finished dereplicate changes to chimera commands. added taxonomy file to subsample...

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index d8e0952a8b9f89cd237946a27ea624f11fa42898..fceef2180163f60e3c33cfecb7e861839c4bd1c7 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -837,6 +837,11 @@ int ChimeraSlayerCommand::execute(){
                        }
                }
                
+        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();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }