X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.cpp;h=7bea292ee6b1dfd7afe9a2ce1300e6b71f2b1324;hb=11c115c802602be50e106aae56969e15d2c49a62;hp=2ffb65598a8fc75041190f764742342202e4ed52;hpb=515c3398ea27e2105f616fc5662b2a7ceb486aa0;p=mothur.git

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 2ffb655..7bea292 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -72,7 +72,7 @@ ClearcutCommand::ClearcutCommand(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 = "";	}
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = hasPath(inputFile);	}
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "version", false);		if (temp == "not found"){	temp = "F";			}
@@ -182,13 +182,8 @@ int ClearcutCommand::execute() {
 		string path = globaldata->argv;
 		path = path.substr(0, (path.find_last_of('m')));
 		
-		string clearcutCommand = "";
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			clearcutCommand = path + "clearcut/clearcut ";
-		#else
-			clearcutCommand = path + "clearcut\\clearcut ";
-		#endif
-		
+		string clearcutCommand = path + "clearcut ";
+				
 		//you gave us a distance matrix
 		if (phylipfile != "") { clearcutCommand += "--distance "; 	}