// File: 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
movq %rsp, %rbp
subq $0x1f0, %rsp            # imm = 0x1F0
movl %edi, -0x4(%rbp)
movq %rsi, -0x10(%rbp)
movb $0x0, -0x11(%rbp)
movl -0x4(%rbp), %edi
movq -0x10(%rbp), %rsi
movq 0x13220c(%rip), %rdx    # 0x199740
leaq 0x12f735(%rip), %rcx    # 0x196c70
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x12(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0x67716
movq 0x131a35(%rip), %rax    # 0x198f90
cmpq $0x0, (%rax)
je 0x67574
movq 0x131a28(%rip), %rax    # 0x198f90
movq (%rax), %rax
movq %rax, -0x1d8(%rbp)
jmp 0x67584
leaq 0xce964(%rip), %rax     # 0x135edf
movq %rax, -0x1d8(%rbp)
jmp 0x67584
movq -0x1d8(%rbp), %rax
movq %rax, -0x1e8(%rbp)
leaq -0x1b9(%rbp), %rdi
movq %rdi, -0x1e0(%rbp)
callq 0xab60
movq -0x1e8(%rbp), %rsi
movq -0x1e0(%rbp), %rdx
leaq -0x1b8(%rbp), %rdi
callq 0x2d6c0
jmp 0x675c1
leaq -0x198(%rbp), %rdi
leaq -0x1b8(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0x675db
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
movsbl -0x12(%rbp), %eax
movl %eax, -0x1ec(%rbp)
testl %eax, %eax
je 0x676bb
jmp 0x67607
movl -0x1ec(%rbp), %eax
subl $0x3f, %eax
je 0x67678
jmp 0x67614
movl -0x1ec(%rbp), %eax
subl $0x68, %eax
je 0x676e9
jmp 0x67625
movl -0x1ec(%rbp), %eax
subl $0x6f, %eax
je 0x67681
jmp 0x67705
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
jmp 0x67667
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
jmp 0x67801
movb $0x1, -0x11(%rbp)
jmp 0x67705
leaq 0x132e68(%rip), %rsi    # 0x19a4f0
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0x67696
jmp 0x67705
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x67801
movb $0x1, 0x132e4e(%rip)    # 0x19a510
leaq -0x198(%rbp), %rdi
leaq -0x1d0(%rbp), %rsi
callq 0xa370
jmp 0x676d7
cmpl $0x1, -0x1d0(%rbp)
jne 0x676e7
movb $0x1, 0x132e2a(%rip)    # 0x19a511
jmp 0x67705
movq 0x132058(%rip), %rsi    # 0x199748
movq 0x1318c1(%rip), %rdi    # 0x198fb8
callq 0xa5c0
jmp 0x676fe
xorl %edi, %edi
callq 0xa700
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x67526
movl -0x4(%rbp), %eax
movq 0x1318a0(%rip), %rcx    # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jge 0x67740
movq 0x1318c2(%rip), %rdi    # 0x198ff0
leaq 0xcacf5(%rip), %rsi     # 0x13242a
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x6776a
movl -0x4(%rbp), %eax
movq 0x131876(%rip), %rcx    # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jle 0x67768
movq 0x131898(%rip), %rdi    # 0x198ff0
leaq 0xcacde(%rip), %rsi     # 0x13243d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x6776a
testb $0x1, -0x11(%rbp)
je 0x6779c
movq 0x131841(%rip), %rdi    # 0x198fb8
leaq 0xc810f(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, %rdi
movq 0x131fbb(%rip), %rsi    # 0x199748
callq 0xa5c0
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0x131819(%rip), %rcx    # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x13180b(%rip), %rdx    # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x132ceb(%rip), %rdi    # 0x19a4b0
callq 0xa810
movq -0x10(%rbp), %rax
movq 0x1317eb(%rip), %rcx    # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x1317dd(%rip), %rdx    # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x132cdd(%rip), %rdi    # 0x19a4d0
callq 0xa810
addq $0x1f0, %rsp            # imm = 0x1F0
popq %rbp
retq
movq -0x1c8(%rbp), %rdi
callq 0xab50
nopl (%rax)