added name option to trim.seqs

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index dad8b98b64f99026388b32c7d47e60dab33e1fba..ed84cc0c60d404b0d7c12eb0c3751a2e2a601706 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -369,7 +369,7 @@ 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;
@@ -680,6 +680,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        }
                                }
                                else{
+                                       if(nameFile != ""){ //needs to be before the currSeq name is changed
+                                               map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                                               if (itName != nameMap.end()) {  scrapNameFile << itName->first << '\t' << itName->second << endl; }
+                                               else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+                                       }
                                        currSeq.setName(currSeq.getName() + '|' + trashCode);
                                        currSeq.setUnaligned(origSeq);
                                        currSeq.setAligned(origSeq);
@@ -687,11 +692,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        if(qFileName != ""){
                                                currQual.printQScores(scrapQualFile);
                                        }
-                                       if(nameFile != ""){
-                                               map<string, string>::iterator itName = nameMap.find(currSeq.getName());
-                                               if (itName != nameMap.end()) {  scrapNameFile << itName->first << '\t' << itName->second << endl; }
-                                                       else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
-                                       }
                                }
                                count++;
                        }
@@ -1143,7 +1143,7 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        
                                        if(qFileName != ""){
                                                qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
-                                               if (uniqueNames.count(fastaFileName) == 0) {
+                                               if (uniqueNames.count(qualFileName) == 0) {
                                                        outputNames.push_back(qualFileName);
                                                        outputTypes["qfile"].push_back(qualFileName);
                                                }
@@ -1154,7 +1154,7 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        
                                        if(nameFile != ""){
                                                nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
-                                               if (uniqueNames.count(fastaFileName) == 0) {
+                                               if (uniqueNames.count(nameFileName) == 0) {
                                                        outputNames.push_back(nameFileName);
                                                        outputTypes["name"].push_back(nameFileName);
                                                }