// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_massoko.cpp
// Function: parseMassokoOptions(int, char**)
void parseMassokoOptions(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 'd': arg >> opt::max_overall_depth; break;
            case 'c': arg >> opt::min_copies; break;
            case 's': arg >> opt::min_depth_in_any_individual; break;
            case '?': die = true; break;   
            case OPT_HELP:
                std::cout << FILTER_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    if (argc - optind < 1) {
        std::cerr << "missing arguments\n";
        die = true;
    } 
    else if (argc - optind > 1) 
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << FILTER_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = 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 %r13
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x5205a(%rip), %rdx     # 0xa296b
leaq 0x8ae48(%rip), %rcx     # 0xdb760
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r15d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x509c5
movq 0x8c658(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x494da(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r14, %rdi
movq %r12, %rsi
movl %r13d, %edx
callq 0x87e0
movsbl %r15b, %r15d
movq %r12, %rdi
callq 0x8978
cmpl $0x3f, %r15d
je 0x50997
leaq 0x8cc0b(%rip), %rsi     # 0xdd588
cmpl $0x63, %r15d
je 0x509b0
cmpl $0x64, %r15d
je 0x509a0
cmpl $0x73, %r15d
je 0x509a9
cmpl $0x1, %r15d
jne 0x509b8
jmp 0x50a06
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x509b8
leaq 0x8cbe5(%rip), %rsi     # 0xdd58c
jmp 0x509b0
leaq 0x8cbe0(%rip), %rsi     # 0xdd590
movq %r14, %rdi
callq 0x82e0
movq %r14, %rdi
callq 0x8220
jmp 0x50905
movq 0x8c5f4(%rip), %rax     # 0xdcfc0
movslq (%rax), %rcx
subl %ecx, %ebp
jle 0x50a20
cmpl $0x1, %ebp
jne 0x50a29
testb $0x1, 0x10(%rsp)
jne 0x50a3c
leal 0x1(%rcx), %edx
movl %edx, (%rax)
movq (%rbx,%rcx,8), %rsi
leaq 0x8d9c9(%rip), %rdi     # 0xde3b8
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x8c5ab(%rip), %rdi     # 0xdcfb8
leaq 0x524ee(%rip), %rsi     # 0xa2f02
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x458fb(%rip), %rsi     # 0x96322
jmp 0x50a30
leaq 0x45905(%rip), %rsi     # 0x96335
movq 0x8c5b1(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0x8c575(%rip), %rdi     # 0xdcfb8
leaq 0x42f03(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x524ac(%rip), %rsi     # 0xa2f02
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x50a68
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x50a89
movq %rax, %rbx
jmp 0x50a89
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870
nop