Merge remote-tracking branch 'mothur/master'

diff --cc shhhercommand.cpp
index d8f538b56109e2faa290cb060c314186e8be318a,89d78288639e6cca3e8eebca34dd01174c3963da..2214c5ea8b4b5f124393067ff2d59dcc3acf931c
--- 1/shhhercommand.cpp
--- 2/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@@ -146,9 -148,11 +148,11 @@@ ShhherCommand::ShhherCommand(string opt
                        }
                        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 = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
 +                              compositeFASTAFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();