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Experimental/merged alternative sequence store

Merge branch 'experimental/alternative_sequence_stores' of https://github.com/Ensembl/ensembl into experimental/alternative_sequence_stores

Seems by passing @_ onwards I broke later initalisation code. Thanks
Travis for picking that up :)

Following on from Alessandro's comments from the pull request.
SequenceAdaptor can now control the cache size and FileFaidx's POD is
now correct.

Specify 5' or 3' UTR in the GTF file

Seems that calling external code could assume the sequence cache is, in
fact, a hash. If the cache is replaced with the wrong data structure
(say a normal hash) then a memory leak will appear as seen in the xref
pipeline whilst dumping sequences.

This reverts commit 38b2e251.

Update GTFSerializer.pm

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