Fixed typo (= instead of eq) that was causing search regions to be deleted when enhancers were loaded!

Prevent race condition which could lead to confusing results if two projections to the same target (e.g. human-dog and mouse-dog) were run in parallel.

commented out by someone foolish).

changes from code review implemented. Principally the reduction of some duplicated code. Also for the generation of display_xref_ids do not use those where the display_label is just a number. Also perl -w now runs with no warnings. Ah yes and also the triage stuff is now done right at the end as this was done before the pair calculation before which made writing the xrefs for the pairs more complicated than was needed.

changed  if ( defined $refseq_io ) to if ( !defined $refseq_io ), otherwise it
could not open the file

replaced 'shares_CDS_with' with two entries 'shares_CDS_with_ENST' and
'shares_CDS_with_OTTT'

message_only_once

script debugged and modified to produce gene, exon,transcript-and translation stable_ids
with correct prefixes . -start option modified !

be undefined.  Removes a whole lot of warnings when running with -w.