while(!m8FileHandle.eof()){
m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
- //cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t';
+ //cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl;
//get rest of junk in line
//while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; }else{ cout << c; } } //
//cout << endl;
m->gobble(m8FileHandle);
- if (searchScore >= minPerID) {
+ if (score >= minPerID) { //this follows broads CS, but probably should be searchScore...
topMatches.push_back(templateAccession);
Scores.push_back(searchScore);
}