paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / sensspeccommand.cpp

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 7c4dc1322e9b69cbc021274a292098c7bbe67b57..213a2ca99da988257a46ba8e91cb5e4123b5bb0e 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -66,6 +66,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        string temp;
@@ -189,7 +190,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                        
                        lineLabel = validParameter.validFile(parameters, "label", false);       if (lineLabel == "not found") { lineLabel = ""; }
                        
-                       sensSpecFileName = listFile.substr(0,listFile.find_last_of('.')) + ".sensspec";
+                       sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + ".sensspec";
                }
        }
        catch(exception& e) {
@@ -208,6 +209,11 @@ int SensSpecCommand::execute(){
                if(format == "phylip")          {       processPhylip();        }
                else if(format == "column")     {       processColumn();        }
                
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(sensSpecFileName); m->mothurOutEndLine();  
+               m->mothurOutEndLine();
+               
                
                return 0;       
        }