X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=0641d3b7bf4ed8abc588467b946d0678766c5fb0;hb=6da6af5c7f43f9f4f602d224af447805fb01c46c;hp=1ef074df88919d9e15ac1655ea217c37b74949f4;hpb=24083a26340293cb3a0e44bcf79edbc9b31f41db;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 1ef074d..0641d3b 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,16 +44,67 @@ QualityScores::QualityScores(ifstream& qFile){
 		else{
 			seqName = seqName.substr(1);
 		}
-		
 		string qScoreString = m->getline(qFile);
+		while(qFile.peek() != '>' && qFile.peek() != EOF){
+			qScoreString += ' ' + m->getline(qFile);
+		}
 		
 		istringstream qScoreStringStream(qScoreString);
+		int count = 0;
 		while(!qScoreStringStream.eof()){
+			if (m->control_pressed) { break; }
 			qScoreStringStream >> score;
 			qScores.push_back(score);
+			count++;
 		}
 		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; }
+//			}
+//			cout << scores << endl;
+//			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();
+		
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "QualityScores", "QualityScores");
@@ -67,6 +118,7 @@ QualityScores::QualityScores(ifstream& qFile){
 string QualityScores::getName(){
 	
 	try {
+		cout << qScores.size() << '\t';
 		return seqName;
 	}
 	catch(exception& e) {
@@ -102,6 +154,8 @@ void QualityScores::trimQScores(int start, int end){
 	try {
 		vector<int> hold;
 		
+		cout << seqName << '\t' << qScores.size() << '\t' << start << '\t' << end << endl;
+		
 		if(end == -1){		
 			hold = vector<int>(qScores.begin()+start, qScores.end());
 			qScores = hold;		
@@ -194,7 +248,6 @@ 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;
 			}
 		}
@@ -310,7 +363,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
 		int seqLength = errorSeq.size();
 		
 		int qIndex = start - 1;
-		cout << start << '\t' << stop << '\t' << seqLength << endl;
+
 		for(int i=0;i<seqLength;i++){
 			
 			if(errorSeq[i] == 'm')		{	qualErrorMap['m'][qScores[qIndex]] += weight;	}