# 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 RShortread(RPackage):
    """FASTQ input and manipulation

       This package implements sampling, iteration, and input of FASTQ files.
       The package includes functions for filtering and trimming reads, and for
       generating a quality assessment report. Data are represented as
       DNAStringSet-derived objects, and easily manipulated for a diversity of
       purposes. The package also contains legacy support for early single-end,
       ungapped alignment formats."""

    homepage = "https://bioconductor.org/packages/ShortRead"
    git      = "https://git.bioconductor.org/packages/ShortRead.git"

    version('1.48.0', commit='ba44cd2517bc0e6f46d2cfcfce393f86eec814d0')
    version('1.42.0', commit='daa2576a48278460caf87f42c022c796652f4908')
    version('1.40.0', commit='0cbe4b62b0be4c5f2e2670da17493423446e008f')
    version('1.38.0', commit='e9498f04b7b4bf0212bbb10ec7e3de2d7699f4bf')
    version('1.36.1', commit='176c34eddf4a416d30c69cb4ac197141ba42e66f')
    version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')

    depends_on('r-biocgenerics@0.22.1:', type=('build', 'run'))
    depends_on('r-biocgenerics@0.23.3:', when='@1.36.1:', type=('build', 'run'))
    depends_on('r-biocparallel', type=('build', 'run'))
    depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
    depends_on('r-biostrings@2.47.6:', when='@1.38.0:', type=('build', 'run'))
    depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
    depends_on('r-rsamtools@1.31.2:', when='@1.38.0:', type=('build', 'run'))
    depends_on('r-genomicalignments@1.5.4:', type=('build', 'run'))
    depends_on('r-genomicalignments@1.15.6:', when='@1.38.0:', type=('build', 'run'))
    depends_on('r-biobase', type=('build', 'run'))
    depends_on('r-s4vectors@0.13.8:', type=('build', 'run'))
    depends_on('r-s4vectors@0.17.25:', when='@1.38.0:', type=('build', 'run'))
    depends_on('r-iranges@2.3.7:', type=('build', 'run'))
    depends_on('r-iranges@2.13.12:', when='@1.38.0:', type=('build', 'run'))
    depends_on('r-genomeinfodb@1.1.19:', type=('build', 'run'))
    depends_on('r-genomeinfodb@1.15.2:', when='@1.38.0:', type=('build', 'run'))
    depends_on('r-genomicranges@1.21.6:', type=('build', 'run'))
    depends_on('r-genomicranges@1.31.8:', when='@1.38.0:', type=('build', 'run'))
    depends_on('r-hwriter', type=('build', 'run'))
    depends_on('r-zlibbioc', type=('build', 'run'))
    depends_on('r-lattice', type=('build', 'run'))
    depends_on('r-latticeextra', type=('build', 'run'))
    depends_on('r-xvector', type=('build', 'run'))
    depends_on('r-rhtslib', when='@1.48.0:', type=('build', 'run'))
