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# Copyright 2013-2023 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"))
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