# 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 RExomecopy(RPackage):
    """Copy number variant detection from exome sequencing read depth.

    Detection of copy number variants (CNV) from exome sequencing samples,
    including unpaired samples. The package implements a hidden Markov model
    which uses positional covariates, such as background read depth and
    GC-content, to simultaneously normalize and segment the samples into
    regions of constant copy count."""

    bioc = "exomeCopy"

    version("1.46.0", commit="b282adb17fb05e1a940d068d27bfd9d4549a53e7")
    version("1.44.0", commit="2dd6598d5fb14d49f7a42e597284c7a929c0cd62")
    version("1.42.0", commit="ba0979cf5fbdefed841022f2dc0604941315c1b8")
    version("1.40.0", commit="ebde39be67baace2c326359421fd17f4a02fd4fe")
    version("1.36.0", commit="cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26")
    version("1.32.0", commit="c9a884427d91b6d62ddc16a939bd808e389d3ea6")

    depends_on("r-iranges@2.5.27:", type=("build", "run"))
    depends_on("r-genomicranges@1.23.16:", type=("build", "run"))
    depends_on("r-rsamtools", type=("build", "run"))
    depends_on("r-genomeinfodb", type=("build", "run"))