Fixed possible undefined behaviour if there are no Blast results for a
particular name.
Extra debug commands
Merge branch 'master' into contig_id_fix
Adding a single $contigID for the accessory genome database insert.
Changed default coreGenomeThreshold to 3
Added a trailing slash to all Directory settings, whether included by
the user or not.
Added additional debugging comments, changed default logfile level to
INFO. Change debug_level=DEBUG in log4p.conf if needed.