fixed bug with trim.seqs- when a file is blank for a grouping mothur removed it,...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5e0541f9cb954575d39d277cdf4a50d6931c21c2..acbead2ed3a77171980ab49e4d8e098dce3c52d8 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -360,10 +360,10 @@ int TrimSeqsCommand::execute(){
                #endif
                
                if (m->control_pressed) {  return 0; }                  
-                                                                               
-               for(int i=0;i<fastaFileNames.size();i++){
                        
-                       if (m->isBlank(fastaFileNames[i])) {  remove(fastaFileNames[i].c_str());        }
+               set<string> blanks;
+               for(int i=0;i<fastaFileNames.size();i++){
+                       if (m->isBlank(fastaFileNames[i])) {   blanks.insert(fastaFileNames[i]);        }
                        else if (filesToRemove.count(fastaFileNames[i]) > 0) {  remove(fastaFileNames[i].c_str()); }
                        else {
                                ifstream inFASTA;
@@ -371,6 +371,10 @@ int TrimSeqsCommand::execute(){
                                m->openInputFile(fastaFileNames[i], inFASTA);
                                ofstream outGroups;
                                string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
+                               
+                               //if the fastafile is on the blanks list then the groups file should be as well
+                               if (blanks.count(fastaFileNames[i]) != 0) { blanks.insert(outGroupFilename); }
+                               
                                m->openOutputFile(outGroupFilename, outGroups);
                                outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);  
                                
@@ -394,30 +398,17 @@ int TrimSeqsCommand::execute(){
                        }
                }
                
+               for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) {  remove((*(itBlanks)).c_str()); }
+               
+               blanks.clear();
                if(qFileName != ""){
                        for(int i=0;i<qualFileNames.size();i++){
-                               if (m->isBlank(qualFileNames[i])) {  remove(qualFileNames[i].c_str());  }
+                               if (m->isBlank(qualFileNames[i])) {  blanks.insert(qualFileNames[i]);   }
                                else if (filesToRemove.count(qualFileNames[i]) > 0) {  remove(qualFileNames[i].c_str()); }
-                               else {
-                                       ifstream inQual;
-                                       string seqName;
-                                       m->openInputFile(qualFileNames[i], inQual);
-//                                     ofstream outGroups;
-//                                     
-//                                     string thisGroup = "";
-//                                     if (i > comboStarts) {
-//                                             map<string, int>::iterator itCombo;
-//                                             for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
-//                                                     if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
-//                                             }
-//                                     }
-//                                     else{ thisGroup = groupVector[i]; }
-                                       
-                                       inQual.close();
-                               }
                        }
                }
                
+               for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) {  remove((*(itBlanks)).c_str()); }
                
                if (m->control_pressed) { 
                        for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }