// File: /workspace/github_cpp_makefile_star2_O1/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 0x2aed5(%rip), %rdx     # 0xe8e91
leaq 0x4c95d(%rip), %rcx     # 0x10a920
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0xbe10c
movq $0x0, 0x8(%rsp)
leaq 0x10(%rsp), %r15
leaq 0x88(%rsp), %r12
movq %r13, %rbx
movq 0x4cf81(%rip), %rax     # 0x10af80
movq (%rax), %r13
testq %r13, %r13
leaq 0x13c73(%rip), %rax     # 0xd1c7f
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 0x28952
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 0xbe060
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
leal -0x66(%r14), %eax
cmpl $0x8, %eax
ja 0xbe095
leaq 0x2ad80(%rip), %rcx     # 0xe8df4
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
leaq 0x4f136(%rip), %rsi     # 0x10d1b8
jmpq *%rax
movq %r12, %rdi
leaq 0x4d552(%rip), %rsi     # 0x10b5e0
callq 0x82b0
jmp 0xbe0c1
testl %r14d, %r14d
je 0xbe0b2
cmpl $0x3f, %r14d
jne 0xbe0c1
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0xbe0c1
movb $0x1, 0x4f148(%rip)     # 0x10d1f8
jmp 0xbe0c1
leaq 0x4f11f(%rip), %rsi     # 0x10d1d8
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0x4cecd(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0x100(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq %r13, %rsi
leaq 0x2ada8(%rip), %rdx     # 0xe8e91
leaq 0x4c830(%rip), %rcx     # 0x10a920
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xbdff5
movq 0x4cead(%rip), %rbx     # 0x10afc0
subl (%rbx), %ebp
cmpl $0x4, %ebp
jge 0xbe128
movl $0x12, %edx
leaq 0x1008c(%rip), %rsi     # 0xce1b2
jmp 0xbe13b
movq 0x8(%rsp), %r14
je 0xbe14a
movl $0x13, %edx
leaq 0x1008a(%rip), %rsi     # 0xce1c5
movb $0x1, %r14b
movq 0x4cea3(%rip), %rdi     # 0x10afe8
callq 0x84e0
testb $0x1, %r14b
jne 0xbe288
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %r14
movq 0x4efd8(%rip), %r15     # 0x10d140
leaq 0x4efc9(%rip), %r12     # 0x10d138
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 0x4efc2(%rip), %r15     # 0x10d160
leaq 0x4efb3(%rip), %r12     # 0x10d158
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 0x4efac(%rip), %r15     # 0x10d180
leaq 0x4ef9d(%rip), %r12     # 0x10d178
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 0x4ef96(%rip), %r14     # 0x10d1a0
leaq 0x4ef87(%rip), %r15     # 0x10d198
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 0x3123c
leaq 0x70(%rsp), %rdi
callq 0x3123c
movq 0x30(%rsp), %rdi
leaq 0x40(%rsp), %rax
cmpq %rax, %rdi
je 0xbe25c
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 0x4cd43(%rip), %rdi     # 0x10afb8
leaq 0x2ac1c(%rip), %rsi     # 0xe8e98
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0x4cd29(%rip), %rdi     # 0x10afb8
leaq 0xe3e7(%rip), %rsi      # 0xcc67d
movl $0x1, %edx
callq 0x84e0
movq 0x4cd11(%rip), %rdi     # 0x10afb8
leaq 0x2abea(%rip), %rsi     # 0xe8e98
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0xbe2c1
jmp 0xbe2e7
movq %rax, %r14
movq 0x4cccd(%rip), %rsi     # 0x10af98
leaq 0x88(%rsp), %rdi
callq 0x8620
leaq 0x100(%rsp), %rdi
callq 0x8190
jmp 0xbe30b
movq %rax, %r14
jmp 0xbe30b
movq %rax, %r14
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
je 0xbe30b
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x50(%rsp), %rdi
callq 0x3123c
leaq 0x70(%rsp), %rdi
callq 0x3123c
movq 0x30(%rsp), %rdi
leaq 0x40(%rsp), %rax
cmpq %rax, %rdi
je 0xbe33b
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840
nop