temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = bdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
if (alnLength == 0) { numDiff = bdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = bdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
if (alnLength == 0) { numDiff = bdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = bdiffs + 100; }
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = bdiffs + 100; }
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = bdiffs + 100; }
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = bdiffs + 100; }
if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
group = it->first;
string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
group = it->first;
string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
group = it->first;
if (!keepForward) {
if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
group = it->first;
if (!keepForward) {
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = pdiffs + 100; }
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = pdiffs + 100; }
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;