X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=54d3dcc5c9b6c93f267478e6491126b3aedff772;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=2bd7054afc33c4f0600683a1b8ebe50a2fd338c4;hpb=196c22d0f93ba48e8ec54ab76608b6e3ba5e68cc;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 2bd7054..54d3dcc 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -358,7 +358,7 @@ int SeqErrorCommand::execute(){
 		if(namesFileName != "")     {	weights = getWeights();         }
         else if (countfile != "")   {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             weights = ct.getNameMap();
         }
 		
@@ -881,7 +881,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 				if (queryFile.eof()) { break; }
 			#endif
 			
-			if(index % 100 == 0){	m->mothurOut(toString(index));	m->mothurOutEndLine(); }
+			if(index % 100 == 0){	m->mothurOutJustToScreen(toString(index)+"\n");	 }
 		}
 		queryFile.close();
 		outChimeraReport.close();
@@ -892,7 +892,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 		else if(qFileName != "" && aligned == false){   qualFile.close();                       }
         
 		//report progress
-		m->mothurOut(toString(index));	m->mothurOutEndLine();
+		m->mothurOutJustToScreen(toString(index)+"\n");	
 		
 		return index;
 	}