added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / clusterfragmentscommand.cpp

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 71ce5eed4e6e21c63210be0e34eb9a6f72dac59b..772113baf83e9fbbd057794103f46ffa21c21fda 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -147,15 +147,20 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                        // ...at some point should added some additional type checking...
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
-                       else if (namefile == "not open") { abort = true; }      
+                       else if (namefile == "not open") { namefile = ""; abort = true; }       
                        else {  readNameFile(); m->setNameFile(namefile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "diffs", false);            if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, diffs); 
+                       m->mothurConvert(temp, diffs); 
                        
                        temp = validParameter.validFile(parameters, "percent", false);          if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, percent);
+                       m->mothurConvert(temp, percent);
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                        
                }
                                
@@ -226,7 +231,7 @@ 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 +243,7 @@ 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();