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# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit python-single-r1
DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
HOMEPAGE="http://www.htslib.org"
SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="
dev-lang/perl
=sci-libs/htslib-${PV}*:=
sys-libs/zlib:=
${PYTHON_DEPS}"
DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}"/${PN}-1.5-buildsystem.patch
"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
)
src_prepare() {
default
python_fix_shebang misc/{guess-ploidy,plot-roh}.py
# remove bundled htslib
rm -r htslib-* || die
}
src_configure() {
econf \
--disable-bcftools-plugins \
--disable-libgsl \
--disable-configure-htslib \
--with-htslib=system
}
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