1.23.0

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cf4256851eb583a78b78fd5ab800bbfa5d46f5e8..cac80b8d775d2e5bd4810198e69a2d5ad625c04d 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -156,11 +156,11 @@ PreClusterCommand::PreClusterCommand(string option) {
                        else {   m->setGroupFile(groupfile); bygroup = true;  }
                        
                        string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
-                       convert(temp, diffs); 
+                       m->mothurConvert(temp, diffs); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        
                }
@@ -372,6 +372,9 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
                
                //append output files
                for(int i=0;i<processIDS.size();i++){
+                       newFName = m->getFullPathName(".\\" + newFName);
+                       newNName = m->getFullPathName(".\\" + newNName);
+                       cout << newFName << endl;
                        m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
                        m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));