added picrust and ref taxonomy parameters to make.biom

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 0408b83ebaf0d79f31e5290278fa29e567c1cb87..0c55650b33149148c80374a0b8c03d41a7a4ea53 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,7 +44,7 @@ QualityScores::QualityScores(ifstream& qFile){
             while(qFile.peek() != '>' && qFile.peek() != EOF){
                 if (m->control_pressed) { break; }
                 string temp = m->getline(qFile); m->gobble(qFile);
-                if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n.");  }
+                //if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n.");  }
                 qScoreString +=  ' ' + temp;
             }
             //cout << "done reading " << endl;
@@ -55,7 +55,7 @@ QualityScores::QualityScores(ifstream& qFile){
                 string temp;
                 qScoreStringStream >> temp;  m->gobble(qScoreStringStream);
                 
-                if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n.");  }
+                //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"; }
@@ -200,7 +200,7 @@ bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
                
                if(seqName != sequence.getName()){
                        m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
-                       m->mothurOutEndLine();  
+                       m->mothurOutEndLine();  m->control_pressed = true;
                }
                
                int end;