// File: /workspace/github_c_makefile_star2_O0/OpenGene[P]pecheck/src/main.cpp
// Function: main
int main(int argc, char* argv[]){
    // display version info if no argument is given
    if(argc == 1) {
        cout << "A tool to check paired-end FASTQ data integrity" << endl << "version " << VERSION_NUM << endl;
    }
    if (argc == 2 && strcmp(argv[1], "test")==0){
        UnitTest tester;
        tester.run();
        return 0;
    }
    cmdline::parser cmd;
    // input/output
    cmd.add<string>("in1", 'i', "read1 file name", true, "");
    cmd.add<string>("in2", 'I', "read2 file name", true, "");
    cmd.add<string>("json", 'j', "json report file name", true, "pecheck.json");

    cmd.parse_check(argc, argv);
    
    stringstream ss;
    for(int i=0;i<argc;i++){
        ss << argv[i] << " ";
    }
    command = ss.str();

    time_t t1 = time(NULL);

    Options opt;

    opt.in1 = cmd.get<string>("in1");
    opt.in2 = cmd.get<string>("in2");
    opt.jsonFile = cmd.get<string>("json");

    opt.validate();

    PECheck pecheck(&opt);
    pecheck.run();

    time_t t2 = time(NULL);

    cerr << endl << "JSON report: " << opt.jsonFile << endl;
    cerr << endl << command << endl;
    cerr << "pecheck v" << VERSION_NUM << ", time used: " << (t2)-t1 << " seconds" << endl;

