X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makebiomcommand.cpp;fp=makebiomcommand.cpp;h=9e8d3e39cb58e31e9f3dca2eeff35257eadd537a;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=03e7baf2b9888fc7f52cbe6076ea8fdfa472b584;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;p=mothur.git

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index 03e7baf..9e8d3e3 100644
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -129,6 +129,27 @@ string MakeBiomCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string MakeBiomCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "biom")             {   outputFileName =  "biom";       }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "MakeBiomCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 MakeBiomCommand::MakeBiomCommand(){	
 	try {
@@ -352,7 +373,7 @@ int MakeBiomCommand::execute(){
 int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
 	try {
         
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".biom";
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("biom");
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);