changed all shared commands so that they read the shared file generated by the read...

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 1b2ec9e750445f7b256b978fec0298d42b3f825c..c8ec791c5c667e1f01bfdc59944ed2811e345d6c 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -51,6 +51,12 @@ int ReadOtuCommand::execute(){
 
                        parselist = new ParseListCommand();
                        parselist->execute();
+                       
+                       //change format to shared  to speed up commands
+                       globaldata->setFormat("sharedfile");
+                       globaldata->setListFile("");
+                       globaldata->setGroupFile("");
+                       globaldata->setSharedFile(getRootName(filename) + "shared");
                }
                return 0;
        }