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

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 1d7e252cb702f58138ae0e756460bb98273b8908..e82dc1bc8dce5ffd0887025d5816b5eec8d0eab9 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -820,6 +820,11 @@ int ChimeraUchimeCommand::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();