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# Copyright 2013-2021 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 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."""
homepage = "http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html"
git = "https://git.bioconductor.org/packages/exomeCopy"
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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