# -*- coding: utf-8 -*-

###########################################################################
# Bioconvert is a project to facilitate the interconversion               #
# of life science data from one format to another.                        #
#                                                                         #
# Authors: see CONTRIBUTORS.rst                                           #
# Copyright © 2018  Institut Pasteur, Paris and CNRS.                     #
# See the COPYRIGHT file for details                                      #
#                                                                         #
# bioconvert is free software: you can redistribute it and/or modify      #
# it under the terms of the GNU General Public License as published by    #
# the Free Software Foundation, either version 3 of the License, or       #
# (at your option) any later version.                                     #
#                                                                         #
# bioconvert is distributed in the hope that it will be useful,           #
# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
# GNU General Public License for more details.                            #
#                                                                         #
# You should have received a copy of the GNU General Public License       #
# along with this program (COPYING file).                                 #
# If not, see <http://www.gnu.org/licenses/>.                             #
###########################################################################

"""Convert :term:`VCF` file to :term:`BCF` file"""
from bioconvert import ConvBase

import colorlog

from bioconvert.core.decorators import requires

logger = colorlog.getLogger(__name__)


__all__ = ["VCF2BCF"]


class VCF2BCF(ConvBase):
    """

    """

    @requires("bcftools")
    def _method_bcftools(self, *args, **kwargs):
        """

        command used::

            bcftools view -Sb

        :param args:
        :param kwargs:
        :return:
        """
        # -S means ignored (input format is VCF)
        # -b output BCF instead of VCF
        #cmd = "bcftools view -Sb {} >  {}".format(self.infile, self.outfile)

        # -O, --output-type b|u|z|v Output compressed BCF (b), uncompressed BCF
        # (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when
        # piping between bcftools subcommands to speed up performance
        cmd = "bcftools view {} -O b -o {}".format(self.infile, self.outfile)
        self.execute(cmd)



