#!/usr/bin/env python
import signal
signal.signal(signal.SIGPIPE, signal.SIG_DFL)

import argparse
from lib_alu_detect import *
import lib_alu_detect_sam as sam

parser = argparse.ArgumentParser(description=sys.argv[0])
parser.add_argument('-v', '--verbose', action='append_const', const=1, default=[], dest='verbose')
parser.add_argument('-p', '--pairing', action='store', default='paired=0', dest='pairing')

args = parser.parse_args()
set_log_level(len(args.verbose))
sam.set_pairing(args.pairing)

sam.get_bowtie_pairing()
