X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=4dd5b38d4f7ab3895d7fa305bdb57f2e9ab5a628;hb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;hp=4b315b1c397d3a42921b0071253065b26b4befe6;hpb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 4b315b1..4dd5b38 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");
@@ -25,32 +26,75 @@ QualityScores::QualityScores(){
 
 /**************************************************************************************************/
 
-QualityScores::QualityScores(ifstream& qFile){
+QualityScores::QualityScores(ifstream& qFile, int l){
 	try {
 		
 		m = MothurOut::getInstance();
 
 		seqName = "";
-		seqLength = -1;
+		seqLength = l;
 		int score;
 		
-		string line;
-		getline(qFile, line);
-		istringstream nameStream(line);
-	
-		nameStream >> seqName;
-		seqName = seqName.substr(1); 
+		qFile >> seqName; 
 
-		getline(qFile, line);
-		istringstream qualStream(line);
+		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;
+		//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);
+		}*/		
+		
+		
+		
+		for(int i=0;i<seqLength;i++){
+			qFile >> score;
 			qScores.push_back(score);
 		}
-		qScores.pop_back();
-		
-		seqLength = qScores.size();	
+		m->gobble(qFile);
+
 	}
 	catch(exception& e) {
 		m->errorOut(e, "QualityScores", "QualityScores");
@@ -58,7 +102,6 @@ QualityScores::QualityScores(ifstream& qFile){
 	}							
 
 }
-
 /**************************************************************************************************/
 
 string QualityScores::getName(){
@@ -104,8 +147,10 @@ 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();
@@ -153,9 +198,12 @@ 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) {
@@ -193,9 +241,11 @@ bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshol
 		
 		if(end == -1){	end = seqLength;	}
 		
+		
 		sequence.setUnaligned(rawSequence.substr(0,end));
 		trimQScores(-1, end);
 		
+		
 		return 1;
 	}
 	catch(exception& e) {
@@ -213,14 +263,15 @@ 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;
 
@@ -230,7 +281,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 			double windowAverage = windowSum / (double)(end-start);
 			
 			if(windowAverage < qThreshold){
-				end = start;
+				end = end - stepSize;
 				break;
 			}
 			start += stepSize;
@@ -241,6 +292,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		
 		if(end == -1){	end = seqLength;	}
 		
+		
 		sequence.setUnaligned(rawSequence.substr(0,end));
 		trimQScores(-1, end);
 		
@@ -287,7 +339,66 @@ 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++;	}
+
+		}	
+	}
+	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);
 	}
 }