From 9e2fce77f5ceb93d9b3d6ef1a6d76770c3e86e0e Mon Sep 17 00:00:00 2001
From: sukanka <su975853527@gmail.com>
Date: Mon, 11 Jul 2022 10:13:49 +0800
Subject: [PATCH] freebayes: update dependencies tabixpp: add libtabixpp.so
 vcflib: build shared library

---
 BioArchLinux/tabixpp/PKGBUILD | 1 +
 BioArchLinux/vcflib/PKGBUILD  | 1 +
 prepare/freebayes/PKGBUILD    | 7 ++++---
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/BioArchLinux/tabixpp/PKGBUILD b/BioArchLinux/tabixpp/PKGBUILD
index d100cabf5a..327ba508ab 100644
--- a/BioArchLinux/tabixpp/PKGBUILD
+++ b/BioArchLinux/tabixpp/PKGBUILD
@@ -29,4 +29,5 @@ package() {
   install -Dm 755 libtabix.a $pkgdir/usr/lib/libtabix.a
 
   ln -s /usr/lib/libtabix.so.1 ${pkgdir}/usr/lib/libtabix.so
+  ln -s /usr/lib/libtabix.so   ${pkgdir}/usr/lib/libtabixpp.so
 }
diff --git a/BioArchLinux/vcflib/PKGBUILD b/BioArchLinux/vcflib/PKGBUILD
index 48b8fa7694..d0fb83e76a 100644
--- a/BioArchLinux/vcflib/PKGBUILD
+++ b/BioArchLinux/vcflib/PKGBUILD
@@ -46,6 +46,7 @@ prepare(){
   done
   cd ${pkgname}
   sed -i 's| contrib/tabixpp/tabix.cpp|/usr/include/tabix/tabix.cpp|g' CMakeLists.txt
+  sed -i 's|vcflib STATIC|vcflib SHARED|g' CMakeLists.txt
   sed -i 's|<tabix.hpp>|<tabix/tabix.hpp>|g' src/Variant.h
 }
 build() {
diff --git a/prepare/freebayes/PKGBUILD b/prepare/freebayes/PKGBUILD
index 27476f86ca..9ddfdaf90d 100644
--- a/prepare/freebayes/PKGBUILD
+++ b/prepare/freebayes/PKGBUILD
@@ -17,12 +17,13 @@ sha256sums=('SKIP')
 prepare() {
   cd "$pkgname"
   git submodule update --init --recursive
+  # find vcflib
+  sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'" CMakeLists.txt
 }
 build() {
   cd "$pkgname"
-  rm -rf build
-  mkdir build
-  meson --prefix=/usr --buildtype=debug build
+  test -d build || mkdir build
+  meson --prefix=/usr --buildtype=release  build -Dprefer_system_deps=true
   cd build
   ninja -v
 }