working on pam

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 0408b83ebaf0d79f31e5290278fa29e567c1cb87..3a1687bf9e174d77ddded9eaf331d6f1a78da734 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,7 +44,7 @@ QualityScores::QualityScores(ifstream& qFile){
             while(qFile.peek() != '>' && qFile.peek() != EOF){
                 if (m->control_pressed) { break; }
                 string temp = m->getline(qFile); m->gobble(qFile);
-                if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n.");  }
+                //if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n.");  }
                 qScoreString +=  ' ' + temp;
             }
             //cout << "done reading " << endl;
@@ -55,7 +55,7 @@ QualityScores::QualityScores(ifstream& qFile){
                 string temp;
                 qScoreStringStream >> temp;  m->gobble(qScoreStringStream);
                 
-                if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n.");  }
+                //if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n.");  }
                 
                 //check temp to make sure its a number
                 if (!m->isContainingOnlyDigits(temp)) { m->mothurOut("[ERROR]: In sequence " + seqName + "'s quality scores, expected a number and got " + temp + ", setting score to 0."); m->mothurOutEndLine(); temp = "0"; }
@@ -130,7 +130,7 @@ string QualityScores::getName(){
 void QualityScores::printQScores(ofstream& qFile){
        try {
                
-               double aveQScore = calculateAverage();
+               double aveQScore = calculateAverage(false);
                
                qFile << '>' << seqName << '\t' << aveQScore << endl;
                
@@ -200,7 +200,7 @@ bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
                
                if(seqName != sequence.getName()){
                        m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
-                       m->mothurOutEndLine();  
+                       m->mothurOutEndLine();  m->control_pressed = true;
                }
                
                int end;
@@ -228,7 +228,7 @@ bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
 
 /**************************************************************************************************/
 
-bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshold){
+bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshold, bool logTransform){
        try {
                string rawSequence = sequence.getUnaligned();
                int seqLength = sequence.getNumBases();
@@ -240,12 +240,22 @@ bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshol
                
                int end = -1;
                double rollingSum = 0.0000;
+        double value = 0.0;
                
                for(int i=0;i<seqLength;i++){
-
-                       rollingSum += (double)qScores[i];
+            
+            if (logTransform)   {
+                rollingSum += (double)pow(10.0, qScores[i]);
+                value = log10(rollingSum / (double)(i+1));
+                
+            } //Sum 10^Q
+            else                {
+                rollingSum += (double)qScores[i];
+                value = rollingSum / (double)(i+1);
+            }
+                       
                        
-                       if(rollingSum / (double)(i+1) < qThreshold){
+                       if(value < qThreshold){
                                end = i;
                                break;
                        }
@@ -269,7 +279,7 @@ bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshol
 
 /**************************************************************************************************/
 
-bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int windowSize, double qThreshold){
+bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int windowSize, double qThreshold, bool logTransform){
        try {
                string rawSequence = sequence.getUnaligned();
                int seqLength = sequence.getNumBases();
@@ -288,9 +298,12 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                        double windowSum = 0.0000;
 
                        for(int i=start;i<end;i++){
-                               windowSum += qScores[i];
+                if (logTransform)   {  windowSum += pow(10.0, qScores[i]);  }
+                else                {  windowSum += qScores[i];             }
                        }
-                       double windowAverage = windowSum / (double)(end-start);
+                       double windowAverage = 0.0;
+            if (logTransform)   { windowAverage = log10(windowSum / (double)(end-start)); }
+            else                { windowAverage = windowSum / (double)(end-start);      }
                                
                        if(windowAverage < qThreshold){
                                end = end - stepSize;
@@ -323,21 +336,25 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 
 /**************************************************************************************************/
 
-double QualityScores::calculateAverage(){
+double QualityScores::calculateAverage(bool logTransform){
        
        double aveQScore = 0.0000;
        
        for(int i=0;i<seqLength;i++){
-               aveQScore += (double) qScores[i];
+        if (logTransform)   {  aveQScore += pow(10.0, qScores[i]);  }
+        else                {  aveQScore += qScores[i];             }
        }
        aveQScore /= (double) seqLength;
+    
+    if (logTransform)   {  aveQScore = log10(aveQScore /(double) seqLength);  }
+    else                {  aveQScore /= (double) seqLength;                 }
        
        return aveQScore;
 }
 
 /**************************************************************************************************/
 
-bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage){
+bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage, bool logTransform){
        try {
                string rawSequence = sequence.getUnaligned();
                bool success = 0;       //guilty until proven innocent
@@ -347,7 +364,7 @@ bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage){
                        m->mothurOutEndLine();  
                } 
                        
-               double aveQScore = calculateAverage();
+               double aveQScore = calculateAverage(logTransform);
                
                if(aveQScore >= qAverage)       {       success = 1;    }
                else                                            {       success = 0;    }