alignment->align(oligo, rawSequence.substr(0,length+diffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
alignment->align(oligo, rawSequence.substr(0,length+diffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
- cout << "found match" << endl;
+ if(compareDNASeq(oligo, temp, length, newStart)){
//use needleman to align first primer.length()+numdiffs of sequence to each primer
alignment->align(oligo, rawSequence.substr(0,length+diffs));
oligo = alignment->getSeqAAln();
//use needleman to align first primer.length()+numdiffs of sequence to each primer
alignment->align(oligo, rawSequence.substr(0,length+diffs));
oligo = alignment->getSeqAAln();
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
+ if(compareDNASeq(oligo, temp, length, newStart)){