finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime...

[mothur.git] / clusterfragmentscommand.cpp

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 71ce5eed4e6e21c63210be0e34eb9a6f72dac59b..8d2d3eac9ba398dbce884d61c99dd81b3f2442b6 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -226,7 +226,7 @@ int ClusterFragmentsCommand::execute(){
                string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
                
                string newFastaFile = fileroot + "fragclust.fasta";
-               string newNamesFile = fileroot + "names";
+               string newNamesFile = fileroot + "fragclust.names";
                
                if (m->control_pressed) { return 0; }
                
@@ -238,7 +238,7 @@ int ClusterFragmentsCommand::execute(){
                
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); 
                
-               if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+               if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();