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Specify 5' or 3' UTR in the GTF file

For trans-spliced transcripts, augment the CDS IDs with the location, to prevent multi-row features having different seq_region names and/or strands

Update GTFSerializer.pm

Skipping trans-splicing transcripts and the gene if it's a single transcript gene with optimisation call.

[ENSCORESW-1451] Stop logger utility from terminating host process. error() can now be caught via try/catch or eval.

Fixed fetch_all_by_Slice_and_external_dbname_link

Need to clean-up the additional lookups too

keep overall count

fastmap expects seq region name not id

$self->get_DBEntryAdaptor() doesn't exist

This reverts commit b6a99d4a, reversing
changes made to ac9e1dc1.

Conflicts:

	modules/Bio/EnsEMBL/DBSQL/BaseSequenceAdaptor.pm