added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 3fa622f01ff2fc334f5cbb9d79851a9ca7f8b30c..3d0c0d51acaac8844b71a3efa40c7925674ad4c5 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -125,9 +125,15 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                        }
                        
                        oldNameMapFName = validParameter.validFile(parameters, "name", true);
-                       if (oldNameMapFName == "not open") { abort = true; }
+                       if (oldNameMapFName == "not open") { oldNameMapFName = ""; abort = true; }
                        else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
                        else { m->setNameFile(oldNameMapFName); }
+                       
+                       if (oldNameMapFName == "") {
+                               vector<string> files; files.push_back(inFastaName);
+                               parser.getNameFile(files);
+                       }
+                       
                }
 
        }
@@ -148,7 +154,10 @@ int DeconvoluteCommand::execute() {
                
                map<string, string> nameMap;
                map<string, string>::iterator itNames;
-               if (oldNameMapFName != "")  {  m->readNames(oldNameMapFName, nameMap); }
+               if (oldNameMapFName != "")  {  
+            m->readNames(oldNameMapFName, nameMap); 
+            if (oldNameMapFName == outNameFile){ outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique.names";   }
+        }
                
                if (m->control_pressed) { return 0; }