From eafae911fdb9b1402fe8526b6df38eb51f828f37 Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Mon, 29 Feb 2016 10:12:23 -0500
Subject: [PATCH] Globalizes inputDir for vsearch methods

#169
---
 source/commands/clustercommand.cpp | 2 +-
 source/commands/clustercommand.h   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/source/commands/clustercommand.cpp b/source/commands/clustercommand.cpp
index f5bee32e3..192e6672c 100644
--- a/source/commands/clustercommand.cpp
+++ b/source/commands/clustercommand.cpp
@@ -133,7 +133,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			//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 = "";		}
 			
-			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			inputDir = validParameter.validFile(parameters, "inputdir", false);		
 			if (inputDir == "not found"){	inputDir = "";		}
 			else {
 				string path;
diff --git a/source/commands/clustercommand.h b/source/commands/clustercommand.h
index 595c7a230..e55cf3d82 100644
--- a/source/commands/clustercommand.h
+++ b/source/commands/clustercommand.h
@@ -54,7 +54,7 @@ class ClusterCommand : public Command {
 
 	bool abort, hard, sim;
 
-	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile, fastafile, vsearchLocation;
+	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile, fastafile, inputDir, vsearchLocation;
 	double cutoff;
     float adjust;
 	string showabund, timing;