X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getseqscommand.cpp;h=142023e7a40881c1c6397a761ba350132490b75c;hp=480bde3222c9057aafecacc208d84eac24573b72;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=859e3a473a3e63e0060c49be70b80f9289253da2

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 480bde3..142023e 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -501,7 +501,7 @@ int GetSeqsCommand::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);
@@ -587,7 +587,7 @@ int GetSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }