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

Make all external_synonym entries unique.

Corrected location from which display_xref .sql files are uploaded.

Fixed calculation of transcript display_xrefs; wasn't considering translation-transcript relationship properly.

Now use | as separator character in composite hash keys; : was a bad choice since it appears in GO xrefs.

Don't write xref/object_xrefs for sources that have no corresponding external_db entry (but warn about this).

Set label to accession if it's not set otherwise (so that something gets displayed on the web site).

Check all object_xrefs are unique.

Still problem with gene display_xrefs.

No longer write external_db table from source table, since external_db is defined in CVS. Now builds source_idd->external_db_id mapping and writes external_db_id to xref.txt.

Added external_db and version to core xref output.