bool TrimOligos::stripLinker(Sequence& seq, QualityScores& qual){
try {
string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ bool success = ldiffs + 1; //guilty until proven innocent
for(int i=0;i<linker.size();i++){
string oligo = linker[i];
if(rawSequence.length() < oligo.length()){
- success = 0;
+ success = ldiffs + 10;
break;
}
if(qual.getName() != ""){
qual.trimQScores(oligo.length(), -1);
}
- success = 1;
+ success = 0;
break;
}
}
try {
string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ bool success = ldiffs +1; //guilty until proven innocent
for(int i=0;i<linker.size();i++){
string oligo = linker[i];
if(rawSequence.length() < oligo.length()){
- success = 0;
+ success = ldiffs +10;
break;
}
if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
seq.setUnaligned(rawSequence.substr(oligo.length()));
- success = 1;
+ success = 0;
break;
}
}
bool TrimOligos::stripSpacer(Sequence& seq, QualityScores& qual){
try {
string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ bool success = sdiffs+1; //guilty until proven innocent
for(int i=0;i<spacer.size();i++){
string oligo = spacer[i];
if(rawSequence.length() < oligo.length()){
- success = 0;
+ success = sdiffs+10;
break;
}
if(qual.getName() != ""){
qual.trimQScores(oligo.length(), -1);
}
- success = 1;
+ success = 0;
break;
}
}
try {
string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ bool success = sdiffs+1; //guilty until proven innocent
for(int i=0;i<spacer.size();i++){
string oligo = spacer[i];
if(rawSequence.length() < oligo.length()){
- success = 0;
+ success = sdiffs+10;
break;
}
if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
seq.setUnaligned(rawSequence.substr(oligo.length()));
- success = 1;
+ success = 0;
break;
}
}