X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraperseuscommand.cpp;h=0547802198960198d9d2a063bc498e79f04bfe33;hp=f7dc597cf8ca514712bf06f29f2010982d6c03c9;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=b0997605981902442138b9309e9c43d95c3ba10a

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index f7dc597..0547802 100644
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -516,7 +516,7 @@ int ChimeraPerseusCommand::execute(){
             
             if (hasCount) {
                 CountTable* ct = new CountTable();
-                ct->readTable(nameFile);
+                ct->readTable(nameFile, true, false);
                 
                 if (ct->hasGroupInfo()) {
                     cparser = new SequenceCountParser(fastaFileNames[s], *ct);
@@ -534,7 +534,7 @@ int ChimeraPerseusCommand::execute(){
                     
                     if(processors == 1)	{	numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
                         if (dups) {
-                            CountTable c; c.readTable(nameFile);
+                            CountTable c; c.readTable(nameFile, true, false);
                             if (!m->isBlank(newCountFile)) {
                                 ifstream in2;
                                 m->openInputFile(newCountFile, in2);
@@ -559,7 +559,7 @@ int ChimeraPerseusCommand::execute(){
                         numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
                     }else {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile);
+                        CountTable c; c.readTable(newCountFile, true, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -1046,10 +1046,10 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
 			}
 	
 			//report progress
-			if((i+1) % 100 == 0){ 	m->mothurOut("Processing sequence: " + toString(i+1) + "\n");		}
+			if((i+1) % 100 == 0){ 	m->mothurOutJustToScreen("Processing sequence: " + toString(i+1) + "\n");		}
 		}
 		
-		if((numSeqs) % 100 != 0){ 	m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n");		}
+		if((numSeqs) % 100 != 0){ 	m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n");		}
 		
 		chimeraFile.close();
 		accnosFile.close();
@@ -1070,7 +1070,7 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
 		int num = 0;
 		
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(name); }
+        if (hasCount && dups) { newCount.readTable(name, true, false); }
         
 		//sanity check
 		if (groups.size() < processors) { processors = groups.size(); }