// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/evo_abba_baba.cpp
// Function: parseAbbaBabaOptions(int, char**)
void parseAbbaBabaOptions(int argc, char** argv) {
    bool die = false;
    for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
    {
        std::istringstream arg(optarg != NULL ? optarg : "");
        switch (c)
        {
            case '?': die = true; break;
            case 's': arg >> opt::sampleNameFile; break;
            case 'f': opt::bFrequency = true; opt::jackKniveWindowSize = JACKKNIVE_WINDOW_SIZE_FREQUENCY; break;
            case 'w': arg >> opt::windowSize; break;
            case 'n': arg >> opt::runName; break;
            case OPT_AA_EQ_O: opt::bAaEqO = true; break;
            case OPT_NO_AA_O: opt::bNoAaO = true; break;
            case 'h':
                std::cout << ABBA_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (opt::runName == "") {
        if (opt::bFrequency) { opt::runName = "frequency"; }
        if (!opt::bFrequency) { opt::runName = "sequence"; }
    }
    if (argc - optind < 2) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 2)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << ABBA_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::setsFile = argv[optind++];
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movq %rsi, %rbx
movl %edi, %ebp
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r12
leaq 0x38(%rsp), %r13
pushq $0x8
popq %r14
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x6917e(%rip), %rdx     # 0x97978
leaq 0xabf8f(%rip), %rcx     # 0xda790
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r15d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x2e8ef
movq 0xae76f(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x6b5f1(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r13, %rdi
movq %r12, %rsi
movl %r14d, %edx
callq 0x87e0
movsbl %r15b, %r15d
movq %r12, %rdi
callq 0x8978
testl %r15d, %r15d
je 0x2e8c9
cmpl $0x1, %r15d
je 0x2e8db
cmpl $0x3f, %r15d
je 0x2e8d2
cmpl $0x66, %r15d
je 0x2e894
leaq 0xaf0f9(%rip), %rsi     # 0xdd970
cmpl $0x6e, %r15d
je 0x2e8bf
cmpl $0x73, %r15d
je 0x2e8b8
cmpl $0x77, %r15d
je 0x2e8a7
cmpl $0x68, %r15d
jne 0x2e8e2
jmp 0x2e999
movb $0x1, 0xaf122(%rip)     # 0xdd9bd
movl $0x1388, 0xaec5b(%rip)  # imm = 0x1388
jmp 0x2e8e2
movq %r13, %rdi
leaq 0xaec53(%rip), %rsi     # 0xdd504
callq 0x82e0
jmp 0x2e8e2
leaq 0xaf091(%rip), %rsi     # 0xdd950
movq %r13, %rdi
callq 0x8570
jmp 0x2e8e2
movb $0x1, 0xaf0ec(%rip)     # 0xdd9bc
jmp 0x2e8e2
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x2e8e2
movb $0x1, 0xaf0dc(%rip)     # 0xdd9be
movq %r13, %rdi
callq 0x8220
jmp 0x2e7ee
leaq 0xaf07a(%rip), %rdi     # 0xdd970
leaq 0x6b522(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
je 0x2e93e
cmpb $0x1, 0xaf0b0(%rip)     # 0xdd9bd
jne 0x2e92b
leaq 0xaf05a(%rip), %rdi     # 0xdd970
leaq 0x75bf7(%rip), %rsi     # 0xa4514
callq 0x88f0
cmpb $0x0, 0xaf094(%rip)     # 0xdd9bd
jne 0x2e93e
leaq 0xaf03e(%rip), %rdi     # 0xdd970
leaq 0x68f85(%rip), %rsi     # 0x978be
callq 0x88f0
movq 0xae67b(%rip), %r14     # 0xdcfc0
movslq (%r14), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0x2e9b3
jne 0x2e9bc
testb $0x1, 0x10(%rsp)
jne 0x2e9cf
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0xaefa7(%rip), %rdi     # 0xdd910
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0xaefae(%rip), %rdi     # 0xdd930
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xae618(%rip), %rdi     # 0xdcfb8
leaq 0x68ffe(%rip), %rsi     # 0x979a5
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x67968(%rip), %rsi     # 0x96322
jmp 0x2e9c3
leaq 0x67972(%rip), %rsi     # 0x96335
movq 0xae61e(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0xae5e2(%rip), %rdi     # 0xdcfb8
leaq 0x64f70(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x68fbc(%rip), %rsi     # 0x979a5
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x2e9fb
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x2ea1c
movq %rax, %rbx
jmp 0x2ea1c
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870