Updated gene count script
Updated columns 4 and 5 to count isolates and not mutations, added all_isolates file under data to read from as default input (has a list of all isolates, when no input file provided, runs with all isolates)
Updated columns 4 and 5 to count isolates and not mutations, added all_isolates file under data to read from as default input (has a list of all isolates, when no input file provided, runs with all isolates)