From 73cec72874510228d8145f3ddf6e5b2f6862491e Mon Sep 17 00:00:00 2001
From: sukanka <su975853527@gmail.com>
Date: Sun, 10 Jul 2022 11:06:52 +0800
Subject: [PATCH] add vcflib

---
 prepare/vcflib/PKGBUILD | 64 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 prepare/vcflib/PKGBUILD

diff --git a/prepare/vcflib/PKGBUILD b/prepare/vcflib/PKGBUILD
new file mode 100644
index 0000000000..ea22268c0b
--- /dev/null
+++ b/prepare/vcflib/PKGBUILD
@@ -0,0 +1,64 @@
+# Maintainer: Guoyi
+pkgname=vcflib
+pkgver=1.0.3
+pkgrel=1
+pkgdesc="C++ library and cmdline tools for parsing and manipulating VCF files doi: 10.1101/2021.05.21.445151"
+arch=('any')
+url="https://github.com/vcflib/vcflib"
+license=('MIT')
+depends=()
+makedepends=('git' 'cmake' 'make' 'htslib'
+'pandoc'
+)
+optdepends=()
+source=("git+https://github.com/vcflib/vcflib.git"
+"git+https://github.com/smarco/WFA2-lib.git"
+"fastahack.tar.gz::https://github.com/ekg/fastahack/archive/refs/tags/v1.0.0.tar.gz"
+"git+https://github.com/ekg/filevercmp.git"
+"git+https://github.com/ekg/fsom.git"
+# "intervaltree.tar.gz::https://github.com/ekg/intervaltree/archive/refs/tags/v0.1.tar.gz"
+"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"
+"https://github.com/vcflib/tabixpp/archive/refs/tags/v1.1.1.tar.gz"
+)
+
+md5sums=('SKIP'
+         'SKIP'
+         'eeb7d046978d7633fe4d07def29f48c3'
+         'SKIP'
+         'SKIP'
+         'SKIP'
+         'SKIP'
+         'SKIP'
+         'SKIP'
+         'SKIP'
+         '6441f3e3bbeb6c642edc7dea1c4cf8c3')
+
+prepare(){
+  cd ${srcdir}
+  cp -rf WFA2-lib/*  ${pkgname}/contrib/WFA2-lib
+  cp -rf tabixpp-1.1.1/*  ${pkgname}/contrib/tabixpp
+  cp -rf  fastahack-1.0.0 fastahack
+  for module in {fastahack,filevercmp,fsom,intervaltree,libVCFH,multichoose,smithwaterman}; do
+    cp -rf ${module}/* ${pkgname}/${module}
+  done
+}
+build() {
+  cd $srcdir/${pkgname}
+  install -d build
+  cd build
+  cmake .. -DCAME_INSTALL_PREFIX=/usr -DPREFIX=/usr -DHTS_HEADERS=/usr/include/htslib  -DHTS_LIB=/usr/lib/libhts.so
+  cmake --build .
+
+}
+
+package() {
+  cd "$pkgname"/build
+  make install DESTDIR="$pkgdir"
+  mv ${pkgdir}/usr/local/* ${pkgdir}/usr/
+  mv ${pkgdir}/usr/lib/pyvcf*  ${pkgdir}/usr/lib/pyvcflib.so
+  rmdir ${pkgdir}/usr/local
+}