chnages now made to check if they exist first etc....    Also stopped dump_comparison from being called

Rationalised database connection; lots of calls to $self->xref()->dbi() and $self->dbi() were causing many database connections to be opened and never closed.

Now only uses one connection per database.

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.

Added generation of gene descriptions. Previously these were done via a separate script, now they are generated as part of the post-xref-mapping phase.

New implementation uses the same precedence rules for deciding which xref description to assign to a gene as the old script.

fix bug that if -dumpcheck set and files not found then the script failed instead of dumping the files