#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
import sys

import pysam

# 提取fr+rr>=2的点
if len(sys.argv) != 3:
    print(" ".join(['usage:python', sys.argv[0], 'outputDir', 'tumor']))
    sys.exit()

# output_dir = sys.argv[1]
# tumor = sys.argv[2]

# infile = "".join([output_dir, '/alignment/', tumor, '.rmdup.bam'])
# outfile = "".join([output_dir, '/alignment/', tumor, '.2r.rmdup.bam'])
samfile = pysam.AlignmentFile(sys.argv[1], "rb")
bamfile = pysam.AlignmentFile(sys.argv[2], "wb", template=samfile)
for s in samfile:
    fr = 0
    rr = 0
    if s.has_tag('FR'):
        fr = s.get_tag('FR')
    if s.has_tag('RR'):
        rr = s.get_tag('RR')
    if fr + rr >= 2:
        bamfile.write(s)

# os.system('samtools index ' + outfile)