modified reportfile class

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 2e20c57e6245cc66f4b4f9483f643aacd6c1201a..db3a4a97c9e9e6f64c828bfab5f66cafecfe3b24 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -310,6 +310,7 @@ 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();
@@ -339,17 +340,23 @@ 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;
                                }
                        }                       
 
@@ -367,6 +374,8 @@ int SeqErrorCommand::execute(){
                        }
 
                        index++;
+                       cout << "end of loop:\t" << index << endl;
+                       
                        if(index % 1000 == 0){  cout << index << endl;  }
                }
                queryFile.close();