X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraperseuscommand.cpp;h=f7dc597cf8ca514712bf06f29f2010982d6c03c9;hp=1835862f6b970ffdf7469002866f33a6682257ad;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=196c22d0f93ba48e8ec54ab76608b6e3ba5e68cc

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 1835862..f7dc597 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);
 		}
 	}
@@ -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();