X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=fceef2180163f60e3c33cfecb7e861839c4bd1c7;hb=037b7fccc64a5c7d5d5c23a949273a912160a400;hp=d8e0952a8b9f89cd237946a27ea624f11fa42898;hpb=196c22d0f93ba48e8ec54ab76608b6e3ba5e68cc;p=mothur.git

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index d8e0952..fceef21 100644
--- 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();	}