fixing minor bugs

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 7c3e1995ecf9315839b5f26ab9f7768d59e6ca08..ba7eae42a668e7fa9bf3a9f8d33c4746b55ce810 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -106,7 +106,7 @@ ReadOtuCommand::ReadOtuCommand(string option){
                        if (abort == false) {
                                //gets whichever one of the above is set
                                filename = globaldata->inputFileName;
-                               read = new ReadOTUFile(filename);
+                               //read = new ReadOTUFile(filename);
                        }
 
                }
@@ -155,7 +155,8 @@ void ReadOtuCommand::help(){
 //**********************************************************************************************************************
 
 ReadOtuCommand::~ReadOtuCommand(){
-       if (abort == false) {  delete read;  }
+       if (abort == false) {  //delete read; 
+        }
 }
 
 //**********************************************************************************************************************
@@ -165,17 +166,20 @@ int ReadOtuCommand::execute(){
        
                if (abort == true) {    return 0;       }
                
-               read->read(&*globaldata); 
+               //read->read(&*globaldata); 
                if (globaldata->getFormat() == "shared") {
                        groupMap->readMap();
                        
                        //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
-                       globaldata->gGroupmap = groupMap;               
-                       shared = new SharedCommand();
-                       shared->execute();
-
+                       globaldata->gGroupmap = groupMap;
+                       
                        parselist = new ParseListCommand();
                        parselist->execute();
+                       delete parselist;
+                       
+                       shared = new SharedCommand();
+                       shared->execute();
+                       delete shared;
                        
                        //change format to shared  to speed up commands
                        globaldata->setFormat("sharedfile");