// File: millanek[P]evo/process_vcf_fill_aa.cpp
// Function: parseFillAaOptions(int, char**)
void parseFillAaOptions(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 'i': arg >> opt::IndividualName; break;
            case 'h':
                std::cout << FILL_AA_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" << FILL_AA_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::ancSeqFile = 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 0x11f4c4(%rip), %rdx    # 0x199768
leaq 0x11cb65(%rip), %rcx    # 0x196e10
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x12(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0x7a46d
movq 0x11ecc5(%rip), %rax    # 0x198f90
cmpq $0x0, (%rax)
je 0x7a2e4
movq 0x11ecb8(%rip), %rax    # 0x198f90
movq (%rax), %rax
movq %rax, -0x1d8(%rbp)
jmp 0x7a2f4
leaq 0xbbbf4(%rip), %rax     # 0x135edf
movq %rax, -0x1d8(%rbp)
jmp 0x7a2f4
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 0x7a331
leaq -0x198(%rbp), %rdi
leaq -0x1b8(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0x7a34b
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
movsbl -0x12(%rbp), %eax
movl %eax, -0x1ec(%rbp)
subl $0x3f, %eax
je 0x7a3e9
jmp 0x7a374
movl -0x1ec(%rbp), %eax
subl $0x68, %eax
je 0x7a440
jmp 0x7a385
movl -0x1ec(%rbp), %eax
subl $0x69, %eax
je 0x7a429
jmp 0x7a396
movl -0x1ec(%rbp), %eax
subl $0x6f, %eax
je 0x7a3ef
jmp 0x7a45c
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
jmp 0x7a3d8
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 0x7a558
movb $0x1, -0x11(%rbp)
jmp 0x7a45c
leaq 0x12025a(%rip), %rsi    # 0x19a650
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0x7a404
jmp 0x7a45c
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x7a558
leaq 0x120240(%rip), %rsi    # 0x19a670
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0x7a43e
jmp 0x7a45c
movq 0x11f329(%rip), %rsi    # 0x199770
movq 0x11eb6a(%rip), %rdi    # 0x198fb8
callq 0xa5c0
jmp 0x7a455
xorl %edi, %edi
callq 0xa700
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x7a296
movl -0x4(%rbp), %eax
movq 0x11eb49(%rip), %rcx    # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jge 0x7a497
movq 0x11eb6b(%rip), %rdi    # 0x198ff0
leaq 0xb7f9e(%rip), %rsi     # 0x13242a
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x7a4c1
movl -0x4(%rbp), %eax
movq 0x11eb1f(%rip), %rcx    # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jle 0x7a4bf
movq 0x11eb41(%rip), %rdi    # 0x198ff0
leaq 0xb7f87(%rip), %rsi     # 0x13243d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x7a4c1
testb $0x1, -0x11(%rbp)
je 0x7a4f3
movq 0x11eaea(%rip), %rdi    # 0x198fb8
leaq 0xb53b8(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, %rdi
movq 0x11f28c(%rip), %rsi    # 0x199770
callq 0xa5c0
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0x11eac2(%rip), %rcx    # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x11eab4(%rip), %rdx    # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x1200f4(%rip), %rdi    # 0x19a610
callq 0xa810
movq -0x10(%rbp), %rax
movq 0x11ea94(%rip), %rcx    # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x11ea86(%rip), %rdx    # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x1200e6(%rip), %rdi    # 0x19a630
callq 0xa810
addq $0x1f0, %rsp            # imm = 0x1F0
popq %rbp
retq
movq -0x1c8(%rbp), %rdi
callq 0xab50
nopw %cs:(%rax,%rax)
nop