X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=3a9f42b22e0715ccf1f68313439342269da81bf8;hb=ffa535cf04326227080b02594616971a2c3a5195;hp=e82dc1bc8dce5ffd0887025d5816b5eec8d0eab9;hpb=037b7fccc64a5c7d5d5c23a949273a912160a400;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index e82dc1b..3a9f42b 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -564,14 +564,12 @@ 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);
 
 			
 			if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+            if (hasCount && (templatefile != "self")) { m->mothurOut("You have provided a countfile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 			if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 			
 			//look for uchime exe
@@ -677,7 +675,7 @@ int ChimeraUchimeCommand::execute(){
                 int error;
                 if (hasCount) {
                     CountTable ct;
-                    ct.readTable(nameFile);
+                    ct.readTable(nameFile, true, false);
                     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 +726,7 @@ 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, false);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -758,7 +756,7 @@ int ChimeraUchimeCommand::execute(){
                     
                     if (hasCount) {
                         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]);
@@ -1798,7 +1796,7 @@ 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, false); }
 		
 		//sanity check
 		if (groups.size() < processors) { processors = groups.size(); }