if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
int oStart = contig.length();
+ //cout << fSeq.getAligned() << endl; cout << rSeq.getAligned() << endl;
for (int i = overlapStart; i < overlapEnd; i++) {
+ //cout << seq1[i] << ' ' << seq2[i] << ' ' << scores1[ABaseMap[i]] << ' ' << scores2[BBaseMap[i]] << endl;
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]; }
}
-
+ //cout << contig << endl;
+ //exit(1);
if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart); if (contig.length() == 0) { trashCode += "l"; } }
if(trashCode.length() == 0){