X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=fee74a719ce9c4d3a988a0a30647f2f1368ca8f9;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=3354665852ce1b5a95b9ecc7cc673d5083b25d8b;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 3354665..fee74a7 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -200,7 +200,7 @@ int AlignCheckCommand::execute(){
 		if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }