modified seqerror and qualscores

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 4dd5b38d4f7ab3895d7fa305bdb57f2e9ab5a628..fca3d9f4c9cd17947116fbdb9a872bfce863fe47 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -26,82 +26,42 @@ QualityScores::QualityScores(){
 
 /**************************************************************************************************/
 
-QualityScores::QualityScores(ifstream& qFile, int l){
+QualityScores::QualityScores(ifstream& qFile){
        try {
                
                m = MothurOut::getInstance();
-
+               
                seqName = "";
-               seqLength = l;
                int score;
                
                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);
-               }*/             
+               m->getline(qFile);
                
+               if (seqName == "")      {
+                       m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg()));
+                       m->mothurOutEndLine(); 
+               }
+               else{
+                       seqName = seqName.substr(1);
+               }
                
+               string qScoreString = m->getline(qFile);
                
-               for(int i=0;i<seqLength;i++){
-                       qFile >> score;
+               istringstream qScoreStringStream(qScoreString);
+               while(!qScoreStringStream.eof()){
+                       qScoreStringStream >> score;
                        qScores.push_back(score);
                }
-               m->gobble(qFile);
-
+               qScores.pop_back();
+               seqLength = qScores.size();
        }
        catch(exception& e) {
                m->errorOut(e, "QualityScores", "QualityScores");
                exit(1);
        }                                                       
-
+       
 }
+
 /**************************************************************************************************/
 
 string QualityScores::getName(){
@@ -271,12 +231,12 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                int start = 0;
                
                if(seqLength < windowSize) {    return 0;       }
-               
+                       
                while(start < seqLength){
                        double windowSum = 0.0000;
 
                        for(int i=start;i<end;i++){
-                               windowSum += qScores[i];                                
+                               windowSum += qScores[i];
                        }
                        double windowAverage = windowSum / (double)(end-start);
                        
@@ -289,10 +249,8 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                        if(end >= seqLength){   end = seqLength - 1;    }
                }
                
-               
                if(end == -1){  end = seqLength;        }
                
-               
                sequence.setUnaligned(rawSequence.substr(0,end));
                trimQScores(-1, end);
                
@@ -350,6 +308,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
        try {
 
                int seqLength = errorSeq.size();
+               
                int qIndex = start - 1;
                for(int i=0;i<seqLength;i++){
                        
@@ -360,7 +319,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
                        else if(errorSeq[i] == 'd')     {       /*      there are no qScores for deletions      */              }
 
                        if(errorSeq[i] != 'd')          {       qIndex++;       }
-
+                       if(qIndex > stop){      break;  }
                }       
        }
        catch(exception& e) {