X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=qualityscores.cpp;h=3a1687bf9e174d77ddded9eaf331d6f1a78da734;hp=8b8e4ec22c68ea406ddcafeee6e4a1abb280566a;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=6973be461c47c057531f447de22003a30cabc193

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 8b8e4ec..3a1687b 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -30,30 +30,46 @@ QualityScores::QualityScores(ifstream& qFile){
 	try {
 		
 		m = MothurOut::getInstance();
-		
-		seqName = "";
+
 		int score;
+		seqName = getSequenceName(qFile); m->gobble(qFile);
+		
+        if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "'\n.");  }
+        
+		if (!m->control_pressed) {
+            string qScoreString = m->getline(qFile); m->gobble(qFile);
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + qScoreString + "'\n.");  }
+            
+            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.");  }
+                qScoreString +=  ' ' + temp;
+            }
+            //cout << "done reading " << endl;
+            istringstream qScoreStringStream(qScoreString);
+            int count = 0;
+            while(!qScoreStringStream.eof()){
+                if (m->control_pressed) { break; }
+                string temp;
+                qScoreStringStream >> temp;  m->gobble(qScoreStringStream);
+                
+                //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"; }
+                convert(temp, score);
+                
+                //cout << count << '\t' << score << endl;
+                qScores.push_back(score);
+                count++;
+            }
+        }
 		
-		qFile >> seqName; 
-		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);
-		
-		istringstream qScoreStringStream(qScoreString);
-		while(!qScoreStringStream.eof()){
-			qScoreStringStream >> score;
-			qScores.push_back(score);
-		}
-		qScores.pop_back();
 		seqLength = qScores.size();
+		//cout << "seqlength = " << seqLength  << endl;
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "QualityScores", "QualityScores");
@@ -61,7 +77,41 @@ QualityScores::QualityScores(ifstream& qFile){
 	}							
 	
 }
-
+//********************************************************************************************************************
+string QualityScores::getSequenceName(ifstream& qFile) {
+	try {
+		string name = "";
+		
+        qFile >> name;
+        m->getline(qFile);
+		
+		if (name.length() != 0) { 
+            
+			name = name.substr(1); 
+            
+            m->checkName(name);
+            
+        }else{ m->mothurOut("Error in reading your qfile, at position " + toString(qFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
+        
+		return name;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "QualityScores", "getSequenceName");
+		exit(1);
+	}
+}
+//********************************************************************************************************************
+void QualityScores::setName(string name) {
+	try {
+      
+        m->checkName(name);   
+        seqName = name;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "QualityScores", "setName");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 
 string QualityScores::getName(){
@@ -80,7 +130,7 @@ string QualityScores::getName(){
 void QualityScores::printQScores(ofstream& qFile){
 	try {
 		
-		double aveQScore = calculateAverage();
+		double aveQScore = calculateAverage(false);
 		
 		qFile << '>' << seqName << '\t' << aveQScore << endl;
 		
@@ -102,6 +152,9 @@ 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;		
@@ -147,7 +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;
@@ -175,7 +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();
@@ -187,12 +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;
 			}
@@ -216,7 +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();
@@ -228,35 +291,44 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		
 		int end = windowSize;
 		int start = 0;
-		
+
 		if(seqLength < windowSize) {	return 0;	}
 			
-		while(start < seqLength){
+		while((start+windowSize) < seqLength){
 			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;
 				break;
 			}
+			
 			start += stepSize;
 			end = start + windowSize;
-			if(end >= seqLength){	end = seqLength - 1;	}
+				
+			if(end >= seqLength){	end = seqLength;	}
+				
 		}
-		
+	
 		if(end == -1){	end = seqLength;	}
 		
+		//failed first window
+		if (end < windowSize) { return 0; }
+			
 		sequence.setUnaligned(rawSequence.substr(0,end));
 		trimQScores(-1, end);
 		
 		return 1;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "QualityScores", "flipQScores");
+		m->errorOut(e, "QualityScores", "stripQualWindowAverage");
 		exit(1);
 	}							
 	
@@ -264,21 +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
@@ -288,7 +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;	}
@@ -315,10 +391,11 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
 			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] == 'a')	{	qualErrorMap['a'][qScores[qIndex]] += weight;	/*if(qScores[qIndex] != 0){	cout << qIndex << '\t';		}*/	}
 			else if(errorSeq[i] == 'd')	{	/*	there are no qScores for deletions	*/		}
 
 			if(errorSeq[i] != 'd')		{	qIndex++;	}
+						
 			if(qIndex > stop){	break;	}
 		}	
 	}
@@ -351,13 +428,13 @@ void QualityScores::updateReverseMap(vector<vector<int> >& reverseMap, int start
 	try {
 		
 		int index = 0;
-		for(int i=stop-1;i>=start;i--){
+		for(int i=stop-1;i>=start-1;i--){
 			reverseMap[index++][qScores[i]] += weight;
 		}
 		
 	}	
 	catch(exception& e) {
-		m->errorOut(e, "QualityScores", "updateForwardMap");
+		m->errorOut(e, "QualityScores", "updateReverseMap");
 		exit(1);
 	}
 }