Now throws if a dependent_xref is found, but the source (EntrezGene|MIM) are not in the xref DB. Without this change we end up with sql execute errors later on

During initial source selection, now selects the species in addition to the species_id. If the source_url is mysql:* the source and species are fed to the parser as additional args to the run method. Species and source specific queries can thus be generated

change to throw if dbpattern isn't found

A mapper method for running exonerate jobs inline on the local machine, without using bsub. Useful for debug

Fixed bug in handling LOCAL: files; now the specified file is checksum-ed, rather than a non-existent file

Fixed bug in validate_sources. Now uses the number of rows returned (rather than the row data) to validate the source

Can now support oligonucleotide microarrays other than Affy.
The three affy_* tables are changed to oligo_* tables. New fields are:
  oligo_array.type (currently either AFFY or OLIGO)
  oligo_probe.length
  oligo_probe.description
The existing Affy objects become subclasses of new Oligo objects, but
the API is backwards compatible, so existing pipeline and Web code won't
need changing.