<reponame>johnsmith2077/kevlar
#!/usr/bin/env python
#
# -----------------------------------------------------------------------------
# Copyright (c) 2019 Battelle National Biodefense Institute
#
# This file is part of kevlar (http://github.com/dib-lab/kevlar) and is
# licensed under the MIT license: see LICENSE.
# -----------------------------------------------------------------------------


def subparser(subparsers):
    subparser = subparsers.add_parser(
        'varfilter', description='Filter out variants falling in the genomic '
        'regions specified by the BED file(s). This can be used to exclude '
        'putative variant calls corresponding to common variants, segmental '
        'duplications, or other problematic loci.'
    )

    subparser.add_argument(
        '-o', '--out', metavar='FILE', help='file to which filtered variants '
        'will be written; default is terminal (standard output)'
    )
    subparser.add_argument(
        'filt', help='BED file containing regions to filter out'
    )
    subparser.add_argument(
        'vcf', nargs='+', help='VCF file(s) with calls to filter'
    )
