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# Copyright 2013-2022 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 RGenomicalignments(RPackage):
"""Representation and manipulation of short genomic alignments.
Provides efficient containers for storing and manipulating short genomic
alignments (typically obtained by aligning short reads to a reference
genome). This includes read counting, computing the coverage, junction
detection, and working with the nucleotide content of the alignments."""
bioc = "GenomicAlignments"
version('1.32.0', commit='7a660a914a04e2eb0758082b6f64c4124a887ef3')
version('1.30.0', commit='2d2c5fce3529c2962fdcefd736d8b7f7c0ec2d54')
version('1.26.0', commit='6c74c74ee53efcd880171126366fee4bd72357bc')
version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd')
version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab')
version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974')
version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r@4.0.0:', type=('build', 'run'), when='@1.30.0:')
depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@1.30.0:')
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.28:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-s4vectors@0.19.11:', type=('build', 'run'), when='@1.18.1:')
depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.26.0:')
depends_on('r-iranges@2.5.36:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.14.2:')
depends_on('r-iranges@2.13.25:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-iranges@2.15.12:', type=('build', 'run'), when='@1.18.1:')
depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@1.26.0:')
depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.14.2:')
depends_on('r-genomicranges@1.27.19:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.14.2:')
depends_on('r-genomicranges@1.31.19:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-genomicranges@1.33.4:', type=('build', 'run'), when='@1.18.1:')
depends_on('r-genomicranges@1.41.5:', type=('build', 'run'), when='@1.26.0:')
depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.9.13:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-biostrings@2.55.7:', type=('build', 'run'), when='@1.26.0:')
depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-biocparallel', type=('build', 'run'))
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