From 06a445cd086f0b7775e2d193e47748218ba1ee4d Mon Sep 17 00:00:00 2001
From: Florian Weimer <fweimer@redhat.com>
Date: Dec 20 2022 12:03:26 +0000
Subject: Apply upstream patch to fix C99 compatibility issue


Related to:

  <https://fedoraproject.org/wiki/Changes/PortingToModernC>
  <https://fedoraproject.org/wiki/Toolchain/PortingToModernC>

---

diff --git a/ugene-c99.patch b/ugene-c99.patch
new file mode 100644
index 0000000..538f5f6
--- /dev/null
+++ b/ugene-c99.patch
@@ -0,0 +1,19 @@
+commit a8c7ed9daaa098410b84b2f81827700cc061c985
+Author: Yuliya Algaer <yalgaer@gmail.com>
+Date:   Wed Dec 14 16:14:44 2022 +0700
+
+    Replace 'ugene_custom_open' with a standard 'open' (#1034)
+
+diff --git a/src/libs_3rdparty/samtools/src/samtools/bgzf.c b/src/libs_3rdparty/samtools/src/samtools/bgzf.c
+index 4a6852e7d9..0df061e2a3 100644
+--- a/src/libs_3rdparty/samtools/src/samtools/bgzf.c
++++ b/src/libs_3rdparty/samtools/src/samtools/bgzf.c
+@@ -210,7 +210,7 @@ bgzf_open(const char* __restrict path, const char* __restrict mode)
+ #ifdef _WIN32
+ 		oflag |= O_BINARY;
+ #endif
+-		fd = ugene_custom_open(path, oflag);
++        fd = open(path, oflag);
+ 		if (fd == -1) return 0;
+         fp = open_read(fd);
+ #endif
diff --git a/ugene.spec b/ugene.spec
index be4f656..cefffb7 100644
--- a/ugene.spec
+++ b/ugene.spec
@@ -35,7 +35,7 @@
 %global	GIT	git
 %endif
 
-%global	mainrel		1
+%global	mainrel		2
 %undefine	prever
 
 %if		0%{?use_release} >= 1
@@ -78,6 +78,7 @@ Patch105:	ugene-40.1-libs_3rdparty-breakpad-arch-port.patch
 Patch106:	ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch
 Patch107:	ugene-40.1-qbswap-bigendian-workaround.patch
 Patch108:	ugene-43.x-wrong-elif-SendReportDialog.patch
+Patch109:	ugene-c99.patch
 
 BuildRequires:	make
 BuildRequires:	gcc-c++
@@ -146,6 +147,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org"
 	%GIT	commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a
 %patch108 -p1 -b .elif -Z
 	%GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a
+%patch109 -p1 -b .c99 -Z
+	%GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a
 
 sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d'
 sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d'
@@ -250,6 +253,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop
 %{_mandir}/man1/%{name}.1*
 
 %changelog
+* Tue Dec 20 2022 Florian Weimer <fweimer@redhat.com> - 45.0-2
+- Apply upstream patch to fix C99 compatibility issue
+
 * Sun Nov 20 2022 Mamoru TASAKA <mtasaka@fedoraproject.org> - 45.0-1
 - 45.0