+ }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 threshold. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores2[BBaseMap[i]] < pDataArray->threshold) { } //
+ else {
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }
+ }else { contig += seq2[i]; }
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores1[ABaseMap[i]] < pDataArray->threshold) { } //
+ else {
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }
+ }else { contig += seq1[i]; }