X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=fee74a719ce9c4d3a988a0a30647f2f1368ca8f9;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=c1cdb6b90c910c2e58c5d016a6c2293f7d7aa8ce;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index c1cdb6b..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);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }