X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=0b7bd0625b914d8a69b298a1b0e88187ddf6757c;hb=20071b183e619c122bf9f63b4bb42722507c4e4a;hp=0641d3b7bf4ed8abc588467b946d0678766c5fb0;hpb=6da6af5c7f43f9f4f602d224af447805fb01c46c;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 0641d3b..0b7bd06 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -36,7 +36,7 @@ QualityScores::QualityScores(ifstream& qFile){
 		
 		qFile >> seqName; 
 		m->getline(qFile);
-		
+		//cout << seqName << endl;	
 		if (seqName == "")	{
 			m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg()));
 			m->mothurOutEndLine(); 
@@ -44,20 +44,32 @@ QualityScores::QualityScores(ifstream& qFile){
 		else{
 			seqName = seqName.substr(1);
 		}
+		
 		string qScoreString = m->getline(qFile);
+		//cout << qScoreString << endl;
 		while(qFile.peek() != '>' && qFile.peek() != EOF){
-			qScoreString += ' ' + m->getline(qFile);
+			if (m->control_pressed) { break; }
+			string temp = m->getline(qFile);
+			//cout << temp << endl;
+			qScoreString +=  ' ' + temp;
 		}
-		
+		//cout << "done reading " << endl;	
 		istringstream qScoreStringStream(qScoreString);
 		int count = 0;
 		while(!qScoreStringStream.eof()){
 			if (m->control_pressed) { break; }
-			qScoreStringStream >> score;
+			string temp;
+			qScoreStringStream >> temp;  m->gobble(qScoreStringStream);
+			
+			//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++;
 		}
-		qScores.pop_back();
+		//qScores.pop_back();
 		
 //		string scores = "";
 //		
@@ -82,7 +94,6 @@ QualityScores::QualityScores(ifstream& qFile){
 //				if((letter == '>')){	qFile.putback(letter);	break;	}
 //				else if (isprint(letter)) { scores += letter; }
 //			}
-//			cout << scores << endl;
 //			m->gobble(qFile);
 //			
 //			break;
@@ -103,7 +114,7 @@ QualityScores::QualityScores(ifstream& qFile){
 //		qScores.pop_back();
 
 		seqLength = qScores.size();
-		
+		//cout << "seqlength = " << seqLength << '\t' << count << endl;
 		
 	}
 	catch(exception& e) {
@@ -118,7 +129,6 @@ QualityScores::QualityScores(ifstream& qFile){
 string QualityScores::getName(){
 	
 	try {
-		cout << qScores.size() << '\t';
 		return seqName;
 	}
 	catch(exception& e) {
@@ -154,8 +164,9 @@ void QualityScores::trimQScores(int start, int end){
 	try {
 		vector<int> hold;
 		
-		cout << seqName << '\t' << qScores.size() << '\t' << start << '\t' << end << endl;
-		
+
+		//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;		
@@ -282,35 +293,41 @@ 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];
 			}
 			double 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);
 	}							
 	
@@ -369,10 +386,11 @@ 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;	}
 		}	
 	}
@@ -405,13 +423,13 @@ 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);
 	}
 }