Force MyISAM engine for job and job_status table to avoid deadlocks
added --checksum option
if used, contig identity is assessed based on checksum rather than name
Fix use vars, removed comma
Merge pull request #6 from swingingsimian/master

Fix use vars, removed comma
Ambiguous codes translated to N during sequence load
store cleaned sequence with ambiguous codes via separate variable
update the seq object during load
removed out of date test runnables
added flag for ambiguous base storage
flag allows replace ambiguous bases control
Bug fix: The protein id for a gene needs to be fetched from the transcripts supporting features, not only from the exons supporting features.
Update farm bin path.
protein_id renamed to hit_name, which is what the code fetches.
Added comment on PAF/DAF priority since this is returning the first hit_name found.
Sort supporting features before getting the hit name so that the PAFs are prioritised over the DAFs.
Reminder that Rfam now have a mirror at EBI and we may wish to use this instead in the future
Merge pull request #5 from magaliruffier/master

added --checksum option
Do not create an input_id for the MT unless "use_mt => 1" is used