X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chopseqscommand.cpp;fp=chopseqscommand.cpp;h=1ebb1f4b631f21d02596aa3e1e528d27cb3587df;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=31fe64f232919ec714eecb3227e2ee946d0c9c12;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 31fe64f..1ebb1f4 100644
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> ChopSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ChopSeqsCommand::ChopSeqsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["accnos"] = tempOutNames;
@@ -62,10 +61,10 @@ vector<string> ChopSeqsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ChopSeqsCommand::ChopSeqsCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -156,7 +155,7 @@ void ChopSeqsCommand::help(){
 int ChopSeqsCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
 		string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";