From a2500064492040eebcf9835849f313fbed48d6a6 Mon Sep 17 00:00:00 2001
From: t-nojiri <68096132+t-nojiri@users.noreply.github.com>
Date: Mon, 14 Sep 2020 13:14:59 +0900
Subject: ngmlr: support for aarch64 (#18621)

* ngmlr: support for aarch64

* ngmlr: Fixed patch file
---
 .../repos/builtin/packages/ngmlr/for_aarch64.patch | 33 ++++++++++++++++++++++
 .../repos/builtin/packages/ngmlr/for_va_list.patch | 22 +++++++++++++++
 var/spack/repos/builtin/packages/ngmlr/package.py  |  4 +++
 3 files changed, 59 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ngmlr/for_aarch64.patch
 create mode 100644 var/spack/repos/builtin/packages/ngmlr/for_va_list.patch

diff --git a/var/spack/repos/builtin/packages/ngmlr/for_aarch64.patch b/var/spack/repos/builtin/packages/ngmlr/for_aarch64.patch
new file mode 100644
index 0000000000..9db5bb838a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ngmlr/for_aarch64.patch
@@ -0,0 +1,33 @@
+--- spack-src/lib/Complete-Striped-Smith-Waterman-Library/src/ssw.h.bak	2017-06-27 02:01:12.000000000 +0900
++++ spack-src/lib/Complete-Striped-Smith-Waterman-Library/src/ssw.h	2020-09-02 16:16:01.835283173 +0900
+@@ -14,7 +14,7 @@
+ #include <stdio.h>
+ #include <stdint.h>
+ #include <string.h>
+-#include <emmintrin.h>
++#include <SSE2NEON.h>
+ 
+ #ifdef __cplusplus
+ extern "C" {
+--- spack-src/lib/Complete-Striped-Smith-Waterman-Library/src/ssw.c.bak	2017-06-27 02:01:12.000000000 +0900
++++ spack-src/lib/Complete-Striped-Smith-Waterman-Library/src/ssw.c	2020-09-08 11:44:57.995497574 +0900
+@@ -35,7 +35,7 @@
+  *
+  */
+ 
+-#include <emmintrin.h>
++#include <SSE2NEON.h>
+ #include <stdint.h>
+ #include <stdlib.h>
+ #include <stdio.h>
+--- spack-src/src/ConvexAlignFast.cpp.bak	2017-06-27 02:01:12.000000000 +0900
++++ spack-src/src/ConvexAlignFast.cpp	2020-09-07 17:03:29.325279688 +0900
+@@ -8,7 +8,7 @@
+ #include <string.h>
+ #include <stdio.h>
+ #include <algorithm>
+-#include <x86intrin.h>
++#include <SSE2NEON.h>
+ 
+ #include "IConfig.h"
+ 
diff --git a/var/spack/repos/builtin/packages/ngmlr/for_va_list.patch b/var/spack/repos/builtin/packages/ngmlr/for_va_list.patch
new file mode 100644
index 0000000000..63fe89bfae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ngmlr/for_va_list.patch
@@ -0,0 +1,22 @@
+--- spack-src/src/AlignmentBuffer.cpp.bak	2017-06-27 02:01:12.000000000 +0900
++++ spack-src/src/AlignmentBuffer.cpp	2020-09-08 11:38:24.075464116 +0900
+@@ -2365,7 +2365,7 @@
+ 		va_list args;
+ 
+ 		va_start(args, s);
+-		if (args != 0)
++		if (va_arg(args, char *) != 0)
+ 			vfprintf(stderr, s, args);
+ 		else
+ 			fprintf(stderr, "%s", s);
+--- spack-src/src/Logging.cpp.bak	2020-09-08 11:30:20.915422258 +0900
++++ spack-src/src/Logging.cpp	2020-09-08 11:32:33.125437676 +0900
+@@ -94,7 +94,7 @@
+ 
+ 	if (color)
+ 		SetConsoleColor((ConsoleColor) (Message + (lvl * 2)));
+-	if (args != 0)
++	if (va_arg(args, char *) != 0)
+ 		vfprintf(stderr, s, args);
+ 	else
+ 		fprintf(stderr, "%s", s);
diff --git a/var/spack/repos/builtin/packages/ngmlr/package.py b/var/spack/repos/builtin/packages/ngmlr/package.py
index fba498e8d8..6dede65ee9 100644
--- a/var/spack/repos/builtin/packages/ngmlr/package.py
+++ b/var/spack/repos/builtin/packages/ngmlr/package.py
@@ -17,3 +17,7 @@ class Ngmlr(CMakePackage):
     version('0.2.5', sha256='719944a35cc7ff9c321eedbf3385a7375ce2301f609b3fd7be0a850cabbb028b')
 
     depends_on('zlib', type='link')
+    depends_on('sse2neon', when='target=aarch64:')
+
+    patch('for_aarch64.patch', when='target=aarch64:')
+    patch('for_va_list.patch')
-- 
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