/**************************************************************************************************/
-QualityScores::QualityScores(ifstream& qFile, int l){
+QualityScores::QualityScores(ifstream& qFile){
try {
m = MothurOut::getInstance();
-
- seqName = "";
- seqLength = l;
+
+ /*seqName = "";
int score;
qFile >> seqName;
-
- while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13 || c == -1){ break; } } // get rest of line
- m->gobble(qFile);
- if (seqName == "") { m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg())); m->mothurOutEndLine(); }
- else {
- seqName = seqName.substr(1);
+ m->getline(qFile);
+
+ if (seqName == "") {
+ m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg()));
+ m->mothurOutEndLine();
+ }
+ else{
+ seqName = seqName.substr(1);
+ }
+ cout << seqName << endl;
+ string qScoreString = m->getline(qFile);
+ cout << qScoreString << endl;
+ istringstream qScoreStringStream(qScoreString);
+ int count = 0;
+ while(!qScoreStringStream.eof()){
+ if (m->control_pressed) { break; }
+ qScoreStringStream >> score;
+ qScores.push_back(score);
+ cout << score << '\t' << count << endl;
+ count++;
}
+ qScores.pop_back();*/
+ string scores = "";
- //m->getline(qFile, line);
- //istringstream qualStream(line);
-
- //while(qualStream){
- // qualStream >> score;
- // qScores.push_back(score);
- //}
- //qScores.pop_back();
-
- //seqLength = qScores.size();
-
- /*while(!in.eof()){
- string saveName = "";
- string name = "";
- string scores = "";
+ while(!qFile.eof()){
- in >> name;
- //cout << name << endl;
- if (name.length() != 0) {
- saveName = name.substr(1);
- while (!in.eof()) {
- char c = in.get();
+ qFile >> seqName;
+
+ //get name
+ if (seqName.length() != 0) {
+ seqName = seqName.substr(1);
+ while (!qFile.eof()) {
+ char c = qFile.get();
+ //gobble junk on line
if (c == 10 || c == 13){ break; }
- else { name += c; }
}
- m->gobble(in);
+ m->gobble(qFile);
}
- while(in){
- char letter= in.get();
- if(letter == '>'){ in.putback(letter); break; }
- else{ scores += letter; }
+ //get scores
+ while(qFile){
+ char letter=qFile.get();
+ if((letter == '>')){ qFile.putback(letter); break; }
+ else if (isprint(letter)) { scores += letter; }
}
- //istringstream iss (scores,istringstream::in);
-
- //int count = 0; int tempScore;
- //while (iss) { iss >> tempScore; count++; }
- //cout << saveName << '\t' << count << endl;
+ m->gobble(qFile);
- m->gobble(in);
- }*/
-
+ break;
+ }
+ //convert scores string to qScores
+ istringstream qScoreStringStream(scores);
- for(int i=0;i<seqLength;i++){
- qFile >> score;
+ int score;
+ while(!qScoreStringStream.eof()){
+
+ if (m->control_pressed) { break; }
+
+ qScoreStringStream >> score;
qScores.push_back(score);
}
- m->gobble(qFile);
-
+
+ qScores.pop_back();
+ seqLength = qScores.size();
+
+
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");
exit(1);
}
-
+
}
+
/**************************************************************************************************/
string QualityScores::getName(){
if(rollingSum / (double)(i+1) < qThreshold){
end = i;
-// cout << i+1 << '\t' << seqName << '\t' << rollingSum / (double)(i+1) << endl;
break;
}
}
try {
int seqLength = errorSeq.size();
+
int qIndex = start - 1;
+
for(int i=0;i<seqLength;i++){
if(errorSeq[i] == 'm') { qualErrorMap['m'][qScores[qIndex]] += weight; }
else if(errorSeq[i] == 'd') { /* there are no qScores for deletions */ }
if(errorSeq[i] != 'd') { qIndex++; }
-
+ if(qIndex > stop){ break; }
}
}
catch(exception& e) {