took out couts

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 1ef074df88919d9e15ac1655ea217c37b74949f4..8b8e4ec22c68ea406ddcafeee6e4a1abb280566a 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -194,7 +194,6 @@ 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 +309,7 @@ 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;   }

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index db3a4a97c9e9e6f64c828bfab5f66cafecfe3b24..407850f6ef80ac0c0d47811b785873d67f03e319 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -310,7 +310,6 @@ int SeqErrorCommand::execute(){
                        if (m->control_pressed) { errorSummaryFile.close();     errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
                
                        Sequence query(queryFile);
-                       cout << "gotQuery" << endl;
                        
                        int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
                        int closestRefIndex = chimeraTest.getClosestRefIndex();
@@ -340,23 +339,17 @@ int SeqErrorCommand::execute(){
 
                        if(qualFileName != "" && reportFileName != ""){
                                report = ReportFile(reportFile);
-                               cout << "gotReport" << endl;
                                
 //                             int origLength = report.getQueryLength();
                                int startBase = report.getQueryStart();
                                int endBase = report.getQueryEnd();
 
                                quality = QualityScores(qualFile);
-                               cout << "gotQuality" << endl;
 
                                if(!ignoreSeq){
-                                       cout << "not ignoring" << endl;
                                        quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
-                                       cout << "updateQScoreErrorMap" << endl;
                                        quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
-                                       cout << "updateForwardMap" << endl;
                                        quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
-                                       cout << "updateReverseMap" << endl;
                                }
                        }                       
 
@@ -374,9 +367,8 @@ int SeqErrorCommand::execute(){
                        }
 
                        index++;
-                       cout << "end of loop:\t" << index << endl;
                        
-                       if(index % 1000 == 0){  cout << index << endl;  }
+                       if(index % 1000 == 0){  m->mothurOut(toString(index) + '\n');   }
                }
                queryFile.close();
                errorSummaryFile.close();