X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mergefilecommand.cpp;h=d5973394e5a097e879bf1526689d137266a417c1;hp=fcf63895b960fa8293df03dcff7c1e5bce28c914;hb=315e38cf393c82be238da5b32574f225a020d25c;hpb=c99f3846e7a7b6f06ab46508baa5409204ad6290

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index fcf6389..d597339 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -21,7 +21,7 @@ MergeFileCommand::MergeFileCommand(string option){
 		}
 		else {
 			//valid paramters for this command
-			string Array[] =  {"input", "output"};
+			string Array[] =  {"input", "output","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -34,10 +34,18 @@ MergeFileCommand::MergeFileCommand(string option){
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			
 			string fileList = validParameter.validFile(parameters, "input", false);			
 			if(fileList == "not found") { mothurOut("you must enter two or more file names"); mothurOutEndLine();  abort=true;  }
 			else{ 	splitAtDash(fileList, fileNames);	}
 			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			string outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found")	{	outputDir = "";		}
+			
+			
 			numInputFiles = fileNames.size();
 			ifstream testFile;
 			if(numInputFiles == 0){
@@ -46,6 +54,12 @@ MergeFileCommand::MergeFileCommand(string option){
 			}
 			else{
 				for(int i=0;i<numInputFiles;i++){
+					if (inputDir != "") {
+						string path = hasPath(fileNames[i]);
+						//if the user has not given a path then, add inputdir. else leave path alone.
+						if (path == "") {	fileNames[i] = inputDir + fileNames[i];		}
+					}
+					
 					if(openInputFile(fileNames[i], testFile)){	abort = true;	}
 					testFile.close();
 				}
@@ -53,6 +67,7 @@ MergeFileCommand::MergeFileCommand(string option){
 			
 			outputFileName = validParameter.validFile(parameters, "output", false);			
 			if (outputFileName == "not found") { mothurOut("you must enter an output file name"); mothurOutEndLine();  abort=true;  }
+			else if (outputDir != "") { outputFileName = outputDir + getSimpleName(outputFileName); }
 		}
 			
 	}