    return 0;
}

// Assembly:
subq $0x608, %rsp            # imm = 0x608
movl $0x0, 0x604(%rsp)
movl %edi, 0x600(%rsp)
movq %rsi, 0x5f8(%rsp)
cmpl $0x1, 0x600(%rsp)
jne 0x741a
movq 0x16bfe(%rip), %rdi     # 0x1dfd0
leaq 0xece9(%rip), %rsi      # 0x160c2
callq 0x4340
movq %rax, %rdi
movq 0x16bc0(%rip), %rsi     # 0x1dfa8
callq 0x43b0
movq %rax, %rdi
leaq 0xecfb(%rip), %rsi      # 0x160f2
callq 0x4340
movq %rax, %rdi
leaq 0xecf5(%rip), %rsi      # 0x160fb
callq 0x4340
movq %rax, %rdi
movq 0x16b93(%rip), %rsi     # 0x1dfa8
callq 0x43b0
cmpl $0x2, 0x600(%rsp)
jne 0x746b
movq 0x5f8(%rsp), %rax
movq 0x8(%rax), %rdi
leaq 0xecca(%rip), %rsi      # 0x16101
callq 0x4530
cmpl $0x0, %eax
jne 0x746b
leaq 0x5f7(%rsp), %rdi
callq 0x159d0
leaq 0x5f7(%rsp), %rdi
callq 0x159e0
movl $0x0, 0x604(%rsp)
jmp 0x7f59
leaq 0x538(%rsp), %rdi
callq 0x7f80
leaq 0x517(%rsp), %rdi
movq %rdi, 0xd0(%rsp)
callq 0x46b0
movq 0xd0(%rsp), %rdx
leaq 0xefc0(%rip), %rsi      # 0x1645c
leaq 0x518(%rsp), %rdi
callq 0x67f0
jmp 0x74ab
leaq 0x4df(%rsp), %rdi
movq %rdi, 0xc8(%rsp)
callq 0x46b0
movq 0xc8(%rsp), %rdx
leaq 0xec37(%rip), %rsi      # 0x16106
leaq 0x4e0(%rsp), %rdi
callq 0x67f0
jmp 0x74de
leaq 0x4b7(%rsp), %rdi
movq %rdi, 0xc0(%rsp)
callq 0x46b0
movq 0xc0(%rsp), %rdx
leaq 0xf80b(%rip), %rsi      # 0x16d0d
leaq 0x4b8(%rsp), %rdi
callq 0x67f0
jmp 0x7511
leaq 0x538(%rsp), %rdi
leaq 0x518(%rsp), %rsi
movl $0x69, %edx
leaq 0x4e0(%rsp), %rcx
movl $0x1, %r8d
leaq 0x4b8(%rsp), %r9
callq 0x7ff0
jmp 0x7543
leaq 0x4b8(%rsp), %rdi
callq 0x4758
leaq 0x4b7(%rsp), %rdi
callq 0x43e0
leaq 0x4e0(%rsp), %rdi
callq 0x4758
leaq 0x4df(%rsp), %rdi
callq 0x43e0
leaq 0x518(%rsp), %rdi
callq 0x4758
leaq 0x517(%rsp), %rdi
callq 0x43e0
leaq 0x48f(%rsp), %rdi
movq %rdi, 0xb8(%rsp)
callq 0x46b0
movq 0xb8(%rsp), %rdx
leaq 0xeed0(%rip), %rsi      # 0x16485
leaq 0x490(%rsp), %rdi
callq 0x67f0
jmp 0x75c4
leaq 0x467(%rsp), %rdi
movq %rdi, 0xb0(%rsp)
callq 0x46b0
movq 0xb0(%rsp), %rdx
leaq 0xeb2e(%rip), %rsi      # 0x16116
leaq 0x468(%rsp), %rdi
callq 0x67f0
jmp 0x75f7
leaq 0x43f(%rsp), %rdi
movq %rdi, 0xa8(%rsp)
callq 0x46b0
movq 0xa8(%rsp), %rdx
leaq 0xf6f2(%rip), %rsi      # 0x16d0d
leaq 0x440(%rsp), %rdi
callq 0x67f0
jmp 0x762a
leaq 0x538(%rsp), %rdi
leaq 0x490(%rsp), %rsi
movl $0x49, %edx
leaq 0x468(%rsp), %rcx
movl $0x1, %r8d
leaq 0x440(%rsp), %r9
callq 0x7ff0
jmp 0x765c
leaq 0x440(%rsp), %rdi
callq 0x4758
leaq 0x43f(%rsp), %rdi
callq 0x43e0
leaq 0x468(%rsp), %rdi
callq 0x4758
leaq 0x467(%rsp), %rdi
callq 0x43e0
leaq 0x490(%rsp), %rdi
callq 0x4758
leaq 0x48f(%rsp), %rdi
callq 0x43e0
leaq 0x417(%rsp), %rdi
movq %rdi, 0xa0(%rsp)
callq 0x46b0
movq 0xa0(%rsp), %rdx
leaq 0xea76(%rip), %rsi      # 0x16144
leaq 0x418(%rsp), %rdi
callq 0x67f0
jmp 0x76dd
leaq 0x3ef(%rsp), %rdi
movq %rdi, 0x98(%rsp)
callq 0x46b0
movq 0x98(%rsp), %rdx
leaq 0xea25(%rip), %rsi      # 0x16126
leaq 0x3f0(%rsp), %rdi
callq 0x67f0
jmp 0x7710
leaq 0x3c7(%rsp), %rdi
movq %rdi, 0x90(%rsp)
callq 0x46b0
movq 0x90(%rsp), %rdx
leaq 0xea08(%rip), %rsi      # 0x1613c
leaq 0x3c8(%rsp), %rdi
callq 0x67f0
jmp 0x7743
leaq 0x538(%rsp), %rdi
leaq 0x418(%rsp), %rsi
movl $0x6a, %edx
leaq 0x3f0(%rsp), %rcx
movl $0x1, %r8d
leaq 0x3c8(%rsp), %r9
callq 0x7ff0
jmp 0x7775
leaq 0x3c8(%rsp), %rdi
callq 0x4758
leaq 0x3c7(%rsp), %rdi
callq 0x43e0
leaq 0x3f0(%rsp), %rdi
callq 0x4758
leaq 0x3ef(%rsp), %rdi
callq 0x43e0
leaq 0x418(%rsp), %rdi
callq 0x4758
leaq 0x417(%rsp), %rdi
callq 0x43e0
movl 0x600(%rsp), %esi
movq 0x5f8(%rsp), %rdx
leaq 0x538(%rsp), %rdi
callq 0x80f0
jmp 0x77e1
leaq 0x238(%rsp), %rdi
callq 0x4260
jmp 0x77f0
movl $0x0, 0x234(%rsp)
movl 0x234(%rsp), %eax
cmpl 0x600(%rsp), %eax
jge 0x7a9b
leaq 0x248(%rsp), %rdi
movq 0x5f8(%rsp), %rax
movslq 0x234(%rsp), %rcx
movq (%rax,%rcx,8), %rsi
callq 0x4340
movq %rax, 0x88(%rsp)
jmp 0x783a
movq 0x88(%rsp), %rdi
leaq 0xe9b8(%rip), %rsi      # 0x16201
callq 0x4340
jmp 0x7850
jmp 0x7852
movl 0x234(%rsp), %eax
addl $0x1, %eax
movl %eax, 0x234(%rsp)
jmp 0x77fb
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x78ff
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x78e5
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x78cb
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
leaq 0x4b8(%rsp), %rdi
callq 0x4758
leaq 0x4b7(%rsp), %rdi
callq 0x43e0
leaq 0x4e0(%rsp), %rdi
callq 0x4758
leaq 0x4df(%rsp), %rdi
callq 0x43e0
leaq 0x518(%rsp), %rdi
callq 0x4758
leaq 0x517(%rsp), %rdi
callq 0x43e0
jmp 0x7f4a
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x79ab
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7991
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7977
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
leaq 0x440(%rsp), %rdi
callq 0x4758
leaq 0x43f(%rsp), %rdi
callq 0x43e0
leaq 0x468(%rsp), %rdi
callq 0x4758
leaq 0x467(%rsp), %rdi
callq 0x43e0
leaq 0x490(%rsp), %rdi
callq 0x4758
leaq 0x48f(%rsp), %rdi
callq 0x43e0
jmp 0x7f4a
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7a57
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7a3d
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7a23
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
leaq 0x3c8(%rsp), %rdi
callq 0x4758
leaq 0x3c7(%rsp), %rdi
callq 0x43e0
leaq 0x3f0(%rsp), %rdi
callq 0x4758
leaq 0x3ef(%rsp), %rdi
callq 0x43e0
leaq 0x418(%rsp), %rdi
callq 0x4758
leaq 0x417(%rsp), %rdi
callq 0x43e0
jmp 0x7f4a
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7f4a
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7f3d
leaq 0x210(%rsp), %rdi
leaq 0x238(%rsp), %rsi
callq 0x4330
jmp 0x7ab2
leaq 0x1691f(%rip), %rdi     # 0x1e3d8
leaq 0x210(%rsp), %rsi
movq %rsi, 0x80(%rsp)
callq 0x4490
movq 0x80(%rsp), %rdi
callq 0x4758
xorl %eax, %eax
movl %eax, %edi
callq 0x4310
movq %rax, 0x208(%rsp)
leaq 0x1a8(%rsp), %rdi
callq 0x10480
jmp 0x7afb
leaq 0x187(%rsp), %rdi
movq %rdi, 0x78(%rsp)
callq 0x46b0
movq 0x78(%rsp), %rdx
leaq 0xe943(%rip), %rsi      # 0x1645c
leaq 0x188(%rsp), %rdi
callq 0x67f0
jmp 0x7b28
leaq 0x538(%rsp), %rdi
leaq 0x188(%rsp), %rsi
callq 0x8340
movq %rax, 0x70(%rsp)
jmp 0x7b44
movq 0x70(%rsp), %rsi
leaq 0x1a8(%rsp), %rdi
callq 0x4070
jmp 0x7b58
leaq 0x188(%rsp), %rdi
callq 0x4758
leaq 0x187(%rsp), %rdi
callq 0x43e0
leaq 0x15f(%rsp), %rdi
movq %rdi, 0x68(%rsp)
callq 0x46b0
movq 0x68(%rsp), %rdx
leaq 0xe8f5(%rip), %rsi      # 0x16485
leaq 0x160(%rsp), %rdi
callq 0x67f0
jmp 0x7b9f
leaq 0x538(%rsp), %rdi
leaq 0x160(%rsp), %rsi
callq 0x8340
movq %rax, 0x60(%rsp)
jmp 0x7bbb
movq 0x60(%rsp), %rsi
leaq 0x1c8(%rsp), %rdi
callq 0x4070
jmp 0x7bcf
leaq 0x160(%rsp), %rdi
