X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=2ee71e066f22e421b7f312be03da1279b2aa3a7a;hb=fe5bbb79f9434df947347881c47b430112f4253e;hp=f76d9826ee0224cb63d3520a30a0f7b100a5cecf;hpb=0746c58a680458c0bc874b3a5fc1334b12ed2f18;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index f76d982..2ee71e0 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -34,11 +34,8 @@ QualityScores::QualityScores(ifstream& qFile, int l){
 		seqLength = l;
 		int score;
 		
-		//string line;
-		//m->getline(qFile, line); 
-		//istringstream nameStream(line);
-	
 		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(); }
@@ -106,8 +103,6 @@ QualityScores::QualityScores(ifstream& qFile, int l){
 }
 /**************************************************************************************************/
 
-/**************************************************************************************************/
-
 string QualityScores::getName(){
 	
 	try {
@@ -151,8 +146,10 @@ 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();
@@ -267,7 +264,8 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		int end = windowSize;
 		int start = 0;
 		
-
+		if(seqLength < windowSize) {	return 0;	}
+		
 		while(start < seqLength){
 			double windowSum = 0.0000;
 
@@ -340,3 +338,24 @@ bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage){
 }
 
 /**************************************************************************************************/
+
+void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap, string errorSeq, int start, int stop, int weight){
+	try {
+	
+		for(int i=start-1;i<stop;i++){
+			
+			if(errorSeq[i] == 'm')		{	qualErrorMap['m'][qScores[i]] += weight;	}
+			else if(errorSeq[i] == 's')	{	qualErrorMap['s'][qScores[i]] += weight;	}
+			else if(errorSeq[i] == 'i')	{	qualErrorMap['i'][qScores[i]] += weight;	}
+			else if(errorSeq[i] == 'a')	{	qualErrorMap['a'][qScores[i]] += weight;	}
+			else if(errorSeq[i] == 'd')	{	/*		nothing		*/						}
+
+		}	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "updateQScoreErrorMap");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/