#!/usr/bin/env python3
#
# -----------------------------------------------------------------------------
# Copyright (c) 2019, Battelle National Biodefense Institute.
#
# This file is part of MicroHapulator (github.com/bioforensics/microhapulator)
# and is licensed under the BSD license: see LICENSE.txt.
# -----------------------------------------------------------------------------


def subparser(subparsers):
    cli = subparsers.add_parser('contrib')
    cli.add_argument(
        '-o', '--out', metavar='FILE', help='write output to "FILE"; by '
        'default, output is written to the terminal (standard output)'
    )
    cli.add_argument(
        '-j', '--json', metavar='FILE', help='precomputed genotype in JSON '
        'format; if not specified, must supply arguments for `--refr-fasta` '
        ' and `--bam` flags'
    )
    cli.add_argument(
        '-r', '--refr', metavar='FILE', help='microhap locus sequences in '
        'Fasta format'
    )
    cli.add_argument(
        '-b', '--bam', metavar='FILE', help='aligned and sorted reads in BAM '
        'format'
    )
