added normalize.shared command

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 8a767f696415737284491fa691a708dd1c011573..320bc41f4816eccb8f4b0fb19cb92864e91055d2 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -224,9 +224,8 @@ int TrimSeqsCommand::execute(){
                string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
                outputNames.push_back(scrapSeqFile);
                string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
-               outputNames.push_back(trimQualFile);
                string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
-               outputNames.push_back(scrapQualFile);
+               if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  }
                string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
                
                vector<string> fastaFileNames;
@@ -315,7 +314,7 @@ int TrimSeqsCommand::execute(){
                                
                                if (m->control_pressed) {  return 0; }
                #else
-                               driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qlines[0]);
+                               driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
                                
                                for (int j = 0; j < fastaFileNames.size(); j++) {
                                        rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
@@ -429,10 +428,10 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                vector<ofstream*> fastaFileNames;
                vector<ofstream*> qualFileNames;
                
-               
                if (oligoFile != "") {          
                        m->openOutputFile(groupFile, outGroups);   
                        for (int i = 0; i < fastaNames.size(); i++) {
+
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
                                if(qFileName != ""){