int openInputFile(string, ifstream&, string); //no error given
bool checkLocations(string&, string); //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location. Returns false if cant be found. If found completes name with location
int openInputFile(string, ifstream&, string); //no error given
bool checkLocations(string&, string); //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location. Returns false if cant be found. If found completes name with location