#!/usr/bin/env python
""" MultiQC module to parse output from bcftools """
from __future__ import print_function
from collections import OrderedDict
import logging

from multiqc.modules.base_module import BaseMultiqcModule

# Import the Samtools submodules
from .stats import StatsReportMixin

# Initialise the logger
log = logging.getLogger(__name__)


class MultiqcModule(BaseMultiqcModule, StatsReportMixin):
    """ Bcftools has a number of different commands and outputs.
    This MultiQC module supports some but not all. The code for
    each script is split into its own file and adds a section to
    the module output if logs are found. """

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(
            name='Bcftools',
            anchor='bcftools', target='Bcftools',
            href='https://samtools.github.io/bcftools/',
            info=(" contains utilities for variant calling and manipulating VCFs and BCFs."))

        # Set up class objects to hold parsed data
        self.general_stats_headers = OrderedDict()
        self.general_stats_data = dict()
        n = dict()

        # Call submodule functions
        n['stats'] = self.parse_bcftools_stats()
        if n['stats'] > 0:
            log.info("Found {} stats reports".format(n['stats']))

        # Exit if we didn't find anything
        if sum(n.values()) == 0:
            raise UserWarning

        # Add to the General Stats table (has to be called once per MultiQC module)
        self.general_stats_addcols(self.general_stats_data, self.general_stats_headers)
