!5 Update to version 0.7.18

From: @wang--ge 
Reviewed-by: @wk333 
Signed-off-by: @wk333

bwa-fix-build-gcc10.patch

@@ -1,28 +0,0 @@
-From 039e5733af162692ad670d5c6fb4a9d8fa5e3d02 Mon Sep 17 00:00:00 2001
-From: David Seifert <soap@gentoo.org>
-Date: Wed, 26 Feb 2020 13:24:17 +0100
-Subject: [PATCH] Fix building against GCC 10
-
-* GCC 10 defaults to `-fno-common`, which makes C behave
-  more like C++ in that you can only ever have one definition
-  of an object per executable.
----
- rle.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/rle.h b/rle.h
-index 0d59484..4f8946d 100644
---- a/rle.h
-+++ b/rle.h
-@@ -30,7 +30,7 @@ extern "C" {
-  *** 43+3 codec ***
-  ******************/
- 
--const uint8_t rle_auxtab[8];
-+extern const uint8_t rle_auxtab[8];
- 
- #define RLE_MIN_SPACE 18
- #define rle_nptr(block) ((uint16_t*)(block))
--- 
-2.25.1
-

bwa-simde.patch

@@ -1,16 +1,16 @@
 diff --git a/ksw.c b/ksw.c
-index 9793e5eb..76f39c98 100644
+index 1e584e9..d433432 100644
 --- a/ksw.c
 +++ b/ksw.c
-@@ -26,7 +26,11 @@
+@@ -30,6 +30,8 @@
- #include <stdlib.h>
- #include <stdint.h>
- #include <assert.h>
-+#ifdef USE_SIMDE
-+#include <simde/x86/sse2.h>
-+#else
  #include <emmintrin.h>
-+#endif
+ #elif defined __ARM_NEON
- #include "ksw.h"
+ #include "neon_sse.h"
- 
++#elif defined USE_SIMDE
- #ifdef USE_MALLOC_WRAPPERS
++#include <simde/x86/sse2.h>
+ #else
+ #include "scalar_sse.h"
+ #endif
+-- 
+2.43.0
+

bwa.spec

@@ -1,11 +1,10 @@
 Name:                bwa
-Version:             0.7.17
+Version:             0.7.18
 Release:             1
 Summary:             Burrows-Wheeler Alignment tool
 License:             GPLv3 and MIT
 URL:                 https://github.com/lh3/bwa
-Source0:             https://github.com/lh3/bwa/releases/download/v%{version}/%{name}-%{version}.tar.bz2
+Source0:             https://github.com/lh3/bwa/releases/download/v%{version}/%{name}-%{version}.tar.gz
-Patch0:              bwa-fix-build-gcc10.patch
 Patch1:              bwa-simde.patch
 BuildRequires:       gcc perl-generators
 %ifnarch x86_64
@@ -25,7 +24,10 @@ for read shorter than 150bp and the other for longer reads.
 CFLAGS="%{optflags} -O3"
 %ifnarch x86_64
 CFLAGS="${CFLAGS} -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP"
+%else
+CFLAGS="${CFLAGS} -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP"
 %endif
+
 %make_build CFLAGS="${CFLAGS}"
 
 %install
@@ -51,5 +53,8 @@ install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1
 %{_mandir}/man1/%{name}.1*
 
 %changelog
+* Mon Jul 8 2024 Ge Wang <wang__ge@126.com> - 0.7.18-1
+- Update to version 0.7.18
+
 * Fri Jan 8 2021 chengzihan <chengzihan2@huawei.com> - 0.7.17-1
 - Package init