Use a different temp directory for each NetMHCcons instance, moved

mutate from epitopes into immuno, parse stdout of NetMHCcons instead of
xls files (to avoid clobbering hardcoded output file path)
This ends up getting tested implicitly quite a bit since, if the index is off by 1, the reference bases wouldn't match what's in the VCF. 

I agree that we should add more unit tests for this function, it's an extremely critical path.