X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=fdc967856043fc8e191c9b3167fb83634f82ec0a;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=d0179be91a5b2eac505632797a8ebb3f74232282;hpb=de2dc9fb831f569b823031d0730f5a0d739e8290;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index d0179be..fdc9678 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -16,12 +16,14 @@
 RareFactSharedCommand::RareFactSharedCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
+		
 		abort = false;
 		allLines = 1;
 		lines.clear();
 		labels.clear();
 		Estimators.clear();
-		
+		Groups.clear();
+				
 		//allow user to run help
 		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
 		
@@ -83,8 +85,8 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 			if (groups == "not found") { groups = ""; }
 			else { 
 				splitAtDash(groups, Groups);
-				globaldata->Groups = Groups;
 			}
+			globaldata->Groups = Groups;
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
@@ -176,7 +178,7 @@ int RareFactSharedCommand::execute(){
 		input = globaldata->ginput;
 		lookup = input->getSharedRAbundVectors();
 		vector<SharedRAbundVector*> lastLookup = lookup;
-		
+
 		if (lookup.size() < 2) { 
 			cout << "I cannot run the command without at least 2 valid groups."; 
 			for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }