diff --git a/bwa-0.7.17.tar.bz2 b/bwa-0.7.17.tar.bz2 deleted file mode 100644 index eb05d75..0000000 Binary files a/bwa-0.7.17.tar.bz2 and /dev/null differ diff --git a/bwa-0.7.18.tar.gz b/bwa-0.7.18.tar.gz new file mode 100644 index 0000000..43ed326 Binary files /dev/null and b/bwa-0.7.18.tar.gz differ diff --git a/bwa-fix-build-gcc10.patch b/bwa-fix-build-gcc10.patch deleted file mode 100644 index 32c9f9b..0000000 --- a/bwa-fix-build-gcc10.patch +++ /dev/null @@ -1,28 +0,0 @@ -From 039e5733af162692ad670d5c6fb4a9d8fa5e3d02 Mon Sep 17 00:00:00 2001 -From: David Seifert -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 - diff --git a/bwa-simde.patch b/bwa-simde.patch index 6be4d66..2e4cfb4 100644 --- a/bwa-simde.patch +++ b/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 @@ - #include - #include - #include -+#ifdef USE_SIMDE -+#include -+#else +@@ -30,6 +30,8 @@ #include -+#endif - #include "ksw.h" - - #ifdef USE_MALLOC_WRAPPERS + #elif defined __ARM_NEON + #include "neon_sse.h" ++#elif defined USE_SIMDE ++#include + #else + #include "scalar_sse.h" + #endif +-- +2.43.0 + diff --git a/bwa.spec b/bwa.spec index de97546..c375616 100644 --- a/bwa.spec +++ b/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 -Patch0: bwa-fix-build-gcc10.patch +Source0: https://github.com/lh3/bwa/releases/download/v%{version}/%{name}-%{version}.tar.gz 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 - 0.7.18-1 +- Update to version 0.7.18 + * Fri Jan 8 2021 chengzihan - 0.7.17-1 - Package init