X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;fp=deconvolutecommand.cpp;h=09e077b57ca8800d3663f6dd5c3515102aaa1129;hb=859e3a473a3e63e0060c49be70b80f9289253da2;hp=f33a1400721093ee642c90d35c70fed703fdb6a5;hpb=0a9b5ee954b60abbd24c797cece23fb4a487cc8a;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index f33a140..09e077b 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -198,17 +198,24 @@ int DeconvoluteCommand::execute() {
 		map<string, string> nameMap;
 		map<string, string>::iterator itNames;
 		if (oldNameMapFName != "")  {  
-            m->readNames(oldNameMapFName, nameMap); 
-            if (oldNameMapFName == outNameFile){ 
-                variables["[tag]"] = "unique";
-                outNameFile = getOutputFileName("name", variables);   }
+            m->readNames(oldNameMapFName, nameMap);
+            if (oldNameMapFName == outNameFile){
+                //prepare filenames and open files
+                map<string, string> mvariables;
+                mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+                mvariables["[tag]"] = "unique";
+                outNameFile = getOutputFileName("name", mvariables);
+            }
         }
         CountTable ct;
         if (countfile != "")  {  
             ct.readTable(countfile);
-            if (countfile == outCountFile){ 
-                variables["[tag]"] = "unique";
-                outCountFile = getOutputFileName("count", variables);   }
+            if (countfile == outCountFile){
+                //prepare filenames and open files
+                map<string, string> mvariables;
+                mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+                mvariables["[tag]"] = "unique";
+                outCountFile = getOutputFileName("count", mvariables);   }
         }
 		
 		if (m->control_pressed) { return 0; }