oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
- int newStart=0;
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
m->openInputFile(flowFileName, in);
in.seekg(spot);
- unsigned long int newSpot = spot;
string dummy = m->getline(in);
-
//there was not another sequence before the end of the file
unsigned long int sanityPos = in.tellg();