fix trim.seqs / qualscores bug

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index d57ef08ae00e6465edf2cdc17a90da26d968d4f5..0641d3b7bf4ed8abc588467b946d0678766c5fb0 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,16 +44,67 @@ QualityScores::QualityScores(ifstream& qFile){
                else{
                        seqName = seqName.substr(1);
                }
-               
                string qScoreString = m->getline(qFile);
+               while(qFile.peek() != '>' && qFile.peek() != EOF){
+                       qScoreString += ' ' + m->getline(qFile);
+               }
                
                istringstream qScoreStringStream(qScoreString);
+               int count = 0;
                while(!qScoreStringStream.eof()){
+                       if (m->control_pressed) { break; }
                        qScoreStringStream >> score;
                        qScores.push_back(score);
+                       count++;
                }
                qScores.pop_back();
+               
+//             string scores = "";
+//             
+//             while(!qFile.eof()){    
+//                     
+//                     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;  }
+//                             } 
+//                             m->gobble(qFile);
+//                     }
+//                     
+//                     //get scores
+//                     while(qFile){
+//                             char letter=qFile.get();
+//                             if((letter == '>')){    qFile.putback(letter);  break;  }
+//                             else if (isprint(letter)) { scores += letter; }
+//                     }
+//                     cout << scores << endl;
+//                     m->gobble(qFile);
+//                     
+//                     break;
+//             }
+//             
+//             //convert scores string to qScores
+//             istringstream qScoreStringStream(scores);
+//             
+//             int score;
+//             while(!qScoreStringStream.eof()){
+//                     
+//                     if (m->control_pressed) { break; }
+//                     
+//                     qScoreStringStream >> score;
+//                     qScores.push_back(score);
+//             }
+//             
+//             qScores.pop_back();
+
                seqLength = qScores.size();
+               
+               
        }
        catch(exception& e) {
                m->errorOut(e, "QualityScores", "QualityScores");
@@ -67,6 +118,7 @@ QualityScores::QualityScores(ifstream& qFile){
 string QualityScores::getName(){
        
        try {
+               cout << qScores.size() << '\t';
                return seqName;
        }
        catch(exception& e) {
@@ -102,6 +154,8 @@ void QualityScores::trimQScores(int start, int end){
        try {
                vector<int> hold;
                
+               cout << seqName << '\t' << qScores.size() << '\t' << start << '\t' << end << endl;
+               
                if(end == -1){          
                        hold = vector<int>(qScores.begin()+start, qScores.end());
                        qScores = hold;         
@@ -194,7 +248,6 @@ bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshol
                        
                        if(rollingSum / (double)(i+1) < qThreshold){
                                end = i;
-//                             cout << i+1 << '\t' << seqName << '\t' << rollingSum / (double)(i+1) << endl;
                                break;
                        }
                }
@@ -308,9 +361,9 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
        try {
 
                int seqLength = errorSeq.size();
-               cout << start << '\t' << stop << '\t' << seqLength << endl;
                
                int qIndex = start - 1;
+
                for(int i=0;i<seqLength;i++){
                        
                        if(errorSeq[i] == 'm')          {       qualErrorMap['m'][qScores[qIndex]] += weight;   }