working on testing for 1.13

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 8a767f696415737284491fa691a708dd1c011573..e47e71d581d9a24f5b4c5ced4ac1875a94b1d269 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());
@@ -429,7 +428,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                vector<ofstream*> fastaFileNames;
                vector<ofstream*> qualFileNames;
                
-               
+       cout << "here" << endl; 
                if (oligoFile != "") {          
                        m->openOutputFile(groupFile, outGroups);   
                        for (int i = 0; i < fastaNames.size(); i++) {
@@ -446,17 +445,17 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        #endif
                        }
                }
-               
+cout << "here " << filename << endl;           
                ifstream inFASTA;
                m->openInputFile(filename, inFASTA);
                inFASTA.seekg(line->start);
-               
+       cout << "here " << qFileName << endl;   
                ifstream qFile;
                if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
                
                bool done = false;
                int count = 0;
-       
+       cout << "here" << endl;
                while (!done) {
                                
                        if (m->control_pressed) {