From 307137b9669fb94e262312864c806b52ae2be27f Mon Sep 17 00:00:00 2001
From: Jun Aruga <jaruga@redhat.com>
Date: Apr 16 2020 20:08:59 +0000
Subject: Update to upstream release 0.7.17


---

diff --git a/.gitignore b/.gitignore
index a35d82f..81e5c7e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ bwa-0.5.8a.tar.bz2
 /bwa-0.7.12.tar.bz2
 /bwa-0.7.13.tar.bz2
 /bwa-0.7.15.tar.bz2
+/bwa-0.7.17.tar.bz2
diff --git a/bwa-fix-build-gcc10.patch b/bwa-fix-build-gcc10.patch
new file mode 100644
index 0000000..32c9f9b
--- /dev/null
+++ b/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
+
diff --git a/bwa-nosse2-i386.patch b/bwa-nosse2-i386.patch
deleted file mode 100644
index b9b9ea5..0000000
--- a/bwa-nosse2-i386.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- bwa-0.6.1/Makefile	2011-11-28 14:55:02.000000000 +0000
-+++ bwa-0.6.1.new/Makefile	2012-05-13 20:52:46.889400339 +0100
-@@ -2,7 +2,7 @@
- CXX=		g++
- CFLAGS=		-g -Wall -O2
- CXXFLAGS=	$(CFLAGS)
--DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
-+DFLAGS=		-DHAVE_PTHREAD -D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
- OBJS=		QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o \
- 			is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o \
- 			bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
diff --git a/bwa.spec b/bwa.spec
index b5dfcc5..6979a46 100644
--- a/bwa.spec
+++ b/bwa.spec
@@ -1,13 +1,16 @@
 Name:           bwa
-Version:        0.7.15
-Release:        10%{?dist}
+Version:        0.7.17
+Release:        1%{?dist}
 Summary:        Burrows-Wheeler Alignment tool
 
 License:        GPLv3
 URL:            http://bio-bwa.sourceforge.net/
 Source0:        http://downloads.sourceforge.net/bio-%{name}/%{name}-%{version}.tar.bz2
+# Fix building against GCC 10.
+# https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284
+Patch0:         bwa-fix-build-gcc10.patch
 # 0.7.x versions only build on x86_64
-ExclusiveArch:	x86_64
+ExclusiveArch:  x86_64
 
 BuildRequires:  gcc
 BuildRequires:  perl-generators
@@ -21,6 +24,7 @@ for read shorter than 150bp and the other for longer reads.
 
 %prep
 %setup -q
+%patch0 -p1
 
 
 %build
@@ -40,6 +44,10 @@ install -m 0755 bwakit/* %{buildroot}/%{_bindir}
 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 
 %{_mandir}/man1/%{name}.1*
@@ -47,6 +55,9 @@ install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1
 
 
 %changelog
+* Sun Mar 22 2020 Jun Aruga <jaruga@redhat.com> - 0.7.17-1
+- Update to upstream release 0.7.17
+
 * Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.15-10
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
 
diff --git a/sources b/sources
index a161cbf..ce3983e 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-fcf470a46a1dbe2f96a1c5b87c530554  bwa-0.7.15.tar.bz2
+SHA512 (bwa-0.7.17.tar.bz2) = 67cccfef1c7aa1b5aad6b59a49390e8d96f64320c414bfffacf232aeb08c15861e98be826c1b42b6222d6ff086eeb055b1318ea2e9eebfd87b2365d06fc89802