initial commit of VEP plugin to produce mutant protein sequence
only create fasta files if we are going to use them, also bugfixes
start using custom MutantProteinSeqs VEP plugin, store resultant fasta files
send working directory to vep plugin, check protein sequence files exist
fix off by one errors.
do not break up sequence in fasta files by newlines.
pass in working directory as option to plugin so the fasta files are created in the correct directory