package init

bwa-fix-build-gcc10.patch

@@ -0,0 +1,28 @@
+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

@@ -0,0 +1,16 @@
+diff --git a/ksw.c b/ksw.c
+index 9793e5eb..76f39c98 100644
+--- a/ksw.c
++++ b/ksw.c
+@@ -26,7 +26,11 @@
+ #include <stdlib.h>
+ #include <stdint.h>
+ #include <assert.h>
++#ifdef USE_SIMDE
++#include <simde/x86/sse2.h>
++#else
+ #include <emmintrin.h>
++#endif
+ #include "ksw.h"
+ 
+ #ifdef USE_MALLOC_WRAPPERS

bwa.spec

@@ -0,0 +1,55 @@
+Name:                bwa
+Version:             0.7.17
+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
+Patch1:              bwa-simde.patch
+BuildRequires:       gcc perl-generators
+%ifnarch x86_64
+BuildRequires:       simde-devel
+%endif
+BuildRequires:       zlib-devel
+
+%description
+BWA is a program for aligning sequencing reads against a large
+reference genome (e.g. human genome). It has two major components, one
+for read shorter than 150bp and the other for longer reads.
+
+%prep
+%autosetup -p1
+
+%build
+CFLAGS="%{optflags} -O3"
+%ifnarch x86_64
+CFLAGS="${CFLAGS} -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP"
+%endif
+%make_build CFLAGS="${CFLAGS}"
+
+%install
+rm -rf %{buildroot}
+mkdir -p %{buildroot}/%{_bindir}
+mkdir -p %{buildroot}/%{_datadir}/%{name}/bwakit
+mkdir -p %{buildroot}/%{_mandir}/man1
+install -m 0755 bwa %{buildroot}/%{_bindir}
+install -m 0755 qualfa2fq.pl %{buildroot}/%{_bindir}
+install -m 0755 xa2multi.pl %{buildroot}/%{_bindir}
+install -m 0755 bwakit/* %{buildroot}/%{_datadir}/%{name}/bwakit
+install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1
+
+%check
+./bwa 2>&1 | grep '^Version: %{version}'
+
+%files
+%doc COPYING NEWS.md README.md README-alt.md
+%{_bindir}/bwa
+%{_bindir}/qualfa2fq.pl
+%{_bindir}/xa2multi.pl
+%{_datadir}/%{name}/*
+%{_mandir}/man1/%{name}.1*
+
+%changelog
+* Fri Jan 8 2021 chengzihan <chengzihan2@huawei.com> - 0.7.17-1
+- Package init

bwa.yaml

@@ -0,0 +1,4 @@
+version_control: github
+src_repo: lh3/bwa
+tag_prefix: "^v"
+separator: "."