map<string, int> nameMap;
struct linePair {
- unsigned long int start;
- unsigned long int end;
- linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
vector<linePair*> lines;
int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
#ifdef USE_MPI
- int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+ int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long long>&);
#endif
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
-typedef struct seqSumData {
- vector<int>* startPosition;
- vector<int>* endPosition;
- vector<int>* seqLength;
- vector<int>* ambigBases;
- vector<int>* longHomoPolymer;
+struct seqSumData {
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
string filename;
string sumFile;
- unsigned long int start;
- unsigned long int end;
+ unsigned long long start;
+ unsigned long long end;
int count;
MothurOut* m;
string namefile;
seqSumData(){}
- seqSumData(vector<int>* s, vector<int>* e, vector<int>* l, vector<int>* a, vector<int>* h, string f, string sf, MothurOut* mout, unsigned long int st, unsigned long int en, string na, map<string, int> nam) {
- startPosition = s;
- endPosition = e;
- seqLength = l;
- ambigBases = a;
- longHomoPolymer = h;
+ seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
filename = f;
sumFile = sf;
m = mout;
//for each sequence this sequence represents
for (int i = 0; i < num; i++) {
- pDataArray->startPosition->push_back(current.getStartPos());
- pDataArray->endPosition->push_back(current.getEndPos());
- pDataArray->seqLength->push_back(current.getNumBases());
- pDataArray->ambigBases->push_back(current.getAmbigBases());
- pDataArray->longHomoPolymer->push_back(current.getLongHomoPolymer());
+ pDataArray->startPosition.push_back(current.getStartPos());
+ pDataArray->endPosition.push_back(current.getEndPos());
+ pDataArray->seqLength.push_back(current.getNumBases());
+ pDataArray->ambigBases.push_back(current.getAmbigBases());
+ pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
}
outSummary << current.getName() << '\t';