// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/evo_AlleleFeq.cpp
// Function: parseAFoptions(int, char**)
void parseAFoptions(int argc, char** argv) {
    bool die = false; string regionArgString; std::vector<string> regionArgs;
    std::vector<string> windowSizeStep;
    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 'n': arg >> opt::runName; break;
            case 'g': opt::useGenotypeProbabilities = true; break;
            case 'h':
                std::cout << AF_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    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" << AF_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 $0x208, %rsp            # imm = 0x208
movq %rsi, %rbx
movl %edi, %ebp
leaq 0x58(%rsp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb $0x0, (%rax)
andq $0x0, 0x40(%rsp)
xorps %xmm0, %xmm0
andq $0x0, 0x20(%rsp)
movaps %xmm0, 0x30(%rsp)
movaps %xmm0, 0x10(%rsp)
movq $0x0, 0x8(%rsp)
leaq 0x68(%rsp), %r12
leaq 0x88(%rsp), %r14
pushq $0x8
popq %r15
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x2961c(%rip), %rdx     # 0xb0add
leaq 0x55378(%rip), %rcx     # 0xdc840
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r13d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x8756b
movq 0x55aa8(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x1292a(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0x7(%rsp), %rdx
callq 0x21904
movq %r14, %rdi
movq %r12, %rsi
movl %r15d, %edx
callq 0x87e0
movsbl %r13b, %r13d
movq %r12, %rdi
callq 0x8978
cmpl $0x3f, %r13d
je 0x8754e
cmpl $0x67, %r13d
je 0x87557
cmpl $0x6e, %r13d
je 0x8753d
cmpl $0x68, %r13d
jne 0x8755e
jmp 0x875f0
movq %r14, %rdi
leaq 0x57b91(%rip), %rsi     # 0xdf0d8
callq 0x8570
jmp 0x8755e
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x8755e
movb $0x1, 0x57b9a(%rip)     # 0xdf0f8
movq %r14, %rdi
callq 0x8220
jmp 0x874b5
movq 0x55a4e(%rip), %r14     # 0xdcfc0
movslq (%r14), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0x8760a
jne 0x87613
testb $0x1, 0x8(%rsp)
jne 0x87626
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x57af6(%rip), %rdi     # 0xdf098
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x57afd(%rip), %rdi     # 0xdf0b8
callq 0x88f0
leaq 0x10(%rsp), %rdi
callq 0x28a08
leaq 0x30(%rsp), %rdi
callq 0x28a08
leaq 0x48(%rsp), %rdi
callq 0x8978
addq $0x208, %rsp            # imm = 0x208
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x559c1(%rip), %rdi     # 0xdcfb8
leaq 0x294fe(%rip), %rsi     # 0xb0afc
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0xed11(%rip), %rsi      # 0x96322
jmp 0x8761a
leaq 0xed1b(%rip), %rsi      # 0x96335
movq 0x559c7(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0x5598b(%rip), %rdi     # 0xdcfb8
leaq 0xc319(%rip), %rsi      # 0x9394d
callq 0x8480
leaq 0x294bc(%rip), %rsi     # 0xb0afc
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x87654
jmp 0x87666
movq %rax, %rbx
leaq 0x88(%rsp), %rdi
callq 0x8220
jmp 0x87678
movq %rax, %rbx
jmp 0x87678
movq %rax, %rbx
leaq 0x68(%rsp), %rdi
callq 0x8978
leaq 0x10(%rsp), %rdi
callq 0x28a08
leaq 0x30(%rsp), %rdi
callq 0x28a08
leaq 0x48(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870
nop