/**************************************************************************************************/
-QualityScores::QualityScores(ifstream& qFile, int l){
+QualityScores::QualityScores(ifstream& qFile){
try {
m = MothurOut::getInstance();
- seqName = "";
- seqLength = l;
int score;
+ seqName = getSequenceName(qFile);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "'\n."); }
+
+ if (!m->control_pressed) {
+ string qScoreString = m->getline(qFile);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + qScoreString + "'\n."); }
+
+ while(qFile.peek() != '>' && qFile.peek() != EOF){
+ if (m->control_pressed) { break; }
+ string temp = m->getline(qFile);
+ if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n."); }
+ qScoreString += ' ' + temp;
+ }
+ //cout << "done reading " << endl;
+ istringstream qScoreStringStream(qScoreString);
+ int count = 0;
+ while(!qScoreStringStream.eof()){
+ if (m->control_pressed) { break; }
+ string temp;
+ qScoreStringStream >> temp; m->gobble(qScoreStringStream);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n."); }
+
+ //check temp to make sure its a number
+ if (!m->isContainingOnlyDigits(temp)) { m->mothurOut("[ERROR]: In sequence " + seqName + "'s quality scores, expected a number and got " + temp + ", setting score to 0."); m->mothurOutEndLine(); temp = "0"; }
+ convert(temp, score);
+
+ //cout << count << '\t' << score << endl;
+ qScores.push_back(score);
+ count++;
+ }
+ }
- 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, 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 = "";
-
- in >> name;
- //cout << name << endl;
- if (name.length() != 0) {
- saveName = name.substr(1);
- while (!in.eof()) {
- char c = in.get();
- if (c == 10 || c == 13){ break; }
- else { name += c; }
- }
- m->gobble(in);
- }
-
- while(in){
- char letter= in.get();
- if(letter == '>'){ in.putback(letter); break; }
- else{ scores += letter; }
- }
-
- //istringstream iss (scores,istringstream::in);
-
- //int count = 0; int tempScore;
- //while (iss) { iss >> tempScore; count++; }
- //cout << saveName << '\t' << count << endl;
-
- m->gobble(in);
- }*/
-
-
+ seqLength = qScores.size();
+ //cout << "seqlength = " << seqLength << '\t' << count << endl;
- for(int i=0;i<seqLength;i++){
- qFile >> score;
- qScores.push_back(score);
- }
- m->gobble(qFile);
-
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");
exit(1);
}
-
+
+}
+//********************************************************************************************************************
+string QualityScores::getSequenceName(ifstream& qFile) {
+ try {
+ string name = "";
+
+ qFile >> name;
+ m->getline(qFile);
+
+ if (name.length() != 0) {
+
+ name = name.substr(1);
+
+ m->checkName(name);
+
+ }else{ m->mothurOut("Error in reading your qfile, at position " + toString(qFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "getSequenceName");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+void QualityScores::setName(string name) {
+ try {
+
+ m->checkName(name);
+ seqName = name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "setName");
+ exit(1);
+ }
}
/**************************************************************************************************/
try {
vector<int> hold;
+
+ //cout << seqName << '\t' << start << '\t' << end << '\t' << qScores.size() << endl;
+ //for (int i = 0; i < qScores.size(); i++) { cout << qScores[i] << end; }
if(end == -1){
hold = vector<int>(qScores.begin()+start, qScores.end());
qScores = hold;
if(rollingSum / (double)(i+1) < qThreshold){
end = i;
-// cout << i+1 << '\t' << seqName << '\t' << rollingSum / (double)(i+1) << endl;
break;
}
}
int end = windowSize;
int start = 0;
-
+
if(seqLength < windowSize) { return 0; }
- while(start < seqLength){
+ while((start+windowSize) < seqLength){
double windowSum = 0.0000;
for(int i=start;i<end;i++){
windowSum += qScores[i];
}
double windowAverage = windowSum / (double)(end-start);
-
+
if(windowAverage < qThreshold){
end = end - stepSize;
break;
}
+
start += stepSize;
end = start + windowSize;
- if(end >= seqLength){ end = seqLength - 1; }
+
+ if(end >= seqLength){ end = seqLength; }
+
}
-
+
if(end == -1){ end = seqLength; }
+ //failed first window
+ if (end < windowSize) { return 0; }
+
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);
return 1;
}
catch(exception& e) {
- m->errorOut(e, "QualityScores", "flipQScores");
+ m->errorOut(e, "QualityScores", "stripQualWindowAverage");
exit(1);
}
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] == 's') { qualErrorMap['s'][qScores[qIndex]] += weight; }
else if(errorSeq[i] == 'i') { qualErrorMap['i'][qScores[qIndex]] += weight; }
- else if(errorSeq[i] == 'a') { qualErrorMap['a'][qScores[qIndex]] += weight; }
+ else if(errorSeq[i] == 'a') { qualErrorMap['a'][qScores[qIndex]] += weight; /*if(qScores[qIndex] != 0){ cout << qIndex << '\t'; }*/ }
else if(errorSeq[i] == 'd') { /* there are no qScores for deletions */ }
if(errorSeq[i] != 'd') { qIndex++; }
-
+
+ if(qIndex > stop){ break; }
}
}
catch(exception& e) {
try {
int index = 0;
- for(int i=stop-1;i>=start;i--){
+ for(int i=stop-1;i>=start-1;i--){
reverseMap[index++][qScores[i]] += weight;
}
}
catch(exception& e) {
- m->errorOut(e, "QualityScores", "updateForwardMap");
+ m->errorOut(e, "QualityScores", "updateReverseMap");
exit(1);
}
}
projects / mothur.git / blobdiff