X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=81b9111b17dd8bba332ad8a8267cc12bf16e235a;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=5a5d445cb8624386e90d4c714c1f460f1be0d509;hpb=b740fb182372143e152143c6cc5b9ac8591f09b7;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5a5d445..81b9111 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -422,7 +422,7 @@ int TrimSeqsCommand::execute(){
 		
 		if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             nameCount = ct.getNameMap();
 			outputNames.push_back(trimCountFile);
 			outputNames.push_back(scrapCountFile);
@@ -540,7 +540,7 @@ int TrimSeqsCommand::execute(){
             
             if (countfile != "") { //create countfile with group info included
                 CountTable* ct = new CountTable();
-                ct->readTable(trimCountFile);
+                ct->readTable(trimCountFile, true);
                 map<string, int> justTrimmedNames = ct->getNameMap();
                 delete ct;