[med-svn] [bcftools] 03/08: Remove backported patches

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository bcftools.

commit d35e058bff988b712593934f95cf1fbdeb669a9f
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Apr 25 21:59:44 2016 -0700

    Remove backported patches
---
 debian/patches/getopt-return-types.patch | 98 --------------------------------
 debian/patches/peakfit-gsl2.patch        | 36 ------------
 debian/patches/series                    |  3 -
 3 files changed, 137 deletions(-)

diff --git a/debian/patches/getopt-return-types.patch b/debian/patches/getopt-return-types.patch
deleted file mode 100644
index 9c1bcf6..0000000
--- a/debian/patches/getopt-return-types.patch
+++ /dev/null
@@ -1,98 +0,0 @@
-From afecb4e96c3abc188e7fc155e35720e01aa13a81 Mon Sep 17 00:00:00 2001
-From: John Marshall <jm18 at sanger.ac.uk>
-Date: Tue, 15 Mar 2016 16:15:48 +0000
-Subject: [PATCH] getopt_long() returns int, not char
-
-Much like fgetc() returning EOF, we need to store getopt_long()'s
-result in an int so that we can reliably check the -1 return value.
-Hat tip @daviesrob; fixes the usage errors part of #389.
----
- consensus.c          | 2 +-
- plugins/GTisec.c     | 2 +-
- plugins/color-chrs.c | 2 +-
- plugins/fill-tags.c  | 2 +-
- plugins/mendelian.c  | 2 +-
- plugins/tag2tag.c    | 2 +-
- plugins/vcf2sex.c    | 3 ++-
- polysomy.c           | 3 ++-
- 8 files changed, 10 insertions(+), 8 deletions(-)
-
---- bcftools.orig/consensus.c
-+++ bcftools/consensus.c
-@@ -623,7 +623,7 @@
-         {"chain",1,0,'c'},
-         {0,0,0,0}
-     };
--    char c;
-+    int c;
-     while ((c = getopt_long(argc, argv, "h?s:1iH:f:o:m:c:",loptions,NULL)) >= 0) 
-     {
-         switch (c) 
---- bcftools.orig/plugins/color-chrs.c
-+++ bcftools/plugins/color-chrs.c
-@@ -159,7 +159,7 @@
-         {"unrelated",1,0,'u'},
-         {0,0,0,0}
-     };
--    char c;
-+    int c;
-     while ((c = getopt_long(argc, argv, "?ht:u:p:",loptions,NULL)) >= 0)
-     {
-         switch (c) 
---- bcftools.orig/plugins/fill-tags.c
-+++ bcftools/plugins/fill-tags.c
-@@ -112,7 +112,7 @@
-         {"tags",1,0,'t'},
-         {0,0,0,0}
-     };
--    char c;
-+    int c;
-     while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
-     {
-         switch (c) 
---- bcftools.orig/plugins/mendelian.c
-+++ bcftools/plugins/mendelian.c
-@@ -100,7 +100,7 @@
-         {"count",0,0,'c'},
-         {0,0,0,0}
-     };
--    char c;
-+    int c;
-     while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
-     {
-         switch (c) 
---- bcftools.orig/plugins/tag2tag.c
-+++ bcftools/plugins/tag2tag.c
-@@ -83,7 +83,7 @@
-         {"gl-to-pl",0,0,2},
-         {0,0,0,0}
-     };
--    char c;
-+    int c;
-     while ((c = getopt_long(argc, argv, "?hr",loptions,NULL)) >= 0)
-     {
-         switch (c) 
---- bcftools.orig/plugins/vcf2sex.c
-+++ bcftools/plugins/vcf2sex.c
-@@ -389,7 +389,8 @@
-         {"background",1,0,'b'},
-         {0,0,0,0}
-     };
--    char c, *tmp, *ploidy_fname = NULL;
-+    char *tmp, *ploidy_fname = NULL;
-+    int c;
-     while ((c = getopt_long(argc, argv, "p:n:g:m:vb:",loptions,NULL)) >= 0)
-     {
-         switch (c) {
---- bcftools.orig/polysomy.c
-+++ bcftools/polysomy.c
-@@ -675,7 +675,8 @@
-         {"regions-file",1,0,'R'},
-         {0,0,0,0}
-     };
--    char c, *tmp;
-+    char *tmp;
-+    int c;
-     while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:n:S:",loptions,NULL)) >= 0)
-     {
-         switch (c)
diff --git a/debian/patches/peakfit-gsl2.patch b/debian/patches/peakfit-gsl2.patch
deleted file mode 100644
index 1ff2e09..0000000
--- a/debian/patches/peakfit-gsl2.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From 681d80c20d078f953ff39140f7e519c94cb4fd1d Mon Sep 17 00:00:00 2001
-From: Petr Danecek <pd3 at sanger.ac.uk>
-Date: Thu, 11 Feb 2016 14:44:32 +0000
-Subject: [PATCH] peakfit build with GSLv2, resolves #378
-
----
- peakfit.c | 6 ++++++
- 1 file changed, 6 insertions(+)
-
-diff --git a/peakfit.c b/peakfit.c
-index 2bc8492..8094b5d 100644
---- a/peakfit.c
-+++ b/peakfit.c
-@@ -26,6 +26,7 @@
- 
- #include "peakfit.h"
- #include <stdio.h>
-+#include <gsl/gsl_version.h>
- #include <gsl/gsl_vector.h>
- #include <gsl/gsl_multifit_nlin.h>
- #include <htslib/hts.h>
-@@ -550,9 +551,14 @@ double peakfit_run(peakfit_t *pkf, int nvals, double *xvals, double *yvals)
-             }
-             if ( ret ) break;
- 
-+#if GSL_MAJOR_VERSION >= 2
-+            int info;
-+            test1 = gsl_multifit_fdfsolver_test(solver, 1e-8,1e-8, 0.0, &info);
-+#else
-             gsl_multifit_gradient(solver->J, solver->f, grad);
-             test1 = gsl_multifit_test_gradient(grad, 1e-8);
-             test2 = gsl_multifit_test_delta(solver->dx, solver->x, 1e-8, 1e-8);
-+#endif
-         }
-         while ((test1==GSL_CONTINUE || test2==GSL_CONTINUE) && ++niter<niter_max);
-         if ( pkf->verbose >1 )
diff --git a/debian/patches/series b/debian/patches/series
index b532fa2..ca9188d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,6 +2,3 @@ external-libs.patch
 compiler-flags.patch
 destdir.patch
 tests-pluginpath.patch
-spelling.patch
-peakfit-gsl2.patch
-getopt-return-types.patch

-- 
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