unsigned long long fend;
int count, start, end, length, pdiffs;
MothurOut* m;
- vector<string> primers;
+ map<string, int> primers;
vector<string> revPrimer;
set<string> badSeqNames;
bool keepprimer, keepdots;
pcrData(){}
- pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, vector<string> pr, vector<string> rpr, string nm, bool kp, bool kd, int st, int en, int l, int pd, unsigned long long fst, unsigned long long fen) {
+ pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, map<string, int> pr, vector<string> rpr, string nm, bool kp, bool kd, int st, int en, int l, int pd, unsigned long long fst, unsigned long long fen) {
filename = f;
goodFasta = gf;
badFasta = bfn;
set<int> lengths;
//pdiffs, bdiffs, primers, barcodes, revPrimers
map<string, int> faked;
- TrimOligos trim(pdiffs, 0, primers, faked, revPrimer);
+ TrimOligos trim(pDataArray->pdiffs, 0, pDataArray->primers, faked, pDataArray->revPrimer);
for(int i = 0; i < pDataArray->fend; i++){ //end is the number of sequences to process
pDataArray->count++;
}
//report progress
- if((i+1) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine(); }
+ if((i+1) % 100 == 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(i+1)+"\n"); }
}
//report progress
- if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOut("Thread Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOutJustToScreen("Thread Processing sequence: " + toString(pDataArray->count)+"\n"); }
goodFile.close();
inFASTA.close();