From cbd9f91c326f5f57fb9dd4374069b215e2e7a5f6 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 27 Apr 2018 01:05:18 +0200
Subject: gnu: bcftools: Update to 1.8.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8.
* gnu/local.mk: Remove patch.
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
---
 gnu/local.mk                                             |  1 -
 gnu/packages/bioinformatics.scm                          |  7 +++----
 gnu/packages/patches/bcftools-regidx-unsigned-char.patch | 16 ----------------
 3 files changed, 3 insertions(+), 21 deletions(-)
 delete mode 100644 gnu/packages/patches/bcftools-regidx-unsigned-char.patch

(limited to 'gnu')

diff --git a/gnu/local.mk b/gnu/local.mk
index 6065d4c96b..3e093b791b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -575,7 +575,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/azr3.patch				\
   %D%/packages/patches/bash-completion-directories.patch	\
   %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
-  %D%/packages/patches/bcftools-regidx-unsigned-char.patch	\
   %D%/packages/patches/binutils-ld-new-dtags.patch		\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blast+-fix-makefile.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc5fe41115..d8b17f51e4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -285,7 +285,7 @@ (define-public bamtools
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.5")
+    (version "1.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -293,12 +293,11 @@ (define-public bcftools
                     version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
-              (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
+                "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled htslib.
-               '(delete-file-recursively "htslib-1.5"))))
+               '(delete-file-recursively "htslib-1.8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
diff --git a/gnu/packages/patches/bcftools-regidx-unsigned-char.patch b/gnu/packages/patches/bcftools-regidx-unsigned-char.patch
deleted file mode 100644
index af5bc160f5..0000000000
--- a/gnu/packages/patches/bcftools-regidx-unsigned-char.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: Fix test-regidx argument parsing on archs with unsigned char
- On architectures where char is unsigned "c >= 0" was always true.
-Author: Adrian Bunk <bunk@debian.org>
-Bug-Debian: https://bugs.debian.org/865060
-
---- a/test/test-regidx.c
-+++ b/test/test-regidx.c
-@@ -336,7 +336,7 @@
-         {"seed",1,0,'s'},
-         {0,0,0,0}
-     };
--    char c;
-+    int c;
-     int seed = (int)time(NULL);
-     while ((c = getopt_long(argc, argv, "hvs:",loptions,NULL)) >= 0) 
-     {
-- 
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