m = MothurOut::getInstance();
seqName = "";
seqLength = -1;
+
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");
seqLength = l;
int score;
- //string line;
- //getline(qFile, line);
- //istringstream nameStream(line);
-
qFile >> seqName;
+
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13 || c == -1){ break; } } // get rest of line
- gobble(qFile);
+ 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);
}
-
- //getline(qFile, line);
+
+ //m->getline(qFile, line);
//istringstream qualStream(line);
//while(qualStream){
//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);
+ }*/
+
+
+
for(int i=0;i<seqLength;i++){
qFile >> score;
qScores.push_back(score);
}
- gobble(qFile);
+ m->gobble(qFile);
}
catch(exception& e) {
}
}
-
/**************************************************************************************************/
string QualityScores::getName(){
qScores = hold;
}
if(start == -1){
- hold = vector<int>(qScores.begin(), qScores.begin()+end); //not sure if indexing is correct
- qScores = hold;
+ if(qScores.size() > end){
+ hold = vector<int>(qScores.begin(), qScores.begin()+end);
+ qScores = hold;
+ }
}
seqLength = qScores.size();
}
}
+ //every score passed
+ if (end == (seqLength-1)) { end = seqLength; }
+
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);
-
+
return 1;
}
catch(exception& e) {
if(end == -1){ end = seqLength; }
+
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);
+
return 1;
}
catch(exception& e) {
int end = windowSize;
int start = 0;
-
+ if(seqLength < windowSize) { return 0; }
+
while(start < seqLength){
double windowSum = 0.0000;
if(end == -1){ end = seqLength; }
+
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);
return success;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+ m->errorOut(e, "QualityScores", "cullQualAverage");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap, string errorSeq, int start, int stop, int weight){
+ 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] == 'd') { /* there are no qScores for deletions */ }
+
+ if(errorSeq[i] != 'd') { qIndex++; }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "updateQScoreErrorMap");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateForwardMap(vector<vector<int> >& forwardMap, int start, int stop, int weight){
+ try {
+
+ int index = 0;
+ for(int i=start-1;i<stop;i++){
+ forwardMap[index++][qScores[i]] += weight;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "updateForwardMap");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateReverseMap(vector<vector<int> >& reverseMap, int start, int stop, int weight){
+ try {
+
+ int index = 0;
+ for(int i=stop-1;i>=start;i--){
+ reverseMap[index++][qScores[i]] += weight;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "updateForwardMap");
exit(1);
}
}