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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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PYTHON_COMPAT=( python2_7 python3_6 )
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inherit distutils-r1
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DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
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HOMEPAGE="
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https://github.com/pysam-developers/pysam
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https://pypi.org/project/pysam/"
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SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
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LICENSE="MIT"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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RDEPEND="=sci-libs/htslib-1.5*:="
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DEPEND="${RDEPEND}
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dev-python/cython[${PYTHON_USEDEP}]
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dev-python/setuptools[${PYTHON_USEDEP}]"
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PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
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python_prepare_all() {
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# unbundle htslib
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export HTSLIB_MODE="external"
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export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
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export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
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rm -r htslib || die
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# prevent setup.py from adding RPATHs
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sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
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-i cy_build.py || die
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sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
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-i setup.py || die
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distutils-r1_python_prepare_all
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}
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src_compile() {
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# TODO
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# empty compile, as the build system runs the whole build again in install
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:
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}
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