First pass merge of the core code base from the current HEAD (which was intended to be 57) into this branch (56). This is for Ensembl Genomes; any problems please contact us ASAP.

Edits have happened in the core object adaptors & Registry. All of the changes are 1:1 copies of code from the current head into this branch. All files have been diffed to ensure that the code is identical.

ensembl-56'.

Sprout from master 2009-09-18 10:53:27 UTC Steve Trevanion <st3@sanger.ac.uk> 'Havana not Vega'
Delete:
    misc-scripts/protein_match/process_pmach.pl

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

only study core, est, cdna and coreexpression databases, better checking of analysis.description file

changed config for elephant

Get the sources to be used for display_xrefs and gene decriptions from the species file if it exists