working on current change

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 99a3043995b429bf4661a776f25f050262905412..0704f55896e835f331eda28446012e62c790904e 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -134,7 +134,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        //check for required parameters
                        designfile = validParameter.validFile(parameters, "design", true);
@@ -144,7 +144,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                designfile = m->getDesignFile(); 
                                if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setDesignFile(designfile); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){