private:
struct linePair {
- int start;
+ unsigned long int start;
int numSeqs;
- linePair(int i, int j) : start(i), numSeqs(j) {}
+ linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
};
vector<int> processIDS; //processid
vector<linePair*> lines;
vector<string> fastaFileNames;
vector<string> namefileNames;
- map<string, int> nameMap;
- map<string, int>::iterator itNames;
+ vector<string> groupfileNames;
+ map<string, vector<string> > nameMap;
+ map<string, vector<string> >::iterator itNames;
Classify* classify;
- string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir;
+ string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
int processors, kmerSize, numWanted, cutoff, iters;
float match, misMatch, gapOpen, gapExtend;
bool abort, probs;
int MPIReadNamesFile(string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
};