working on current change

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 99687701436dc5ffac7e71a444d97b42f4b6815a..06e199f7a93c96e71ba5cb15f1cafd21c8ca2d8e 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -148,7 +148,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                                        m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); 
                                        abort = true;
                                }
-                       }else {  format = "list";       }
+                       }else {  format = "list";       m->setListFile(listfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
@@ -159,7 +159,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                                        m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); 
                                        abort = true;
                                }
-                       }
+                       }else { m->setGroupFile(groupfile); }
                                                
                        if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
                        
@@ -197,7 +197,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
-                               
+                       else { m->setFastaFile(fastafile); }
                }
 
        }