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

import click
import logging

import astair
import astair.phred as phred
import astair.mbias as mbias
import astair.caller as caller
import astair.aligner as aligner
import astair.simulator as simulator

# TODO make this config properly configurable using command line options
# For example, we could use a global option -v to change the log level to
# DEBUG and produce verbose output for all commands
logging.basicConfig(level=logging.WARNING)
logs = logging.getLogger(__name__)

@click.group()
def cli():
    """
    asTair (tools for processing cytosine modification sequencing data)
    """
    pass

cli.epilog = """
__________________________________About__________________________________
asTair was written by Gergana V. Velikova and Benjamin Schuster-Boeckler.
This code is made available under the GNU General Public License, see 
LICENSE.txt for more details.

                                                         Version: __version__
"""
cli.epilog = cli.epilog.replace('__version__', astair.__version__)

cli.add_command(aligner.align)
cli.add_command(caller.call)
cli.add_command(simulator.simulate)
cli.add_command(phred.phred)
cli.add_command(mbias.mbias)

if __name__ == '__main__':
    cli()
