Various changes - in the middle of fixes/tidying/all sorts of nonsense.
Various changes - in the middle of fixes/tidying/all sorts of nonsense.

- checks transcripts for non translator/mixed exon strands/long introns before
starting to try to cluster them instead of after. Should get rid of long genscan
intron nightmare

- no longer produces duplicate exons

- started to tidy prune methods - prunes on a per cluster basis now as the rejection
of dodgy transcritps is done before we cluster so should be no need to recluster.

- reduced STDERR output - eventually I'll sort out the debug level flag system thingy
but not right now.

Ensembl/ensembl-pipeline,Ensembl/ensembl-pipeline,Ensembl/ensembl-pipeline