if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
int oStart = contig.length();
if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
int oStart = contig.length();
if (seq1[i] == seq2[i]) { //match, add base and choose highest score
contig += seq1[i];
}else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base
if (seq1[i] == seq2[i]) { //match, add base and choose highest score
contig += seq1[i];
}else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base
}else { //seq2 ends before seq1 so take from overlap to length from seq1
for (int i = overlapEnd; i < length; i++) { contig += seq1[i]; }
}
}else { //seq2 ends before seq1 so take from overlap to length from seq1
for (int i = overlapEnd; i < length; i++) { contig += seq1[i]; }
}
if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart); if (contig.length() == 0) { trashCode += "l"; } }
if(trashCode.length() == 0){
if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart); if (contig.length() == 0) { trashCode += "l"; } }
if(trashCode.length() == 0){
if (uniques.size() != 0) {
for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
if (uniques.size() != 0) {
for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
}
for (map<string, pairFastqRead>:: iterator it = pairUniques.begin(); it != pairUniques.end(); it++) {
m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
}
for (map<string, pairFastqRead>:: iterator it = pairUniques.begin(); it != pairUniques.end(); it++) {
else { uniquePrimers.insert(tempPair); }
if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
else { uniquePrimers.insert(tempPair); }
if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
primers[indexPrimer]=newPrimer; indexPrimer++;
primerNameVector.push_back(group);
}else if(type == "BARCODE"){
primers[indexPrimer]=newPrimer; indexPrimer++;
primerNameVector.push_back(group);
}else if(type == "BARCODE"){