#!/usr/bin/env python
# -*- coding: utf-8

"""A client to access short reads in BAM files.

   See https://github.com/meren/anvio/issues/173 for details."""

import sys

import anvio

from anvio.errors import ConfigError, FilesNPathsError
from anvio.bamops import GetReadsFromBAM


__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"


if __name__ == '__main__':
    import argparse

    parser = argparse.ArgumentParser(description='Get short reads back from a BAM file.')

    parser.add_argument('input_bams', metavar = 'BAM FILE[S]', nargs='+',
                        help = 'BAM file(s) to access to recover short reads')

    output_file_kwargs = {'help': 'File path(s) to store results. Multiple files should be separated by commas (no spaces).'}

    parser.add_argument(*anvio.A('profile-db'), **anvio.K('profile-db'))
    parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db'))
    parser.add_argument(*anvio.A('collection-name'), **anvio.K('collection-name'))
    parser.add_argument(*anvio.A('bin-id'), **anvio.K('bin-id'))
    parser.add_argument(*anvio.A('bin-ids-file'), **anvio.K('bin-ids-file'))
    parser.add_argument(*anvio.A('output-file'), **anvio.K('output-file'))
    parser.add_argument(*anvio.A('output-file-prefix'), **anvio.K('output-file-prefix'))
    parser.add_argument(*anvio.A('gzip-output'), **anvio.K('gzip-output'))
    parser.add_argument(*anvio.A('split-R1-and-R2'), **anvio.K('split-R1-and-R2'))

    args = anvio.get_args(parser)

    try:
        r = GetReadsFromBAM(args)
        r.init()
        r.store_short_reads_for_splits()
    except ConfigError as e:
        print(e)
        sys.exit(-1)
    except FilesNPathsError as e:
        print(e)
        sys.exit(-2)
