fixed indicator grouping problem

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index fce4763dcb891ef56a57f24644b9574ffa51cd1a..3c0d378f709042cc3e1c2ca2b87e730a62dbf359 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -360,12 +360,12 @@ int TrimSeqsCommand::execute(){
                #endif
                
                if (m->control_pressed) {  return 0; }                  
-               cout << "done with driver " << endl;                                                                    
+                                                                               
                for(int i=0;i<fastaFileNames.size();i++){
                        cout << fastaFileNames[i] << endl;
                        
-                       if (m->isBlank(fastaFileNames[i])) { cout << fastaFileNames[i] << " was blank" << endl; remove(fastaFileNames[i].c_str());      }
-                       else if (filesToRemove.count(fastaFileNames[i]) > 0) { cout << fastaFileNames[i] << " was on the remove list" << endl; remove(fastaFileNames[i].c_str()); }
+                       if (m->isBlank(fastaFileNames[i])) {  remove(fastaFileNames[i].c_str());        }
+                       else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
                        else {
                                ifstream inFASTA;
                                string seqName;
@@ -382,7 +382,7 @@ int TrimSeqsCommand::execute(){
                                                if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
                                        }
                                }else{ thisGroup = groupVector[i]; }
-                               cout << thisGroup << '\t' << i  << '\t' << comboStarts << endl; 
+                                       
                                while(!inFASTA.eof()){
                                        if(inFASTA.get() == '>'){
                                                inFASTA >> seqName;
@@ -394,12 +394,12 @@ int TrimSeqsCommand::execute(){
                                inFASTA.close();
                        }
                }
-       cout << "done with fastaFileNames " << endl;            
+               
                if(qFileName != ""){
                        for(int i=0;i<qualFileNames.size();i++){
                                cout << qualFileNames[i] << endl;
-                               if (m->isBlank(qualFileNames[i])) { cout << qualFileNames[i] << " was blank" << endl; remove(qualFileNames[i].c_str()); }
-                               else if (filesToRemove.count(qualFileNames[i]) > 0) { cout << qualFileNames[i] << " was on the remove list" << endl; remove(qualFileNames[i].c_str()); }
+                               if (m->isBlank(qualFileNames[i])) {  remove(qualFileNames[i].c_str());  }
+                               else if (filesToRemove.count(qualFileNames[i]) > 0) {  remove(qualFileNames[i].c_str()); }
                                else {
                                        ifstream inQual;
                                        string seqName;
@@ -419,7 +419,7 @@ int TrimSeqsCommand::execute(){
                                }
                        }
                }
-               cout << "done with qualFileNames " << endl;
+               
                
                if (m->control_pressed) { 
                        for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
@@ -460,8 +460,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                }
                
                ofstream outGroups;
-               //vector<ofstream*> fastaFileNames;
-               //vector<ofstream*> qualFileNames;
                
                if (oligoFile != "") {          
                        m->openOutputFile(groupFile, outGroups);   
@@ -753,7 +751,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                }
                        }
                        
-                       if (allFiles) { m->mothurOut("Done with allfile"); m->mothurOutEndLine(); }
+                       if (allFiles) { m->mothurOut("Done with allfiles"); m->mothurOutEndLine(); }
                }
        
                return exitCommand;