X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=b311821b3e8d293daac13107eb9e6771be360bf0;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=8b6a77b4936b0095741747cb255e143a1cd78e64;hpb=feb0fbef36b8a681efc04e9b5e3efb1647b99021;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 8b6a77b..b311821 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -812,7 +812,7 @@ int ClassifySeqsCommand::execute(){
                 PhyloSummary* taxaSum;
                 if (hasCount) { 
                     ct = new CountTable();
-                    ct->readTable(countfileNames[s]);
+                    ct->readTable(countfileNames[s], true);
                     taxaSum = new PhyloSummary(taxonomyFileName, ct);
                     taxaSum->summarize(tempTaxonomyFile);
                 }else {
@@ -1151,11 +1151,11 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count) +"\n"); 		}
 			
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); 		}
 			
 		inFASTA.close();
 		outTax.close();