freebayes: updated to 1.3.9

BioArchLinux/freebayes/PKGBUILD

@@ -1,27 +1,30 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 # Contributor: Clint Valentine <valentine.clint@gmail.com>
 pkgname=freebayes
-pkgver=1.3.8
-pkgrel=7
+pkgver=1.3.9
+pkgrel=0
 pkgdesc="About Bayesian haplotype-based genetic polymorphism discovery and genotyping"
 arch=('x86_64')
 url="https://github.com/freebayes/freebayes"
 license=('MIT')
 depends=('tabixpp' 'seqlib' 'vcflib')
 makedepends=('ninja' 'meson' 'git' 'cmake' 'make'
-  'vcftools' 'samtools' 'parallel' 'bc' 'perl'
+  'vcftools' 'samtools' 'parallel' 'bc' 'perl' 'patch'
 )
 source=(
   "${pkgname}-${pkgver}.tar.gz::${url}/archive/refs/tags/v${pkgver}.tar.gz"
   "fastahack.zip::https://github.com/ekg/fastahack/archive/refs/tags/v1.0.0.tar.gz"
   "multichoose.zip::https://github.com/vcflib/multichoose/archive/255192edd49cfe36557f7f4f0d2d6ee1c702ffbb.zip"
   "smithwaterman.zip::https://github.com/ekg/smithwaterman/archive/2610e259611ae4cde8f03c72499d28f03f6d38a7.zip"
+  "meson.patch::https://github.com/freebayes/freebayes/pull/823.patch"
 )
-sha256sums=('d1c24b1d1b35277e7403cd67063557998218a105c916b01a745e7704715fce67'
-            'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae'
-            '799ce24cf3784090df39dd9552d515bda9c9e7d3f24e7712dd08565680b5c8ed'
-            '0806976c46a5117c7b7a6d4e174e267f05bc652885ca72a82b91e5a87600d4f9')
+sha256sums=('41ed3074c7648375286168a6708e02dac6788eaca4ca6039ff5a7ed91f257b53'
+  'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae'
+  '799ce24cf3784090df39dd9552d515bda9c9e7d3f24e7712dd08565680b5c8ed'
+  '0806976c46a5117c7b7a6d4e174e267f05bc652885ca72a82b91e5a87600d4f9'
+  '910d79a9c3c1cb81936db3c34241334d2635abcd4b38f4dd080580c6cb921e9c')
 prepare() {
+  patch -p1 -i ${srcdir}/meson.patch -d "${pkgname}-${pkgver}"
   mv fastahack-*/* "${pkgname}-${pkgver}"/contrib/fastahack
   mv multichoose-*/* "${pkgname}-${pkgver}"/contrib/multichoose
   mv smithwaterman-*/* "${pkgname}-${pkgver}"/contrib/smithwaterman
@@ -34,6 +37,7 @@ prepare() {
   sed -i src/{*.cpp,*.h} \
     -e 's|#include "../intervaltree/IntervalTree.h"|#include <vcflib/IntervalTree.h>|g' \
     -e 's|<IntervalTree.h>|<vcflib/IntervalTree.h>|g' \
+    -e 's|<intervaltree/IntervalTree.h>|<vcflib/IntervalTree.h>|g' \
     -e 's|"join.h"|<vcflib/join.h>|g' \
     -e 's|"Variant.h"|<vcflib/Variant.h>|g'
 }
@@ -41,7 +45,7 @@ build() {
   cd "${pkgname}-${pkgver}"
   test -d build || mkdir build
   meson setup --prefix=/usr --buildtype=release \
-    -Dprefer_system_deps=true -Dstatic=false \
+    -Dprefer_system_deps=false -Dstatic=false \
     --default-library=shared \
     build
   cd build