Index: jellyfish/jellyfish/cite_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/cite_cmdline.cc	2011-10-10 13:15:50.000000000 -0700
+++ jellyfish/jellyfish/cite_cmdline.cc	2011-10-10 13:12:17.000000000 -0700
@@ -337,13 +337,11 @@
                const char *long_opt, char short_opt,
                const char *additional_error)
 {
-  char *stop_char = 0;
   const char *val = value;
   int found;
   char **string_field;
   FIX_UNUSED (field);
 
-  stop_char = 0;
   found = 0;
 
   if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
@@ -420,14 +418,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
Index: jellyfish/jellyfish/query_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/query_cmdline.cc	2011-10-10 13:18:39.000000000 -0700
+++ jellyfish/jellyfish/query_cmdline.cc	2011-10-10 13:18:06.000000000 -0700
@@ -354,13 +354,11 @@
                const char *long_opt, char short_opt,
                const char *additional_error)
 {
-  char *stop_char = 0;
   const char *val = value;
   int found;
   char **string_field;
   FIX_UNUSED (field);
 
-  stop_char = 0;
   found = 0;
 
   if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
@@ -437,14 +435,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
Index: jellyfish/jellyfish/hash_merge_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/hash_merge_cmdline.cc	2011-10-10 13:21:16.000000000 -0700
+++ jellyfish/jellyfish/hash_merge_cmdline.cc	2011-10-10 13:21:32.000000000 -0700
@@ -472,14 +472,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
Index: jellyfish/jellyfish/histo_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/histo_cmdline.cc	2011-10-10 13:22:17.000000000 -0700
+++ jellyfish/jellyfish/histo_cmdline.cc	2011-10-10 13:22:22.000000000 -0700
@@ -488,14 +488,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
Index: jellyfish/jellyfish/stats_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/stats_cmdline.cc	2011-10-10 13:23:21.000000000 -0700
+++ jellyfish/jellyfish/stats_cmdline.cc	2011-10-10 13:23:28.000000000 -0700
@@ -493,14 +493,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
Index: jellyfish/jellyfish/histo_fastq_main_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/histo_fastq_main_cmdline.cc	2011-10-10 13:24:05.000000000 -0700
+++ jellyfish/jellyfish/histo_fastq_main_cmdline.cc	2011-10-10 13:24:13.000000000 -0700
@@ -448,14 +448,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
Index: jellyfish/jellyfish/dump_fastq_main_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/dump_fastq_main_cmdline.cc	2011-10-10 13:25:26.000000000 -0700
+++ jellyfish/jellyfish/dump_fastq_main_cmdline.cc	2011-10-10 13:25:43.000000000 -0700
@@ -469,14 +469,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
Index: jellyfish/jellyfish/dump_cmdline.cc
===================================================================
--- jellyfish.orig/jellyfish/dump_cmdline.cc	2011-10-10 13:26:40.000000000 -0700
+++ jellyfish/jellyfish/dump_cmdline.cc	2011-10-10 13:26:46.000000000 -0700
@@ -463,14 +463,12 @@
   
   int override;
   int initialize;
-  int check_required;
   int check_ambiguity;
   
   package_name = argv[0];
   
   override = params->override;
   initialize = params->initialize;
-  check_required = params->check_required;
   check_ambiguity = params->check_ambiguity;
 
   if (initialize)
