fixed bug in seqerrorcommand

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index db3a4a97c9e9e6f64c828bfab5f66cafecfe3b24..18b0b72f9ae536e01c889315d2d753b421ee6bb0 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -230,6 +230,8 @@ int SeqErrorCommand::execute(){
        try{
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
+               maxLength = 2000;
+               
                string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
                m->openOutputFile(errorSummaryFileName, errorSummaryFile);
                outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
@@ -259,11 +261,11 @@ int SeqErrorCommand::execute(){
                        m->openInputFile(qualFileName, qualFile);
                        report = ReportFile(reportFile, reportFileName);
                        
-                       qualForwardMap.resize(1000);
-                       qualReverseMap.resize(1000);
-                       for(int i=0;i<1000;i++){
-                               qualForwardMap[i].assign(100,0);
-                               qualReverseMap[i].assign(100,0);
+                       qualForwardMap.resize(maxLength);
+                       qualReverseMap.resize(maxLength);
+                       for(int i=0;i<maxLength;i++){
+                               qualForwardMap[i].assign(maxLength,0);
+                               qualReverseMap[i].assign(maxLength,0);
                        }                               
                }
                
@@ -282,18 +284,18 @@ int SeqErrorCommand::execute(){
                qScoreErrorMap['a'].assign(41, 0);
                
                map<char, vector<int> > errorForward;
-               errorForward['m'].assign(1000,0);
-               errorForward['s'].assign(1000,0);
-               errorForward['i'].assign(1000,0);
-               errorForward['d'].assign(1000,0);
-               errorForward['a'].assign(1000,0);
+               errorForward['m'].assign(maxLength,0);
+               errorForward['s'].assign(maxLength,0);
+               errorForward['i'].assign(maxLength,0);
+               errorForward['d'].assign(maxLength,0);
+               errorForward['a'].assign(maxLength,0);
                
                map<char, vector<int> > errorReverse;
-               errorReverse['m'].assign(1000,0);
-               errorReverse['s'].assign(1000,0);
-               errorReverse['i'].assign(1000,0);
-               errorReverse['d'].assign(1000,0);
-               errorReverse['a'].assign(1000,0);       
+               errorReverse['m'].assign(maxLength,0);
+               errorReverse['s'].assign(maxLength,0);
+               errorReverse['i'].assign(maxLength,0);
+               errorReverse['d'].assign(maxLength,0);
+               errorReverse['a'].assign(maxLength,0);  
                
 
                string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
@@ -310,7 +312,6 @@ 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 +341,17 @@ 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 +369,8 @@ 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();       
@@ -724,7 +718,7 @@ void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map
                outputNames.push_back(errorForwardFileName);  outputTypes["error.forward"].push_back(errorForwardFileName);
 
                errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
-               for(int i=0;i<1000;i++){
+               for(int i=0;i<maxLength;i++){
                        float match = (float)errorForward['m'][i];
                        float subst = (float)errorForward['s'][i];
                        float insert = (float)errorForward['i'][i];
@@ -742,7 +736,7 @@ void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map
                outputNames.push_back(errorReverseFileName);  outputTypes["error.reverse"].push_back(errorReverseFileName);
 
                errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
-               for(int i=0;i<1000;i++){
+               for(int i=0;i<maxLength;i++){
                        float match = (float)errorReverse['m'][i];
                        float subst = (float)errorReverse['s'][i];
                        float insert = (float)errorReverse['i'][i];