sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 1835862f6b970ffdf7469002866f33a6682257ad..f7dc597cf8ca514712bf06f29f2010982d6c03c9 100644 (file)
--- 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();