fixed bug with trim.seqs allfiles=t

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6d87f89c88b1055e033f3cce1cc18e0700377ff1..61a58a4aaeddcdbde6a0b9bdd6f57c56c4079fe9 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -314,7 +314,7 @@ int TrimSeqsCommand::execute(){
                        outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        getOligos(fastaFileNames, qualFileNames);
                }
-
+               
                vector<unsigned long int> fastaFilePos;
                vector<unsigned long int> qFilePos;
                
@@ -337,7 +337,7 @@ int TrimSeqsCommand::execute(){
                #endif
                
                if (m->control_pressed) {  return 0; }                  
-                       
+       
                if(allFiles){
                        map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
                        map<string, string>::iterator it;
@@ -345,19 +345,21 @@ int TrimSeqsCommand::execute(){
                        for(int i=0;i<fastaFileNames.size();i++){
                                for(int j=0;j<fastaFileNames[0].size();j++){
                                        if (fastaFileNames[i][j] != "") {
-                                               if(m->isBlank(fastaFileNames[i][j])){
-                                                       remove(fastaFileNames[i][j].c_str());
-                                                       namesToRemove.insert(fastaFileNames[i][j]);
+                                               if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
+                                                       if(m->isBlank(fastaFileNames[i][j])){
+                                                               remove(fastaFileNames[i][j].c_str());
+                                                               namesToRemove.insert(fastaFileNames[i][j]);
                                                        
-                                                       if(qFileName != ""){
-                                                               remove(qualFileNames[i][j].c_str());
-                                                               namesToRemove.insert(qualFileNames[i][j]);
+                                                               if(qFileName != ""){
+                                                                       remove(qualFileNames[i][j].c_str());
+                                                                       namesToRemove.insert(qualFileNames[i][j]);
+                                                               }
+                                                       }else{  
+                                                               it = uniqueFastaNames.find(fastaFileNames[i][j]);
+                                                               if (it == uniqueFastaNames.end()) {     
+                                                                       uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];  
+                                                               }       
                                                        }
-                                               }else{  
-                                                       it = uniqueFastaNames.find(fastaFileNames[i][j]);
-                                                       if (it == uniqueFastaNames.end()) {     
-                                                               uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];  
-                                                       }       
                                                }
                                        }
                                }
@@ -1027,27 +1029,30 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                                        comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
                                                }
                                        }
-
-                                       ofstream temp;
-                                       fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
-                                       if (uniqueNames.count(fastaFileName) == 0) {
-                                               outputNames.push_back(fastaFileName);
-                                               outputTypes["fasta"].push_back(fastaFileName);
-                                               uniqueNames.insert(fastaFileName);
-                                       }
                                        
-                                       fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
-                                       m->openOutputFile(fastaFileName, temp);         temp.close();
-
-                                       if(qFileName != ""){
-                                               qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
+                                       if ((comboGroupName == "") || (comboGroupName == ".")) {}
+                                       else {
+                                               ofstream temp;
+                                               fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
                                                if (uniqueNames.count(fastaFileName) == 0) {
-                                                       outputNames.push_back(qualFileName);
-                                                       outputTypes["qfile"].push_back(qualFileName);
+                                                       outputNames.push_back(fastaFileName);
+                                                       outputTypes["fasta"].push_back(fastaFileName);
+                                                       uniqueNames.insert(fastaFileName);
                                                }
                                                
-                                               qualFileNames[itBar->second][itPrimer->second] = qualFileName;
-                                               m->openOutputFile(qualFileName, temp);          temp.close();
+                                               fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
+                                               m->openOutputFile(fastaFileName, temp);         temp.close();
+                                               
+                                               if(qFileName != ""){
+                                                       qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
+                                                       if (uniqueNames.count(fastaFileName) == 0) {
+                                                               outputNames.push_back(qualFileName);
+                                                               outputTypes["qfile"].push_back(qualFileName);
+                                                       }
+                                                       
+                                                       qualFileNames[itBar->second][itPrimer->second] = qualFileName;
+                                                       m->openOutputFile(qualFileName, temp);          temp.close();
+                                               }
                                        }
                                }
                        }