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# Maintainer: Clint Valentine <valentine.clint@gmail.com>
pkgname=vcflib-git
_pkgname=vcflib
pkgver=1.0.3.r330.ga36dbe9
pkgrel=1
pkgdesc="C++ library and cmdline tools for parsing and manipulating VCF files doi: 10.1101/2021.05.21.445151"
arch=('x86_64')
url="https://github.com/vcflib/vcflib"
license=('MIT')
provides=(${_pkgname})
depends=('python' 'htslib')
makedepends=('git' 'cmake' 'make' 'pybind11' 'tabixpp'
'pandoc'
)
optdepends=('r: running R scripts'
'perl: running Perl scripts'
)
source=("git+https://github.com/vcflib/vcflib.git"
"git+https://github.com/smarco/WFA2-lib.git"
"git+https://github.com/ekg/fastahack.git"
"git+https://github.com/ekg/filevercmp.git"
"git+https://github.com/ekg/fsom.git"
"git+https://github.com/ekg/intervaltree.git"
"git+https://github.com/edawson/libVCFH.git"
"git+https://github.com/ekg/multichoose.git"
"git+https://github.com/ekg/smithwaterman.git"
"simde::git+https://github.com/simd-everywhere/simde-no-tests.git"
)
md5sums=('SKIP'
'SKIP'
'SKIP'
'SKIP'
'SKIP'
'SKIP'
'SKIP'
'SKIP'
'SKIP'
'SKIP')
pkgver() {
cd "${_pkgname//-git/}"
git describe --long --tags | sed 's/\([^-]*-g\)/r\1/;s/-/./g' | cut -d'v' -f2
}
prepare(){
cd ${srcdir}
cp -rf WFA2-lib/* ${_pkgname}/contrib/WFA2-lib
for module in {fastahack,filevercmp,fsom,intervaltree,libVCFH,multichoose,smithwaterman}; do
cp -rf ${module}/* ${_pkgname}/${module}
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() {
cd $srcdir/${_pkgname}
install -d build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/usr
cmake --build . -- PREFIX=/usr HTS_HEADERS=/usr/include/htslib HTS_LIB=/usr/lib/libhts.so
}
package() {
cd "$_pkgname"/build
make install DESTDIR="$pkgdir"
mv ${pkgdir}/usr/lib/pyvcf* ${pkgdir}/usr/lib/pyvcflib.so
mkdir ${pkgdir}/usr/share
mv ${pkgdir}/usr/man ${pkgdir}/usr/share
# sed -i 's|bindings/cpp/WFAligner.hpp|WFA2/bindings/cpp/WFAligner.hpp|g' ${pkgdir}/usr/include/Variant.h
# install -d ${pkgdir}/usr/include/vcflib
# mv ${pkgdir}/usr/include/{*.h,*.hpp} ${pkgdir}/usr/include/vcflib
# another packages called wfa2lib
install -Dm644 $srcdir/${_pkgname}/contrib/WFA2-lib/bindings/cpp/*.hpp -t ${pkgdir}/usr/include/bindings/cpp
install -Dm644 $srcdir/${_pkgname}/contrib/WFA2-lib/wavefront/*.h -t ${pkgdir}/usr/include/wavefront
install -Dm644 $srcdir/${_pkgname}/contrib/WFA2-lib/utils/*.h -t ${pkgdir}/usr/include/utils
install -Dm644 $srcdir/${_pkgname}/contrib/WFA2-lib/system/*.h -t ${pkgdir}/usr/include/system
install -Dm644 $srcdir/${_pkgname}/contrib/WFA2-lib/alignment/*.h -t ${pkgdir}/usr/include/alignment
}
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