#!/usr/bin/env python3.7

# Author: Roujia Li
# email: Roujia.li@mail.utoronto.ca
import argparse

from TileSeqMut.mergeruns import merge_main

parser = argparse.ArgumentParser(description='TileSeq mutation counts - Merge two runs')
# user input arguments
parser.add_argument("-p1", "--paramOne", help="Path to parameter sheet (JSON) for the first run", type=str)
parser.add_argument("-p2", "--paramTwo", help="Path to parameter sheet (JSON) for the second run", type=str)
parser.add_argument("-d1", "--dir1", help="Path to *_mut_count folder for the first run", type=str)
parser.add_argument("-d2", "--dir2", help="Path to *_mut_count folder for the second run", type=str)
parser.add_argument("-o", "--output", help="Output folder", type=str, required=True)
# user input arguments with default values set
parser.add_argument("--covOverride", help="Ignore coverage files", action="store_true")
parser.add_argument("--subtractWT", help="Subtract wt counts from non-select before merging", action="store_true")
parser.add_argument("-log", "--log_level", help="set log level: debug, \
        info, warning, error, critical. (default = debug)", type=str, default="debug")

args = parser.parse_args()

merge_main(args)