X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=ae85d86199c3ce9fbec09aac5525b17db3c4297a;hb=59814dd1de1def2b7d162c27c21190d8f1199cba;hp=fca3d9f4c9cd17947116fbdb9a872bfce863fe47;hpb=662c0b60d65f79f672ab199300b7ee4975233465;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index fca3d9f..ae85d86 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -46,14 +46,66 @@ QualityScores::QualityScores(ifstream& qFile){
 		}
 		
 		string qScoreString = m->getline(qFile);
+		while(qFile.peek() != '>' && qFile.peek() != EOF){
+			qScoreString +=  ' ' + m->getline(qFile);
+		}
 		
 		istringstream qScoreStringStream(qScoreString);
+		int count = 0;
 		while(!qScoreStringStream.eof()){
-			qScoreStringStream >> score;
+			if (m->control_pressed) { break; }
+			qScoreStringStream >> score;  m->gobble(qScoreStringStream);
+
 			qScores.push_back(score);
+			count++;
 		}
-		qScores.pop_back();
+		//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();
+		//cout << "seqlenght = " << 	seqLength << '\t' << count << endl;
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "QualityScores", "QualityScores");
@@ -102,6 +154,9 @@ void QualityScores::trimQScores(int start, int end){
 	try {
 		vector<int> hold;
 		
+
+		//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;		
@@ -194,7 +249,6 @@ 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;
 			}
 		}
@@ -229,28 +283,34 @@ 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);
 		
@@ -310,6 +370,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
 		int seqLength = errorSeq.size();
 		
 		int qIndex = start - 1;
+
 		for(int i=0;i<seqLength;i++){
 			
 			if(errorSeq[i] == 'm')		{	qualErrorMap['m'][qScores[qIndex]] += weight;	}