This is an option for turning on or off exonerate.  You might want to do
this if the assembly hasn't changed.

Use seq_region mappings correctly by getting all external seq_region_ids
for our internal seq_region_id and then using an IN-list in the
subsequent query.

add_xref now takes a hash instead  of a list for easy maintainance. Lots of docs and removal of old subroutines. perlcritic fixes.

parameter parsing changed for some routines. Added docs to all routines and removed those no longer used

Replaced XrefParser::BaseParser with self. Lots of parameters changes, going from list to hash based parsing for easy maintainance

Edge case support for hive which allows for non-scheme URIs. We now treat these as if they are DB URIs.

Adding support for SQLite since the URI scheme does not take into account the fact that SQLite is a path and the concept of table does not play well with this

output to stdout rather than stderr the list of masters not found. This is to keep the error file for serious problems

DBNAME is no longer a required attribute as we now allow for direct DB connections. SQLHelper is now an attribute of a DBConnection. Methods added to avoid unintentional DB disconnections, working with the DBH safely and quote DB identifiers if required (useful to avoid SQL injection attacks with auto-generated code). Equals method also improved. Associated test cases written.

Added RefSeq_mRNA, RefSeq_mRNA_predicted, RefSeq_ncRNA and RefSeq_ncRNA_predicted external db names to the nucleotide sql.

Removing URIParser sub-package. It was nice in theory but I'd rather support different schemes using extensions to the URI package

Minor POD corrections

Changes to get_official_domain_name, if we can't eliminate multiple HGNCs based on priority, and most common name not found via vega, eliminate HGNCs with worse % identity.

Removing URIParser sub-package. It was nice in theory but I'd rather support different schemes using extensions to the URI package

Remove getting species_id from filename if they are not set. As these have to be set or it dies before that bit is reached.

Remove getting source_id or species_id from filename if they are not set. As these have to be set or it dies before that bit is reached.