get.oturep change and trim.seqs fix

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 7ee5c99dd86775124a83400a92f3ac1d9e24ad16..5e0541f9cb954575d39d277cdf4a50d6931c21c2 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -364,7 +364,7 @@ int TrimSeqsCommand::execute(){
                for(int i=0;i<fastaFileNames.size();i++){
                        
                        if (m->isBlank(fastaFileNames[i])) {  remove(fastaFileNames[i].c_str());        }
-                       else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
+                       else if (filesToRemove.count(fastaFileNames[i]) > 0) {  remove(fastaFileNames[i].c_str()); }
                        else {
                                ifstream inFASTA;
                                string seqName;
@@ -470,6 +470,19 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                ifstream qFile;
                if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
                
+               
+               for (int i = 0; i < fastaNames.size(); i++) { //clears old file
+                       ofstream temp;
+                       m->openOutputFile(fastaNames[i], temp);
+                       temp.close();
+               }
+               for (int i = 0; i < qualNames.size(); i++) { //clears old file
+                       ofstream temp;
+                       m->openOutputFile(qualNames[i], temp);
+                       temp.close();
+               }
+               
+                       
                bool done = false;
                int count = 0;