From b7ed6b4fe05f8eb555bf2932c2523d2309867f22 Mon Sep 17 00:00:00 2001
From: t-nojiri <68096132+t-nojiri@users.noreply.github.com>
Date: Sun, 11 Oct 2020 10:33:08 +0900
Subject: jellyfish@1.1.11: Change the type of the array dna_codes to the
 signed type. (#19019)

* jellyfish@1.1.11: Change the type of the array dna_codes to the signed type.

* jellyfish@1.1.11: Add patch file
---
 .../builtin/packages/jellyfish/dna_codes.patch     | 22 ++++++++++++++++++++++
 .../repos/builtin/packages/jellyfish/package.py    |  2 ++
 2 files changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/jellyfish/dna_codes.patch

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/jellyfish/dna_codes.patch b/var/spack/repos/builtin/packages/jellyfish/dna_codes.patch
new file mode 100644
index 0000000000..59bcce3e93
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jellyfish/dna_codes.patch
@@ -0,0 +1,22 @@
+--- spack-src/jellyfish/dna_codes.hpp.bak	2013-05-30 04:45:57.000000000 +0900
++++ spack-src/jellyfish/dna_codes.hpp	2020-09-28 10:37:14.580832234 +0900
+@@ -14,7 +14,7 @@
+ static const uint_t CODE_IGNORE  = (uint_t)-2;
+ static const uint_t CODE_COMMENT = (uint_t)-3;
+ static const uint_t CODE_NOT_DNA = ((uint_t)1) << (bsizeof(uint_t) - 1);
+-extern const char   dna_codes[256];
++extern const signed char   dna_codes[256];
+ };
+ 
+ #endif /* __DNA_CODE_HPP__ */
+--- spack-src/jellyfish/dna_codes.cc.bak	2013-05-30 04:45:57.000000000 +0900
++++ spack-src/jellyfish/dna_codes.cc	2020-09-28 10:29:08.810848835 +0900
+@@ -7,7 +7,7 @@
+ #define C 1
+ #define G 2
+ #define T 3
+-const char jellyfish::dna_codes[256] = {
++const signed char jellyfish::dna_codes[256] = {
+   O, O, O, O, O, O, O, O, O, O, I, O, O, O, O, O, 
+   O, O, O, O, O, O, O, O, O, O, O, O, O, O, O, O, 
+   O, O, O, O, O, O, O, O, O, O, O, O, O, R, O, O, 
diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py
index 67092a81ad..1d5b7febc1 100644
--- a/var/spack/repos/builtin/packages/jellyfish/package.py
+++ b/var/spack/repos/builtin/packages/jellyfish/package.py
@@ -20,3 +20,5 @@ class Jellyfish(AutotoolsPackage):
 
     depends_on('perl', type=('build', 'run'))
     depends_on('python', type=('build', 'run'))
+
+    patch('dna_codes.patch', when='@1.1.11')
-- 
cgit v1.2.3-70-g09d2