X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=a11465d669a55de0c5555f616c36f51caef74ea2;hb=5a1e62397b91f57d0d3aff635891df04b8999a88;hp=09f899b947bf9bb4b455de86479d34ffa709d46f;hpb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;p=mothur.git

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 09f899b..a11465d 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -87,7 +87,7 @@ ReadTreeCommand::ReadTreeCommand(string option){
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }
-			else if (namefile == "not found") { treefile = ""; }
+			else if (namefile == "not found") { namefile = ""; }
 			else { readNamesFile(); }	
 			
 			if (abort == false) {
@@ -162,6 +162,7 @@ int ReadTreeCommand::execute(){
 					if (it == nameMap.end()) {
 						mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); mothurOutEndLine();
 						treeMap->removeSeq(treeMap->namesOfSeqs[i]);
+						i--; //need this because removeSeq removes name from namesOfSeqs
 					}
 				}
 			}