#!python

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

import argparse
from bfg_analysis import main

parser = argparse.ArgumentParser(description='BFG-Y2H')

# parameters for cluster
parser.add_argument("--fastq", help="Path to all fastq files you want to analyze")
parser.add_argument("--output", help="Output path for sam files")
parser.add_argument("--mode", help="pick yeast or human or virus or hedgy", required=True)

parser.add_argument("--alignment", action="store_true", help= "turn on alignment")
parser.add_argument("--ref", help="path to all reference files", default="/home/rothlab/rli/02_dev/08_bfg_y2h/bfg_data/reference/")
#parser.add_argument("--readCount", action="store_true", help= "turn on read counting")
parser.add_argument("--cutOff", type=int, help = "assign cut off", default=20)

args = parser.parse_args()

main.main(args)
