bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
bool abort, keepprimer, keepdots;
string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch;
- int start, end, pdiffs, processors, length;
+ int start, end, processors, length;
vector<string> revPrimer, outputNames;
vector<string> primers;
pDataArray->m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); pDataArray->m->control_pressed = true; break;
}else {
if (pDataArray->keepdots) {
- currSeq.filterToPos(start);
- currSeq.filterFromPos(end);
+ currSeq.filterToPos(pDataArray->start);
+ currSeq.filterFromPos(pDataArray->end);
}else {
- string seqString = currSeq.getAligned().substr(0, end);
- seqString = seqString.substr(start);
+ string seqString = currSeq.getAligned().substr(0, pDataArray->end);
+ seqString = seqString.substr(pDataArray->start);
currSeq.setAligned(seqString);
}
}
if (pDataArray->end != -1) {
if (pDataArray->end > currSeq.getAligned().length()) { pDataArray->m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); pDataArray->m->control_pressed = true; break; }
else {
- if (pDataArray->keepdots) { currSeq.filterFromPos(end); }
+ if (pDataArray->keepdots) { currSeq.filterFromPos(pDataArray->end); }
else {
- string seqString = currSeq.getAligned().substr(0, end);
+ string seqString = currSeq.getAligned().substr(0, pDataArray->end);
currSeq.setAligned(seqString);
}
}
}
if (pDataArray->start != -1) {
- if (pDataArray->keepdots) { currSeq.filterToPos(start); }
+ if (pDataArray->keepdots) { currSeq.filterToPos(pDataArray->start); }
else {
- string seqString = currSeq.getAligned().substr(start);
+ string seqString = currSeq.getAligned().substr(pDataArray->start);
currSeq.setAligned(seqString);
}
}