X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraperseuscommand.cpp;h=0547802198960198d9d2a063bc498e79f04bfe33;hp=1835862f6b970ffdf7469002866f33a6682257ad;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=196c22d0f93ba48e8ec54ab76608b6e3ba5e68cc

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 1835862..0547802 100644
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -469,10 +469,7 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
 			m->mothurConvert(temp, beta);
             
 			temp = validParameter.validFile(parameters, "dereplicate", false);	
-			if (temp == "not found") { 
-				if (groupfile != "")    {  temp = "false";					}
-				else                    {  temp = "true"; 	}
-			}
+			if (temp == "not found") { temp = "false";			}
 			dups = m->isTrue(temp);
 		}
 	}
@@ -519,7 +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);
@@ -537,7 +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);
@@ -562,7 +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]);
@@ -649,6 +646,11 @@ int ChimeraPerseusCommand::execute(){
 		if (itTypes != outputTypes.end()) {
 			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 		}
+        
+        itTypes = outputTypes.find("count");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+		}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -1044,10 +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();
@@ -1068,7 +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(); }