X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerauchimecommand.cpp;h=422792a68525b495008694360c393e26ba358c09;hp=1d7e252cb702f58138ae0e756460bb98273b8908;hb=615301e57c25e241356a9c2380648d117709458d;hpb=859e3a473a3e63e0060c49be70b80f9289253da2

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 1d7e252..422792a 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -564,10 +564,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
             
             
 			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);
 
 			
@@ -677,7 +674,7 @@ int ChimeraUchimeCommand::execute(){
                 int error;
                 if (hasCount) {
                     CountTable ct;
-                    ct.readTable(nameFile);
+                    ct.readTable(nameFile, true);
                     for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
                         int num = ct.getNumSeqs(it->first);
                         if (num == 0) { error = 1; }
@@ -728,7 +725,7 @@ int ChimeraUchimeCommand::execute(){
 				if(processors == 1)	{	totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
                     
                     if (hasCount && dups) {
-                        CountTable c; c.readTable(nameFile);
+                        CountTable c; c.readTable(nameFile, true);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -758,7 +755,7 @@ int ChimeraUchimeCommand::execute(){
                     
                     if (hasCount) {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile);
+                        CountTable c; c.readTable(newCountFile, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -820,6 +817,11 @@ int ChimeraUchimeCommand::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();
@@ -1793,7 +1795,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 		int num = 0;
         
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(nameFile); }
+        if (hasCount && dups) { newCount.readTable(nameFile, true); }
 		
 		//sanity check
 		if (groups.size() < processors) { processors = groups.size(); }