vector<unsigned long long> setFilePosFasta(string, int&);
string sortFile(string, string);
int appendFiles(string, string);
+ int appendBinaryFiles(string, string);
int appendFilesWithoutHeaders(string, string);
int renameFile(string, string); //oldname, newname
string getFullPathName(string);
int openOutputFileAppend(string, ofstream&);
int openOutputFileBinaryAppend(string, ofstream&);
int openInputFile(string, ifstream&);
+ int openInputFileBinary(string, ifstream&);
+ int openInputFileBinary(string, ifstream&, string);
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