working on testing for 1.13

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 637eccedfc77e74556de6bf3f201270b28874d96..3403b9934dfb9366d066a64ed5552484b2e4275c 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -50,8 +50,6 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
-                       globaldata->newRead();
-                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -88,12 +86,12 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  format = "phylip";  globaldata->setPhylipFile(phylipfile);      }
+                       else {  globaldata->newRead(); format = "phylip";  globaldata->setPhylipFile(phylipfile);       }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  format = "column"; globaldata->setColumnFile(columnfile);       }
+                       else {  globaldata->newRead(); format = "column"; globaldata->setColumnFile(columnfile);        }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }