X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=metastatscommand.cpp;h=0704f55896e835f331eda28446012e62c790904e;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=99a3043995b429bf4661a776f25f050262905412;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 99a3043..0704f55 100644
--- 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"){