fixed bug with windows version of trim.seqs when run with 1 processor. fixed file...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 6ef9532790a5fc63905cb598f1e7bc4baa4c9871..89d78288639e6cca3e8eebca34dd01174c3963da 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -128,8 +128,10 @@ ShhherCommand::ShhherCommand(string option) {
                                        if (path == "") {       parameters["file"] = inputDir + it->second;             }
                                }
                        }
-                       
-                       
+            
+            //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
+            
                        //check for required parameters
                        flowFileName = validParameter.validFile(parameters, "flow", true);
                        flowFilesFileName = validParameter.validFile(parameters, "file", true);
@@ -146,13 +148,15 @@ ShhherCommand::ShhherCommand(string option) {
                        }
                        else{
                                ofstream temp;
-
+                
+                string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+                
                                //flow.files = 9 character offset
-                               compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+                               compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }
@@ -214,17 +218,10 @@ ShhherCommand::ShhherCommand(string option) {
                 if (flowFileVector.size() == 0) {  m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
             }
             else{
+                outputDir += m->hasPath(flowFileName);
                 flowFileVector.push_back(flowFileName);
             }
-
-                       
-                       //if the user changes the output directory command factory will send this info to us in the output parameter 
-                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
-                               outputDir = ""; 
-                               outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it    
-                       }
-                       
-                       
+               
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        string temp;