// File: /workspace/github_cpp_makefile_star2_O2/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
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 %r15
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x3e4b9(%rip), %rdx     # 0xa611f
leaq 0x74033(%rip), %rcx     # 0xdbca0
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r13d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x67d0f
movq 0x75303(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x32185(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r14, %rdi
movq %r12, %rsi
movl %r15d, %edx
callq 0x87e0
movsbl %r13b, %r13d
movq %r12, %rdi
callq 0x8978
testl %r13d, %r13d
je 0x67cf2
cmpl $0x3f, %r13d
je 0x67cfb
cmpl $0x73, %r13d
je 0x67ce1
cmpl $0x68, %r13d
jne 0x67d02
jmp 0x67d6a
movq %r14, %rdi
leaq 0x76b75(%rip), %rsi     # 0xde860
callq 0x8570
jmp 0x67d02
movb $0x1, 0x76b87(%rip)     # 0xde880
jmp 0x67d02
movb $0x1, %al
movq %rax, 0x10(%rsp)
movq %r14, %rdi
callq 0x8220
jmp 0x67c5a
movq 0x752aa(%rip), %r14     # 0xdcfc0
movslq (%r14), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0x67d84
jne 0x67d8d
testb $0x1, 0x10(%rsp)
jne 0x67da0
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x76ae6(%rip), %rdi     # 0xde820
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x76aed(%rip), %rdi     # 0xde840
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x75247(%rip), %rdi     # 0xdcfb8
leaq 0x4155a(%rip), %rsi     # 0xa92d2
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x2e597(%rip), %rsi     # 0x96322
jmp 0x67d94
leaq 0x2e5a1(%rip), %rsi     # 0x96335
movq 0x7524d(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0x75211(%rip), %rdi     # 0xdcfb8
leaq 0x2bb9f(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x41518(%rip), %rsi     # 0xa92d2
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x67dcc
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x67ded
movq %rax, %rbx
jmp 0x67ded
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870
nopl (%rax)