// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_get_aa_seq.cpp
// Function: parseAaSeqOptions(int, char**)
void parseAaSeqOptions(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 'o': arg >> opt::out; break;
            case OPT_ANC_FROM_MAF: opt::bAncFromMaf = true; int a; arg >> a; if (a == 1) opt::deletionAsN = true; break;
            case 'h':
                std::cout << AA_SEQ_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" << AA_SEQ_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::refFastaFile = argv[optind++];
    opt::ancWithGapsFile = 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), %r14
pushq $0x8
popq %r13
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x64808(%rip), %rdx     # 0x9ce39
leaq 0xa2638(%rip), %rcx     # 0xdac70
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r15d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x386f5
movq 0xa4938(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x617ba(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xb(%rsp), %rdx
callq 0x21904
movq %r14, %rdi
movq %r12, %rsi
movl %r13d, %edx
callq 0x87e0
movsbl %r15b, %r15d
movq %r12, %rdi
callq 0x8978
testl %r15d, %r15d
je 0x386bd
cmpl $0x3f, %r15d
je 0x386e1
cmpl $0x6f, %r15d
je 0x386ac
cmpl $0x68, %r15d
jne 0x386e8
jmp 0x38750
movq %r14, %rdi
leaq 0xa598a(%rip), %rsi     # 0xde040
callq 0x8570
jmp 0x386e8
movb $0x1, 0xa599c(%rip)     # 0xde060
movq %r14, %rdi
leaq 0xc(%rsp), %rsi
callq 0x82e0
cmpl $0x1, 0xc(%rsp)
jne 0x386e8
movb $0x1, 0xa5982(%rip)     # 0xde061
jmp 0x386e8
movb $0x1, %al
movq %rax, 0x10(%rsp)
movq %r14, %rdi
callq 0x8220
jmp 0x38625
movq 0xa48c4(%rip), %r14     # 0xdcfc0
movslq (%r14), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0x3876a
jne 0x38773
testb $0x1, 0x10(%rsp)
jne 0x38786
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0xa58e0(%rip), %rdi     # 0xde000
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0xa58e7(%rip), %rdi     # 0xde020
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xa4861(%rip), %rdi     # 0xdcfb8
leaq 0x646f0(%rip), %rsi     # 0x9ce4e
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x5dbb1(%rip), %rsi     # 0x96322
jmp 0x3877a
leaq 0x5dbbb(%rip), %rsi     # 0x96335
movq 0xa4867(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0xa482b(%rip), %rdi     # 0xdcfb8
leaq 0x5b1b9(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x646ae(%rip), %rsi     # 0x9ce4e
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x387b2
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x387d3
movq %rax, %rbx
jmp 0x387d3
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870
nop