X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=3f8722f34f83416aa143f21a5a81e99c7329a7d8;hb=5b3eaca079ab3cd055d447bcaf9ea61f7b225621;hp=dd5d6de8da69a000882eadd86f8d2c50f853454f;hpb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index dd5d6de..3f8722f 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -16,6 +16,7 @@ QualityScores::QualityScores(){
 		m = MothurOut::getInstance();
 		seqName = "";
 		seqLength = -1;
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "QualityScores", "QualityScores");
@@ -25,45 +26,90 @@ QualityScores::QualityScores(){
 
 /**************************************************************************************************/
 
-QualityScores::QualityScores(ifstream& qFile, int l){
+QualityScores::QualityScores(ifstream& qFile){
 	try {
 		
 		m = MothurOut::getInstance();
-
+		
 		seqName = "";
-		seqLength = l;
 		int score;
 		
-		string line;
-		getline(qFile, line); gobble(qFile);
-		istringstream nameStream(line);
-	
-		nameStream >> seqName;
-		seqName = seqName.substr(1); 
-
-		//getline(qFile, line);
-		//istringstream qualStream(line);
-	
-		//while(qualStream){
-		//	qualStream >> score;
-		//	qScores.push_back(score);
-		//}
-		//qScores.pop_back();
+		qFile >> seqName; 
+		m->getline(qFile);
 		
-		//seqLength = qScores.size();	
+		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);
+		while(qFile.peek() != '>' && qFile.peek() != EOF){
+			qScoreString += ' ' + m->getline(qFile);
+		}
 		
-		for(int i=0;i<seqLength;i++){
-			qFile >> score;
+		istringstream qScoreStringStream(qScoreString);
+		int count = 0;
+		while(!qScoreStringStream.eof()){
+			if (m->control_pressed) { break; }
+			qScoreStringStream >> score;
 			qScores.push_back(score);
+			count++;
 		}
-		gobble(qFile);
+		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; }
+//			}
+//			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");
 		exit(1);
 	}							
-
+	
 }
 
 /**************************************************************************************************/
@@ -105,14 +151,16 @@ void QualityScores::printQScores(ofstream& qFile){
 void QualityScores::trimQScores(int start, int end){
 	try {
 		vector<int> hold;
-		
+			
 		if(end == -1){		
 			hold = vector<int>(qScores.begin()+start, qScores.end());
 			qScores = hold;		
 		}
 		if(start == -1){
-			hold = vector<int>(qScores.begin(), qScores.begin()+end);	//not sure if indexing is correct
-			qScores = hold;		
+			if(qScores.size() > end){
+				hold = vector<int>(qScores.begin(), qScores.begin()+end);
+				qScores = hold;		
+			}
 		}
 
 		seqLength = qScores.size();
@@ -160,9 +208,12 @@ bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
 			}
 		}
 		
+		//every score passed
+		if (end == (seqLength-1)) { end = seqLength; }
+		
 		sequence.setUnaligned(rawSequence.substr(0,end));
 		trimQScores(-1, end);
-	
+		
 		return 1;
 	}
 	catch(exception& e) {
@@ -193,16 +244,17 @@ 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;
 			}
 		}
 		
 		if(end == -1){	end = seqLength;	}
 		
+		
 		sequence.setUnaligned(rawSequence.substr(0,end));
 		trimQScores(-1, end);
 		
+		
 		return 1;
 	}
 	catch(exception& e) {
@@ -220,24 +272,25 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		int seqLength = sequence.getNumBases();
 		
 		if(seqName != sequence.getName()){
-			m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
-			m->mothurOutEndLine();	
+			m->mothurOut("sequence name mismatch between fasta: " + sequence.getName() + " and qual file: " + seqName);
+			m->mothurOutEndLine();
 		}
 		
 		int end = windowSize;
 		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);
 			
 			if(windowAverage < qThreshold){
-				end = start;
+				end = end - stepSize;
 				break;
 			}
 			start += stepSize;
@@ -245,7 +298,6 @@ 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));
@@ -294,7 +346,68 @@ bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage){
 		return success;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+		m->errorOut(e, "QualityScores", "cullQualAverage");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap, string errorSeq, int start, int stop, int weight){
+	try {
+
+		int seqLength = errorSeq.size();
+		
+		int qIndex = start - 1;
+
+		for(int i=0;i<seqLength;i++){
+			
+			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] == 'd')	{	/*	there are no qScores for deletions	*/		}
+
+			if(errorSeq[i] != 'd')		{	qIndex++;	}
+			if(qIndex > stop){	break;	}
+		}	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "QualityScores", "updateQScoreErrorMap");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateForwardMap(vector<vector<int> >& forwardMap, int start, int stop, int weight){
+	try {
+		
+		int index = 0;
+		for(int i=start-1;i<stop;i++){
+			forwardMap[index++][qScores[i]] += weight;
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "QualityScores", "updateForwardMap");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateReverseMap(vector<vector<int> >& reverseMap, int start, int stop, int weight){
+	try {
+		
+		int index = 0;
+		for(int i=stop-1;i>=start;i--){
+			reverseMap[index++][qScores[i]] += weight;
+		}
+		
+	}	
+	catch(exception& e) {
+		m->errorOut(e, "QualityScores", "updateForwardMap");
 		exit(1);
 	}
 }