callq 0x4758
leaq 0x15f(%rsp), %rdi
callq 0x43e0
leaq 0x137(%rsp), %rdi
movq %rdi, 0x58(%rsp)
callq 0x46b0
movq 0x58(%rsp), %rdx
leaq 0xe53d(%rip), %rsi      # 0x16144
leaq 0x138(%rsp), %rdi
callq 0x67f0
jmp 0x7c16
leaq 0x538(%rsp), %rdi
leaq 0x138(%rsp), %rsi
callq 0x8340
movq %rax, 0x50(%rsp)
jmp 0x7c32
movq 0x50(%rsp), %rsi
leaq 0x1e8(%rsp), %rdi
callq 0x4070
jmp 0x7c46
leaq 0x138(%rsp), %rdi
callq 0x4758
leaq 0x137(%rsp), %rdi
callq 0x43e0
leaq 0x1a8(%rsp), %rdi
callq 0x10930
jmp 0x7c6f
leaq 0xe0(%rsp), %rdi
leaq 0x1a8(%rsp), %rsi
callq 0x10c30
jmp 0x7c86
leaq 0xe0(%rsp), %rdi
callq 0x10c90
jmp 0x7c95
xorl %eax, %eax
movl %eax, %edi
callq 0x4310
movq %rax, 0xd8(%rsp)
movq 0x16343(%rip), %rdi     # 0x1dff0
movq 0x162f4(%rip), %rsi     # 0x1dfa8
callq 0x43b0
movq %rax, 0x48(%rsp)
jmp 0x7cc0
movq 0x48(%rsp), %rdi
leaq 0xe47d(%rip), %rsi      # 0x16149
callq 0x4340
movq %rax, 0x40(%rsp)
jmp 0x7cd8
movq 0x40(%rsp), %rdi
leaq 0x1e8(%rsp), %rsi
callq 0x42f0
movq %rax, 0x38(%rsp)
jmp 0x7cf1
movq 0x38(%rsp), %rdi
movq 0x162ab(%rip), %rsi     # 0x1dfa8
callq 0x43b0
jmp 0x7d04
movq 0x162e5(%rip), %rdi     # 0x1dff0
movq 0x16296(%rip), %rsi     # 0x1dfa8
callq 0x43b0
movq %rax, 0x30(%rsp)
jmp 0x7d1e
movq 0x30(%rsp), %rdi
leaq 0x166ae(%rip), %rsi     # 0x1e3d8
callq 0x42f0
movq %rax, 0x28(%rsp)
jmp 0x7d36
movq 0x28(%rsp), %rdi
movq 0x16266(%rip), %rsi     # 0x1dfa8
callq 0x43b0
jmp 0x7d49
movq 0x162a0(%rip), %rdi     # 0x1dff0
leaq 0xe400(%rip), %rsi      # 0x16157
callq 0x4340
movq %rax, 0x20(%rsp)
jmp 0x7d63
movq 0x20(%rsp), %rdi
leaq 0xe38c(%rip), %rsi      # 0x160fb
callq 0x4340
movq %rax, 0x18(%rsp)
jmp 0x7d7b
movq 0x18(%rsp), %rdi
leaq 0xe3da(%rip), %rsi      # 0x16161
callq 0x4340
movq %rax, 0x10(%rsp)
jmp 0x7d93
movq 0x10(%rsp), %rdi
movq 0xd8(%rsp), %rsi
movq 0x208(%rsp), %rax
subq %rax, %rsi
callq 0x46d0
movq %rax, 0x8(%rsp)
jmp 0x7db7
movq 0x8(%rsp), %rdi
leaq 0xe3ac(%rip), %rsi      # 0x1616f
callq 0x4340
movq %rax, (%rsp)
jmp 0x7dce
movq (%rsp), %rdi
movq 0x161cf(%rip), %rsi     # 0x1dfa8
callq 0x43b0
jmp 0x7de0
movl $0x0, 0x604(%rsp)
leaq 0xe0(%rsp), %rdi
callq 0x85c0
leaq 0x1a8(%rsp), %rdi
callq 0x85e0
leaq 0x238(%rsp), %rdi
callq 0x4290
leaq 0x538(%rsp), %rdi
callq 0x8620
jmp 0x7f59
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7e5b
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
leaq 0x188(%rsp), %rdi
callq 0x4758
leaq 0x187(%rsp), %rdi
callq 0x43e0
jmp 0x7f30
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7ea4
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
leaq 0x160(%rsp), %rdi
callq 0x4758
leaq 0x15f(%rsp), %rdi
callq 0x43e0
jmp 0x7f30
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7eea
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
leaq 0x138(%rsp), %rdi
callq 0x4758
leaq 0x137(%rsp), %rdi
callq 0x43e0
jmp 0x7f30
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
jmp 0x7f30
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x508(%rsp)
movl %eax, 0x504(%rsp)
leaq 0xe0(%rsp), %rdi
callq 0x85c0
leaq 0x1a8(%rsp), %rdi
callq 0x85e0
leaq 0x238(%rsp), %rdi
callq 0x4290
leaq 0x538(%rsp), %rdi
callq 0x8620
jmp 0x7f68
movl 0x604(%rsp), %eax
addq $0x608, %rsp            # imm = 0x608
retq
movq 0x508(%rsp), %rdi
callq 0x46a0
nopw %cs:(%rax,%rax)
nop