private:
struct linePair {
- int start;
+ unsigned long int start;
int numSeqs;
- linePair(long 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;
int createProcesses(string, string, 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
- bool abort, realign, MPIWroteAccnos;
+ bool abort, realign;
string fastafile, templatefile, outputDir, search;
int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
float divR;