working on current change

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index c9c65042843bffddf5c6d3d7acca4ab38754ac5e..520d0bb56eae9c66a936311ca71aa5330bf29aa1 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,20 +44,22 @@ QualityScores::QualityScores(ifstream& qFile){
                else{
                        seqName = seqName.substr(1);
                }
+               
                string qScoreString = m->getline(qFile);
                while(qFile.peek() != '>' && qFile.peek() != EOF){
-                       qScoreString += ' ' + m->getline(qFile);
+                       qScoreString +=  ' ' + m->getline(qFile);
                }
                
                istringstream qScoreStringStream(qScoreString);
                int count = 0;
                while(!qScoreStringStream.eof()){
                        if (m->control_pressed) { break; }
-                       qScoreStringStream >> score;
+                       qScoreStringStream >> score;  m->gobble(qScoreStringStream);
+
                        qScores.push_back(score);
                        count++;
                }
-               qScores.pop_back();
+               //qScores.pop_back();
                
 //             string scores = "";
 //             
@@ -102,7 +104,7 @@ QualityScores::QualityScores(ifstream& qFile){
 //             qScores.pop_back();
 
                seqLength = qScores.size();
-               
+               //cout << "seqlenght = " <<     seqLength << '\t' << count << endl;
                
        }
        catch(exception& e) {
@@ -151,7 +153,10 @@ void QualityScores::printQScores(ofstream& qFile){
 void QualityScores::trimQScores(int start, int end){
        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;