// File: /workspace/github_cpp_makefile_star2_O3/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
movl %edi, %ebp
leaq 0x8ae3f(%rip), %rdx     # 0xce9c1
leaq 0xbbfc7(%rip), %rcx     # 0xffb50
movq $0x0, (%rsp)
movq %rsi, 0x10(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0x43cd3
leaq 0x28(%rsp), %rbx
movq $0x0, (%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0xbe3b0(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x89dee(%rip), %rax     # 0xcd9cb
cmoveq %rax, %r13
movq %rbx, 0x18(%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 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x43c24
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x67, %r14d
jg 0x43c41
testl %r14d, %r14d
je 0x43c58
cmpl $0x3f, %r14d
jne 0x43c86
movb $0x1, %al
movq %rax, (%rsp)
jmp 0x43c86
cmpl $0x6f, %r14d
jne 0x43c7c
movq %r12, %rdi
leaq 0xbf3bf(%rip), %rsi     # 0x103010
callq 0x8560
jmp 0x43c86
movb $0x1, 0xbf3d1(%rip)     # 0x103030
movq %r12, %rdi
leaq 0xc(%rsp), %rsi
callq 0x82b0
cmpl $0x1, 0xc(%rsp)
jne 0x43c86
movb $0x1, 0xbf3b7(%rip)     # 0x103031
jmp 0x43c86
cmpl $0x68, %r14d
je 0x43d78
movq %r12, %rdi
movq 0xbe308(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x8ad11(%rip), %rdx     # 0xce9c1
leaq 0xbbe99(%rip), %rcx     # 0xffb50
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x43bc9
movq 0xbe2e6(%rip), %rbx     # 0x101fc0
movslq (%rbx), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0x43d92
jne 0x43da0
testb $0x1, (%rsp)
jne 0x43db8
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %r13
movq (%r13,%rax,8), %r14
movq 0xbf2ca(%rip), %r15     # 0x102fd8
leaq 0xbf2bb(%rip), %r12     # 0x102fd0
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 0xbf2b4(%rip), %r14     # 0x102ff8
leaq 0xbf2a5(%rip), %r15     # 0x102ff0
movq %rbx, %rdi
callq 0x81f0
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x86c0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xbe239(%rip), %rdi     # 0x101fb8
leaq 0x8ac50(%rip), %rsi     # 0xce9d6
callq 0x8460
xorl %edi, %edi
callq 0x8530
leaq 0x88149(%rip), %rsi     # 0xcbee2
movl $0x12, %edx
jmp 0x43dac
leaq 0x8814e(%rip), %rsi     # 0xcbef5
movl $0x13, %edx
movq 0xbe235(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0xbe1f9(%rip), %rdi     # 0x101fb8
leaq 0x87677(%rip), %rsi     # 0xcb43d
callq 0x8460
leaq 0x8ac04(%rip), %rsi     # 0xce9d6
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x43de6
movq %rax, %r14
movq 0xbe1a8(%rip), %rsi     # 0x101f98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x43e28
movq %rax, %r14
jmp 0x43e28
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x43e28
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840