X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=54d3dcc5c9b6c93f267478e6491126b3aedff772;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=00897dcfee5881be8dfd37d00bbbe705a3d034f3;hpb=859e3a473a3e63e0060c49be70b80f9289253da2;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 00897dc..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();
         }
 		
@@ -666,7 +666,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 			int misMatchSize;
 			in >> misMatchSize; m->gobble(in);
 			if (misMatchSize > misMatchCounts.size()) {	misMatchCounts.resize(misMatchSize, 0);	}
-			for (int j = 0; j < misMatchCounts.size(); j++) {
+			for (int j = 0; j < misMatchSize; j++) {
 				in >> tempNum; misMatchCounts[j] += tempNum;
 			}
 			m->gobble(in);
@@ -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;
 	}