X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cmdargs.cpp;h=929b4aac886d97135f7d9883396e9a2a3fb292b5;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=416ced88ddb1a0dc765b73a5c973570f7925709b;hpb=1b4aa03040e61f4c2d47ce32cb12726dcdadb917;p=mothur.git

diff --git a/cmdargs.cpp b/cmdargs.cpp
index 416ced8..929b4aa 100644
--- a/cmdargs.cpp
+++ b/cmdargs.cpp
@@ -70,6 +70,8 @@ NJ_handle_args(int argc,
   
   static NJ_ARGS nj_args;
   int option_index, c;
+  
+  optind = 0;  //neccasary to read in arguments if code is run more than once
 
   struct option NJ_long_options[] = {
 
@@ -139,7 +141,8 @@ NJ_handle_args(int argc,
     if(c == -1) {
       break;
     }
-
+//printf("%d\t%d\n", option_index, argc);
+//for (int red = 0; red < argc; red++) { printf("%s\n", argv[red]); }
     switch(c) {
 
     case 0:
@@ -256,12 +259,12 @@ NJ_handle_args(int argc,
   
   if(nj_args.version) {
     printf("Clearcut Version: %s\n", NJ_VERSION);
-    exit(0);
+   //exit(0);
   }
   
   if(nj_args.help) {
     NJ_usage();
-    exit(0);
+    //exit(0);
   }
   
   /* if stdin & explicit filename are specified for input */