X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=fbbe4bb3a2fc5c99f77875292849e0a0e95f1043;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=bbf8df27ac5ee691f091f150638b781f85486a11;hpb=c48d91112209b841444923670dca5454da0e2a4d;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index bbf8df2..fbbe4bb 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -192,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) {
 			else if (countfile == "not open") { abort = true; countfile =  ""; }	
 			else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { bygroup = true; }
                 else { bygroup = false;  }
             }
@@ -903,15 +903,9 @@ void PreClusterCommand::readNameFile(){
 		while (!in.eof()) {
 			in >> firstCol >> secondCol; m->gobble(in);
             
-            for (int i = 0; i < firstCol.length(); i++) {
-                if (firstCol[i] == ':') { firstCol[i] = '_'; m->changedSeqNames = true; }
-            }
-            
-            int size = 1;
-            for (int i = 0; i < secondCol.length(); i++) {
-                if (secondCol[i] == ':') { secondCol[i] = '_'; m->changedSeqNames = true; }
-                else if(secondCol[i] == ','){	size++;	}
-            }
+            m->checkName(firstCol);
+            m->checkName(secondCol);
+            int size = m->getNumNames(secondCol);
             
 			names[firstCol] = secondCol;
             sizes[firstCol] = size;