X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=719bf3dc6c44cd3880ebc8b1c4d3dc352a448ee1;hb=e840ba0e90a2b2be39e0910e4be23dde6a14cbac;hp=fa78b69d653cb841c33833d6249bab6b6ecaf18c;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index fa78b69..719bf3d 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");
@@ -25,50 +26,88 @@ QualityScores::QualityScores(){
 
 /**************************************************************************************************/
 
-QualityScores::QualityScores(ifstream& qFile, int l){
+QualityScores::QualityScores(ifstream& qFile){
 	try {
 		
 		m = MothurOut::getInstance();
-
-		seqName = "";
-		seqLength = l;
+		
+		/*seqName = "";
 		int score;
 		
-		//string line;
-		//m->getline(qFile, line); 
-		//istringstream nameStream(line);
-	
 		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);
+		
+		if (seqName == "")	{
+			m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg()));
+			m->mothurOutEndLine(); 
 		}
-
-		//m->getline(qFile, line);
-		//istringstream qualStream(line);
-	
-		//while(qualStream){
-		//	qualStream >> score;
-		//	qScores.push_back(score);
-		//}
-		//qScores.pop_back();
+		else{
+			seqName = seqName.substr(1);
+		}
+		cout << seqName << endl;	
+		string qScoreString = m->getline(qFile);
+		cout << qScoreString << endl;	
+		istringstream qScoreStringStream(qScoreString);
+		int count = 0;
+		while(!qScoreStringStream.eof()){
+			if (m->control_pressed) { break; }
+			qScoreStringStream >> score;
+			qScores.push_back(score);
+			cout << score << '\t' << count << endl;
+			count++;
+		}
+		qScores.pop_back();*/
+		string scores = "";
 		
-		//seqLength = qScores.size();	
+		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;
+		}
 		
-		for(int i=0;i<seqLength;i++){
-			qFile >> score;
+		//convert scores string to qScores
+		istringstream qScoreStringStream(scores);
+		
+		int score;
+		while(!qScoreStringStream.eof()){
+			
+			if (m->control_pressed) { break; }
+			
+			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);
 	}							
-
+	
 }
 
 /**************************************************************************************************/
@@ -116,8 +155,10 @@ void QualityScores::trimQScores(int start, int 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();
@@ -165,9 +206,12 @@ 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) {
@@ -198,16 +242,17 @@ 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) {
@@ -232,12 +277,13 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		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);
 			
@@ -250,7 +296,6 @@ 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));
@@ -299,7 +344,68 @@ 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);
 	}
 }