contigScores.push_back(scores1[ABaseMap[i]]);
if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[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 threshold. In that case eliminate base
contigScores.push_back(scores1[ABaseMap[i]]);
if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[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 threshold. In that case eliminate base