m = MothurOut::getInstance();
seqName = "";
seqLength = -1;
+
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");
seqLength = l;
int score;
- //string line;
- //m->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
m->gobble(qFile);
if (seqName == "") { m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg())); m->mothurOutEndLine(); }
}
/**************************************************************************************************/
-/**************************************************************************************************/
-
string QualityScores::getName(){
try {
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);
}
}