fixing outputdir bug in shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 70aee3c2dc4c54bcd082c378a6dee4d2847d70f6..d8f538b56109e2faa290cb060c314186e8be318a 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -148,11 +148,11 @@ ShhherCommand::ShhherCommand(string option) {
                                ofstream temp;
 
                                //flow.files = 9 character offset
-                               compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+                               compositeFASTAFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               compositeNamesFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }
@@ -1734,7 +1734,7 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
         outputNames.push_back(fastaFileName);
         
         if(compositeFASTAFileName != ""){
-            m->appendFiles(fastaFileName, thisOutputDir + compositeFASTAFileName);
+            m->appendFiles(fastaFileName, compositeFASTAFileName);
         }
     }
     catch(exception& e) {
@@ -1772,7 +1772,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
         
         
         if(compositeNamesFileName != ""){
-            m->appendFiles(nameFileName, thisOutputDir + uchimecompositeNamesFileName);
+            m->appendFiles(nameFileName, uchimecompositeNamesFileName);
         }              
     }
     catch(exception& e) {