# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack.package import *


class LumpySv(MakefilePackage):
    """A probabilistic framework for structural variant discovery."""

    homepage = "https://github.com/arq5x/lumpy-sv"
    url = "https://github.com/arq5x/lumpy-sv/archive/0.2.13.tar.gz"

    license("MIT")

    version("0.2.13", sha256="3672b86ef0190ebe520648a6140077ee9f15b0549cb233dca18036e63bbf6375")

    depends_on("htslib")

    def edit(self, spec, prefix):
        makefile = FileFilter("Makefile")
        makefile.filter("export CXX .*", "")

    def install(self, spec, prefix):
        install_tree("bin", prefix.bin)