}else{
//if you wanted the sfftxt then you already converted the bases to the right case
if (!sfftxt) {
//make the bases you want to clip lowercase and the bases you want to keep upper case
for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { seq[i] = toupper(seq[i]); }
}else{
//if you wanted the sfftxt then you already converted the bases to the right case
if (!sfftxt) {
//make the bases you want to clip lowercase and the bases you want to keep upper case
for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { seq[i] = toupper(seq[i]); }