make sure each transcript even if it is in a differernt gene have differernt transcript ext for the same gene name

used to process the mappings if species.pm file is not found.

MGI have added -ps to psuedo gene names but havana have not doen this yet so check for this when getting descriptions etc

For offical naming take the gene name of the most comman transcript name. Also remove any version numbers from the transcripts

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

use priority level as well as the list. Things like MGI and HGNC can come form many places so make sure you get the best one

added master_xref_id to object_xrefs to fix problems with only one entry in the dependent_xref table. Also new routines added to reset the database to specific points in the xref process

Only use the source from the display_xref calculation for the calculation of the gene/transcripts status

query_identity is now xref_identity and target_identity is ensembl_identity in the identity_xref table

make sure if we use clone name for the gene name that we only get each clone anem once, else add -201 at the end and increment for each one.