rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index b23ee1924d1a69ef8783a2d4f343f8b2cec74499..5b64b133a0c3df43cfb018c03d9867136661f100 100644 (file)
--- 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(); 
@@ -46,16 +46,26 @@ QualityScores::QualityScores(ifstream& qFile){
                }
                
                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;  m->gobble(qScoreStringStream);
-
+                       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++;
                }
@@ -104,7 +114,7 @@ QualityScores::QualityScores(ifstream& qFile){
 //             qScores.pop_back();
 
                seqLength = qScores.size();
-               //cout << "seqlenght = " <<     seqLength << '\t' << count << endl;
+               //cout << "seqlength = " << seqLength << '\t' << count << endl;
                
        }
        catch(exception& e) {