Exit if an unknown option is used. recalc_display_xrefs added to just do that bit. Some general tiding up too

if noxref_database is specified do not try to write to the xref database. Needed for -recalc_display_xrefs option

if no xref database is specified in the config file then do not try to connect to it. Needed for -recalc_display_xrefs option

so it can be easily identified which evidence was used by ensembl or havana in
a merged transcript

the xref table, not from the external_db table.

fixed.

identifiers (probably there due to copying and pasting).

the program used to align these cDNAs was Exonerate, not GeneWise.

check that all .gz and .Z files are not corrupt as messages are misseed bu users. The code now does a gzip -t test and if it fails causes an error. Takes alot longer now due to the test but it may save time in th elong run from users missing not very obvious messages

change dependent_xref removal back to working and check for 'FAILED_PRIORITY' in the unmapped_object creation as these are NOT unmapped