// File: /workspace/github_cpp_makefile_star2_O3/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, %r13
movl %edi, %ebp
leaq 0x40(%rsp), %rax
movq %rax, -0x10(%rax)
xorl %ecx, %ecx
movq %rcx, -0x8(%rax)
movb $0x0, (%rax)
movq %rcx, 0x80(%rsp)
xorps %xmm0, %xmm0
movaps %xmm0, 0x70(%rsp)
movq $0x0, 0x8(%rsp)
movq %rcx, 0x60(%rsp)
movaps %xmm0, 0x50(%rsp)
leaq 0x25949(%rip), %rdx     # 0xdf885
leaq 0x478dd(%rip), %rcx     # 0x101820
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0xba074
movq $0x0, 0x8(%rsp)
leaq 0x10(%rsp), %r15
leaq 0x88(%rsp), %r12
movq %r13, %rbx
movq 0x48001(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x13a3f(%rip), %rax     # 0xcd9cb
cmoveq %rax, %r13
leaq 0x20(%rsp), %rax
movq %rax, 0x10(%rsp)
movq %r13, %rdi
callq 0x81f0
leaq (%rax,%r13), %rdx
movq %r15, %rdi
movq %r13, %rsi
callq 0x28a52
movq %r12, %rdi
movq %r15, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
movq %rbx, %r13
je 0xb9fe0
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x67, %r14d
jg 0xb9fff
cmpl $0x3f, %r14d
je 0xba016
cmpl $0x67, %r14d
jne 0xba029
movb $0x1, 0x4a0d3(%rip)     # 0x1040d0
jmp 0xba029
cmpl $0x6e, %r14d
jne 0xba01f
movq %r12, %rdi
leaq 0x4a0a1(%rip), %rsi     # 0x1040b0
callq 0x8560
jmp 0xba029
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0xba029
cmpl $0x68, %r14d
je 0xba145
movq %r12, %rdi
movq 0x47f65(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0x100(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq %r13, %rsi
leaq 0x25834(%rip), %rdx     # 0xdf885
leaq 0x477c8(%rip), %rcx     # 0x101820
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xb9f75
movq 0x47f45(%rip), %rbx     # 0x101fc0
movslq (%rbx), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0xba15f
jne 0xba16d
testb $0x1, 0x8(%rsp)
jne 0xba185
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %r14
movq 0x49fcd(%rip), %r15     # 0x104078
leaq 0x49fbe(%rip), %r12     # 0x104070
movq %r14, %rdi
callq 0x81f0
movq %r12, %rdi
xorl %esi, %esi
movq %r15, %rdx
movq %r14, %rcx
movq %rax, %r8
callq 0x86c0
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %rbx
movq 0x49fb7(%rip), %r14     # 0x104098
leaq 0x49fa8(%rip), %r15     # 0x104090
movq %rbx, %rdi
callq 0x81f0
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x86c0
leaq 0x50(%rsp), %rdi
callq 0x2e784
leaq 0x70(%rsp), %rdi
callq 0x2e784
movq 0x30(%rsp), %rdi
leaq 0x40(%rsp), %rax
cmpq %rax, %rdi
je 0xba133
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
addq $0x208, %rsp            # imm = 0x208
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x47e6c(%rip), %rdi     # 0x101fb8
leaq 0x25751(%rip), %rsi     # 0xdf8a4
callq 0x8460
xorl %edi, %edi
callq 0x8530
movl $0x12, %edx
leaq 0x11d77(%rip), %rsi     # 0xcbee2
jmp 0xba179
movl $0x13, %edx
leaq 0x11d7c(%rip), %rsi     # 0xcbef5
movq 0x47e68(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0x47e2c(%rip), %rdi     # 0x101fb8
leaq 0x112aa(%rip), %rsi     # 0xcb43d
movl $0x1, %edx
callq 0x84e0
movq 0x47e14(%rip), %rdi     # 0x101fb8
leaq 0x256f9(%rip), %rsi     # 0xdf8a4
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0xba1bc
movq %rax, %r14
movq 0x47dd2(%rip), %rsi     # 0x101f98
leaq 0x88(%rsp), %rdi
callq 0x8620
leaq 0x100(%rsp), %rdi
callq 0x8190
jmp 0xba208
jmp 0xba1e4
movq %rax, %r14
jmp 0xba208
movq %rax, %r14
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
je 0xba208
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x50(%rsp), %rdi
callq 0x2e784
leaq 0x70(%rsp), %rdi
callq 0x2e784
movq 0x30(%rsp), %rdi
leaq 0x40(%rsp), %rax
cmpq %rax, %rdi
je 0xba238
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840