temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
+ if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " aligned fragment =" + temp + ", barcode =" + oligo + ", numDiffs = " + toString(numDiff) + "\n"); }
+
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
+ if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
+
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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reverse " + forwardSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
+
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; }
- //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+ if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
if(numDiff < minDiff){
minDiff = numDiff;
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = bdiffs + 100; }
+ if (m->debug) { m->mothurOut("[DEBUG]: reverse " + reverseSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
+
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
if(numDiff < minDiff){
minDiff = numDiff;
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+ if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
+
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
int numDiff = countDiffs(oligo, temp);
if (alnLength == 0) { numDiff = pdiffs + 100; }
+ if (m->debug) { m->mothurOut("[DEBUG]: reverse " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
+
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
if(numDiff < minDiff){
minDiff = numDiff;
temp = temp.substr(0,alnLength);
int numDiff = countDiffs(oligo, temp);
+ if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
+
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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reverse " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n"); }
+
if (alnLength == 0) { numDiff = pdiffs + 100; }
//cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
int numDiff = countDiffs(oligo, temp);
+ if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " aligned fragment =" + temp + ", barcode =" + oligo + ", numDiffs = " + toString(numDiff) + "\n"); }
+
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;