char buffer5 [2];
in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
+ if(header.clipQualRight == 0){ header.clipQualRight = numBases; }
//read clipAdapterLeft
char buffer6 [2];
string seq = read.bases;
if (trim) {
- if(header.clipQualRight != 0){
- seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft+1));
- }
- else{
- seq = seq.substr(header.clipQualLeft-1);
- }
+ seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft+1));
}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]); }
-
- if(header.clipQualRight != 0){
- for (int i = (header.clipQualRight-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
- }
+ for (int i = (header.clipQualRight-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
}
}