X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=trimseqscommand.cpp;h=5e0541f9cb954575d39d277cdf4a50d6931c21c2;hb=def6801aad4aadbbaa7cc615b11554e47dad5ce0;hp=7ee5c99dd86775124a83400a92f3ac1d9e24ad16;hpb=76f67ac1d1236dde0f7b4689d2d45fecf6d652cf;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 7ee5c99..5e0541f 100644
--- 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;