// File: /workspace/github_cpp_makefile_star2_O3/millanek[P]evo/evo_distanceToOutgroups.cpp
// Function: parseDistOutOptions(int, char**)
void parseDistOutOptions(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 'f': arg >> opt::fixedWindowSize; break;
            case 'n': arg >> opt::runName; break;
            case 'i': opt::allowIndels = true; break;
            case OPT_ACC_GEN_BED: arg >> opt::accesibleGenBedFile; break;
            case 'h':
                std::cout << DISTOUT_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (argc - optind < 4) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 4)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << DISTOUT_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::setsFile = argv[optind++];
    opt::outgroupFile = argv[optind++];
    opt::ingroupFile = 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 0x22f2a(%rip), %rdx     # 0xdff09
leaq 0x4493a(%rip), %rcx     # 0x101920
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0xbd12f
movq $0x0, 0x8(%rsp)
leaq 0x10(%rsp), %r15
leaq 0x88(%rsp), %r12
movq %r13, %rbx
movq 0x44f5e(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x1099c(%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 0xbd083
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
leal -0x66(%r14), %eax
cmpl $0x8, %eax
ja 0xbd0b8
leaq 0x22dd5(%rip), %rcx     # 0xdfe6c
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
leaq 0x47123(%rip), %rsi     # 0x1041c8
jmpq *%rax
movq %r12, %rdi
leaq 0x4552f(%rip), %rsi     # 0x1025e0
callq 0x82b0
jmp 0xbd0e4
testl %r14d, %r14d
je 0xbd0d5
cmpl $0x3f, %r14d
jne 0xbd0e4
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0xbd0e4
movb $0x1, 0x47135(%rip)     # 0x104208
jmp 0xbd0e4
leaq 0x4710c(%rip), %rsi     # 0x1041e8
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0x44eaa(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0x100(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq %r13, %rsi
leaq 0x22dfd(%rip), %rdx     # 0xdff09
leaq 0x4480d(%rip), %rcx     # 0x101920
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xbd018
movq 0x44e8a(%rip), %rbx     # 0x101fc0
movslq (%rbx), %rax
subl %eax, %ebp
cmpl $0x4, %ebp
jl 0xbd286
jne 0xbd294
testb $0x1, 0x8(%rsp)
jne 0xbd2ac
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %r14
movq 0x46fea(%rip), %r15     # 0x104150
leaq 0x46fdb(%rip), %r12     # 0x104148
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), %r14
movq 0x46fd4(%rip), %r15     # 0x104170
leaq 0x46fc5(%rip), %r12     # 0x104168
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), %r14
movq 0x46fbe(%rip), %r15     # 0x104190
leaq 0x46faf(%rip), %r12     # 0x104188
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 0x46fa8(%rip), %r14     # 0x1041b0
leaq 0x46f99(%rip), %r15     # 0x1041a8
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 0xbd25a
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 0x44d45(%rip), %rdi     # 0x101fb8
leaq 0x22c96(%rip), %rsi     # 0xdff10
callq 0x8460
xorl %edi, %edi
callq 0x8530
movl $0x12, %edx
leaq 0xec50(%rip), %rsi      # 0xcbee2
jmp 0xbd2a0
movl $0x13, %edx
leaq 0xec55(%rip), %rsi      # 0xcbef5
movq 0x44d41(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0x44d05(%rip), %rdi     # 0x101fb8
leaq 0xe183(%rip), %rsi      # 0xcb43d
movl $0x1, %edx
callq 0x84e0
movq 0x44ced(%rip), %rdi     # 0x101fb8
leaq 0x22c3e(%rip), %rsi     # 0xdff10
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0xbd2e5
jmp 0xbd30b
movq %rax, %r14
movq 0x44ca9(%rip), %rsi     # 0x101f98
leaq 0x88(%rsp), %rdi
callq 0x8620
leaq 0x100(%rsp), %rdi
callq 0x8190
jmp 0xbd32f
movq %rax, %r14
jmp 0xbd32f
movq %rax, %r14
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
je 0xbd32f
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 0xbd35f
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840
nop