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# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
PYTHON_COMPAT=( python3_{10..12} )
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}/${P}.tar.bz2"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="
dev-lang/perl
$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
=sci-libs/htslib-$(ver_cut 1-2)*:=
sys-libs/zlib
${PYTHON_DEPS}"
DEPEND="${RDEPEND}"
BDEPEND="${PYTHON_DEPS}"
src_prepare() {
default
python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
# remove bundled htslib
rm -r htslib-* || die
}
src_configure() {
econf \
--disable-bcftools-plugins \
--disable-libgsl \
--with-htslib=system
}
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