fixed a trimming bug in sffinfo which occurs when the right trim point is smaller...

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 89c62faba2f0d3350d3dea797bd2bebbe23074c3..de7d761dc68169f3f0df446f42ca07cd9f3b16aa 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -755,7 +755,7 @@ int GetOTURepCommand::processNames(string filename, string label) {
 
                        if (sequence != "not found") {
                                if (sorted == "") { //print them out
-                                       rep = rep + "|" + toString(i+1);
+                                       rep = rep + "\t" + toString(i+1);
                                        rep = rep + "|" + toString(binsize);
                                        if (groupfile != "") {
                                                rep = rep + "|" + group;
@@ -781,7 +781,7 @@ int GetOTURepCommand::processNames(string filename, string label) {
                        //print them
                        for (int i = 0; i < reps.size(); i++) {
                                string sequence = fasta->getSequence(reps[i].name);
-                               string outputName = reps[i].name + "|" + toString(reps[i].bin);
+                               string outputName = reps[i].name + "\t" + toString(reps[i].bin);
                                outputName = outputName + "|" + toString(reps[i].size);
                                if (groupfile != "") {
                                        outputName = outputName + "|" + reps[i].group;
@@ -790,10 +790,12 @@ int GetOTURepCommand::processNames(string filename, string label) {
                                out << sequence << endl;
                        }
                }
-                       
+               
+               in.close();
                out.close();
                out2.close();
                
+               remove(filename.c_str());
                rename(tempNameFile.c_str(), filename.c_str());
                
                return 0;