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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 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("1.36.0", commit="cdc1aa49f14d3effe2540380a04fe1fc72c00f04")
version("1.34.0", commit="c6eb78079c8aa21d47c95b3d16a606e8c2c5d799")
version("1.32.1", commit="2553580d0b8a8a5fd7835c1446616b39f707b8a9")
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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