X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=b1bc4fd508576c04126206b4e178798c088cb91d;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=b4fb467d6e395ce9b1655e043859cff0e2c77f67;hpb=037b7fccc64a5c7d5d5c23a949273a912160a400;p=mothur.git

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index b4fb467..b1bc4fd 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -469,7 +469,7 @@ int RemoveSeqsCommand::readQual(){
 				saveName = name.substr(1);
 				while (!in.eof())	{	
 					char c = in.get(); 
-					if (c == 10 || c == 13){	break;	}
+					if (c == 10 || c == 13 || c == -1){	break;	}
 					else { name += c; }	
 				} 
 				m->gobble(in);
@@ -557,7 +557,7 @@ int RemoveSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }