X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=9c1408c9a112dcc3ad9ed579026e2528c334a102;hp=ef199ccdf0a11efba99eaf0299ff50413b70b89f;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index ef199cc..9c1408c 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -181,7 +181,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
             countfile = validParameter.validFile(parameters, "count", true);
 			if (countfile == "not open") { abort = true; countfile = ""; }	
 			else if (countfile == "not found") { countfile = ""; }
-			else { ct.readTable(countfile); m->setCountTableFile(countfile); }
+			else { ct.readTable(countfile, true); m->setCountTableFile(countfile); }
 			
             if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 			
@@ -262,10 +262,10 @@ int ClusterFragmentsCommand::execute(){
 				alignSeqs[i].active = 0;
 				
 			}//end if active i
-			if(i % 100 == 0)	{ m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();	}
+			if(i % 100 == 0)	{ m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); 	}
 		}
 		
-		if(numSeqs % 100 != 0)	{ m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();	}
+		if(numSeqs % 100 != 0)	{ m->mothurOutJustToScreen(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n");	}
 	
 		
 		string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));