// File: millanek[P]evo/process_vcf_mt_sequences.cpp
// Function: parseGetMtSeqOptions(int, char**)
void parseGetMtSeqOptions(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 's': arg >> opt::sampleNameFile; break;
            case OPT_LDHAT: opt::bLDhat = true; break;
            case 'h':
                std::cout << GETMTSEQ_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" << GETMTSEQ_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::genomeFile = 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 0xc713c(%rip), %rdx     # 0x1998f0
leaq 0xc54e5(%rip), %rcx     # 0x197ca0
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x12(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0xd296e
movq 0xc67b5(%rip), %rax     # 0x198f90
cmpq $0x0, (%rax)
je 0xd27f4
movq 0xc67a8(%rip), %rax     # 0x198f90
movq (%rax), %rax
movq %rax, -0x1d8(%rbp)
jmp 0xd2804
leaq 0x636e4(%rip), %rax     # 0x135edf
movq %rax, -0x1d8(%rbp)
jmp 0xd2804
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 0xd2841
leaq -0x198(%rbp), %rdi
leaq -0x1b8(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0xd285b
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
movsbl -0x12(%rbp), %eax
movl %eax, -0x1ec(%rbp)
testl %eax, %eax
je 0xd2938
jmp 0xd2887
movl -0x1ec(%rbp), %eax
subl $0x3f, %eax
je 0xd28f8
jmp 0xd2894
movl -0x1ec(%rbp), %eax
subl $0x68, %eax
je 0xd2941
jmp 0xd28a5
movl -0x1ec(%rbp), %eax
subl $0x73, %eax
je 0xd28fe
jmp 0xd295d
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
jmp 0xd28e7
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 0xd2a59
movb $0x1, -0x11(%rbp)
jmp 0xd295d
leaq 0xc841b(%rip), %rsi     # 0x19ad20
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0xd2913
jmp 0xd295d
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0xd2a59
movb $0x1, 0xc8401(%rip)     # 0x19ad40
jmp 0xd295d
movq 0xc6fb0(%rip), %rsi     # 0x1998f8
movq 0xc6669(%rip), %rdi     # 0x198fb8
callq 0xa5c0
jmp 0xd2956
xorl %edi, %edi
callq 0xa700
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0xd27a6
movl -0x4(%rbp), %eax
movq 0xc6648(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jge 0xd2998
movq 0xc666a(%rip), %rdi     # 0x198ff0
leaq 0x5fa9d(%rip), %rsi     # 0x13242a
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0xd29c2
movl -0x4(%rbp), %eax
movq 0xc661e(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jle 0xd29c0
movq 0xc6640(%rip), %rdi     # 0x198ff0
leaq 0x5fa86(%rip), %rsi     # 0x13243d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0xd29c2
testb $0x1, -0x11(%rbp)
je 0xd29f4
movq 0xc65e9(%rip), %rdi     # 0x198fb8
leaq 0x5ceb7(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, %rdi
movq 0xc6f13(%rip), %rsi     # 0x1998f8
callq 0xa5c0
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0xc65c1(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0xc65b3(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0xc82c3(%rip), %rdi     # 0x19ace0
callq 0xa810
movq -0x10(%rbp), %rax
movq 0xc6593(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0xc6585(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0xc82b5(%rip), %rdi     # 0x19ad00
callq 0xa810
addq $0x1f0, %rsp            # imm = 0x1F0
popq %rbp
retq
movq -0x1c8(%rbp), %rdi
callq 0xab50
nopw %cs:(%rax,%rax)
nop