X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=1f86efc51304cc81fa2f359c8b2c996da52e8c30;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=4998b3d1c4dabd18b97fb8f33e36860127e757e5;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 4998b3d..1f86efc 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -32,18 +32,22 @@ QualityScores::QualityScores(ifstream& qFile){
 		m = MothurOut::getInstance();
 
 		int score;
-		seqName = getSequenceName(qFile);
+		seqName = getSequenceName(qFile); m->gobble(qFile);
 		
+        if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "'\n.");  }
+        
 		if (!m->control_pressed) {
-            string qScoreString = m->getline(qFile);
-            //cout << qScoreString << endl;
+            string qScoreString = m->getline(qFile); m->gobble(qFile);
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + qScoreString + "'\n.");  }
+            
             while(qFile.peek() != '>' && qFile.peek() != EOF){
                 if (m->control_pressed) { break; }
-                string temp = m->getline(qFile);
-                //cout << temp << endl;
+                string temp = m->getline(qFile); m->gobble(qFile);
+                //if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n.");  }
                 qScoreString +=  ' ' + temp;
             }
-            //cout << "done reading " << endl;	
+            //cout << "done reading " << endl;
             istringstream qScoreStringStream(qScoreString);
             int count = 0;
             while(!qScoreStringStream.eof()){
@@ -51,6 +55,8 @@ QualityScores::QualityScores(ifstream& qFile){
                 string temp;
                 qScoreStringStream >> temp;  m->gobble(qScoreStringStream);
                 
+                //if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n.");  }
+                
                 //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);
@@ -62,7 +68,7 @@ QualityScores::QualityScores(ifstream& qFile){
         }
 		
 		seqLength = qScores.size();
-		//cout << "seqlength = " << seqLength << '\t' << count << endl;
+		//cout << "seqlength = " << seqLength  << endl;
 		
 	}
 	catch(exception& e) {
@@ -83,9 +89,7 @@ string QualityScores::getSequenceName(ifstream& qFile) {
             
 			name = name.substr(1); 
             
-            for (int i = 0; i < name.length(); i++) {
-                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-            }
+            m->checkName(name);
             
         }else{ m->mothurOut("Error in reading your qfile, at position " + toString(qFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
         
@@ -100,10 +104,7 @@ string QualityScores::getSequenceName(ifstream& qFile) {
 void QualityScores::setName(string name) {
 	try {
       
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-        }     
-    
+        m->checkName(name);   
         seqName = name;
 	}
 	catch(exception& e) {