[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.2-10-g8607d56

[Andreas Tille]

The following commit has been merged in the master branch:
commit ccb48f4d606b785dd37dd768b65de974867c5b42
Author: Andreas Tille <tille at debian.org>
Date:   Sat Mar 31 08:19:34 2012 +0200

    Removed patch that became unnecessary

diff --git a/debian/changelog b/debian/changelog
index 988e45f..ea2bd1e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,8 @@ jellyfish (1.1.4-1) UNRELEASED; urgency=low
 
   * New upstream version
   * debian/patches/ptrdiff_t: Removed because applied upstream
+  * debian/patches/cmdline: Removed because upstream code was changed
+    in a way that it becomes superflous
 
  -- Andreas Tille <tille at debian.org>  Sat, 31 Mar 2012 00:25:12 +0200
 
diff --git a/debian/patches/cmdline b/debian/patches/cmdline
deleted file mode 100644
index e658e69..0000000
--- a/debian/patches/cmdline
+++ /dev/null
@@ -1,180 +0,0 @@
-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)
diff --git a/debian/patches/series b/debian/patches/series
index 8e9cfaf..2a3700c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
 man
-cmdline

-- 
count k-mers of DNA