X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=fca3d9f4c9cd17947116fbdb9a872bfce863fe47;hb=662c0b60d65f79f672ab199300b7ee4975233465;hp=aafa5794e206b936793cf6ffce6109f66eebaf86;hpb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index aafa579..fca3d9f 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");
@@ -25,82 +26,42 @@ QualityScores::QualityScores(){
 
 /**************************************************************************************************/
 
-QualityScores::QualityScores(ifstream& qFile, int l){
+QualityScores::QualityScores(ifstream& qFile){
 	try {
 		
 		m = MothurOut::getInstance();
-
+		
 		seqName = "";
-		seqLength = l;
 		int score;
 		
 		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, line);
-		//istringstream qualStream(line);
-	
-		//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);
-		}*/		
+		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);
 		
-		for(int i=0;i<seqLength;i++){
-			qFile >> score;
+		istringstream qScoreStringStream(qScoreString);
+		while(!qScoreStringStream.eof()){
+			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);
 	}							
-
+	
 }
+
 /**************************************************************************************************/
 
 string QualityScores::getName(){
@@ -197,9 +158,12 @@ 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) {
@@ -237,9 +201,11 @@ 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) {
@@ -265,12 +231,12 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		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);
 			
@@ -283,7 +249,6 @@ 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));
@@ -343,6 +308,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
 	try {
 
 		int seqLength = errorSeq.size();
+		
 		int qIndex = start - 1;
 		for(int i=0;i<seqLength;i++){
 			
@@ -353,7 +319,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
 			else if(errorSeq[i] == 'd')	{	/*	there are no qScores for deletions	*/		}
 
 			if(errorSeq[i] != 'd')		{	qIndex++;	}
-
+			if(qIndex > stop){	break;	}
 		}	
 	}
 	catch(exception& e) {