From 118948cb0abd78cfca59799a48454a4cd9525a78 Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Tue, 4 Aug 2020 17:52:51 -0400
Subject: [PATCH] [bowtie] added version 1.3.0. Patch fixed for new version
 (#17744)

---
 .../packages/bowtie/fix_narrowing_err_1.3.0.patch     | 11 +++++++++++
 var/spack/repos/builtin/packages/bowtie/package.py    |  4 +++-
 2 files changed, 14 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch

diff --git a/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch
new file mode 100644
index 0000000000..0da7fe0de3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch
@@ -0,0 +1,11 @@
+--- a/alphabet.cpp	2020-07-28 15:02:56.137635525 -0400
++++ b/alphabet.cpp	2020-07-28 15:05:32.385589360 -0400
+@@ -274,7 +274,7 @@
+ const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";
+ 
+ signed char mask2iupac[16] = {
+-	-1,
++	static_cast<char>(-1),
+ 	'A', // 0001
+ 	'C', // 0010
+ 	'M', // 0011
diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py
index ce7f8b03a0..737ae8c893 100644
--- a/var/spack/repos/builtin/packages/bowtie/package.py
+++ b/var/spack/repos/builtin/packages/bowtie/package.py
@@ -13,6 +13,7 @@ class Bowtie(MakefilePackage):
     homepage = "https://sourceforge.net/projects/bowtie-bio/"
     url      = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
 
+    version('1.3.0', sha256='d7c2d982a67884909f284a0ff150b56b20127cd7a1ced461c3c4c03e6a6374c5')
     version('1.2.3', sha256='86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823')
     # The bowtie project git tagged and GitHub released a v1.2.2,
     # discovered/fixed a bug, git tagged a v1.2.2_p1 and moved the
@@ -50,7 +51,8 @@ class Bowtie(MakefilePackage):
     patch('for_aarch64.patch', when='target=aarch64:')
 
     # measures for narrowing error
-    patch('fix_narrowing_err.patch')
+    patch('fix_narrowing_err.patch', when='@:1.2.3')
+    patch('fix_narrowing_err_1.3.0.patch', when='@1.3.0:')
 
     def edit(self, spec, prefix):
         makefile = FileFilter('Makefile')
-- 
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