X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=304848179331ab980730713c5a35998bb54a80bc;hb=c3396974063d6efc5e5850ddf4ed8ab65cc94bb9;hp=39408427d87d439d6cdf8e637dd656df5049becd;hpb=fe5bbb79f9434df947347881c47b430112f4253e;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 3940842..3048481 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -64,8 +64,7 @@ vector<string> AlignCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["alignreport"] = tempOutNames;
@@ -79,10 +78,10 @@ AlignCommand::AlignCommand(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(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 {
 			
@@ -279,7 +278,7 @@ void AlignCommand::help(){
 
 int AlignCommand::execute(){
 	try {
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 
 		templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 		int longestBase = templateDB->getLongestBase();
@@ -310,7 +309,7 @@ int AlignCommand::execute(){
 			int start = time(NULL);
 		
 #ifdef USE_MPI	
-				int pid, end, numSeqsPerProcessor; 
+				int pid, numSeqsPerProcessor; 
 				int tag = 2001;
 				vector<unsigned long int> MPIPos;
 				MPIWroteAccnos = false;