From: Pat Schloss <pschloss@umich.edu>
Date: Tue, 1 May 2012 15:08:53 +0000 (-0400)
Subject: Merge remote-tracking branch 'mothur/master'
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=d2390ede25cc211f95f99e377d5654bad7e6950e

Merge remote-tracking branch 'mothur/master'
---

d2390ede25cc211f95f99e377d5654bad7e6950e
diff --cc shhhercommand.cpp
index d8f538b,89d7828..2214c5e
--- a/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();