// File: /workspace/github_cpp_makefile_star2_O3/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
movl %edi, %ebp
leaq 0x6d56e(%rip), %rdx     # 0xd422b
leaq 0x99a7c(%rip), %rcx     # 0x100740
movq $0x0, 0x8(%rsp)
movq %rsi, 0x10(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0x66e03
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0x9b273(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x66cb1(%rip), %rax     # 0xcd9cb
cmoveq %rax, %r13
movq %rbx, 0x18(%rsp)
movq %r13, %rdi
callq 0x81f0
leaq (%rax,%r13), %rdx
movq %r15, %rdi
movq %r13, %rsi
callq 0x28a52
movq %r12, %rdi
movq %r15, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x66d61
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x63, %r14d
jg 0x66d89
cmpl $0x3f, %r14d
je 0x66daf
leaq 0x9b7e0(%rip), %rsi     # 0x102558
cmpl $0x63, %r14d
je 0x66da5
cmpl $0x1, %r14d
jne 0x66db6
jmp 0x66e6a
cmpl $0x64, %r14d
je 0x66d9e
cmpl $0x73, %r14d
jne 0x66db6
leaq 0x9b7c4(%rip), %rsi     # 0x102560
jmp 0x66da5
leaq 0x9b7b7(%rip), %rsi     # 0x10255c
movq %r12, %rdi
callq 0x82b0
jmp 0x66db6
movb $0x1, %al
movq %rax, 0x8(%rsp)
movq %r12, %rdi
movq 0x9b1d8(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x6d44b(%rip), %rdx     # 0xd422b
leaq 0x99959(%rip), %rcx     # 0x100740
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x66d06
movq 0x9b1b6(%rip), %rax     # 0x101fc0
movslq (%rax), %rcx
subl %ecx, %ebp
jle 0x66e84
cmpl $0x1, %ebp
jne 0x66e92
testb $0x1, 0x8(%rsp)
jne 0x66eaa
leal 0x1(%rcx), %edx
movl %edx, (%rax)
movq 0x10(%rsp), %rax
movq (%rax,%rcx,8), %rbx
movq 0x9c55a(%rip), %r14     # 0x103390
leaq 0x9c54b(%rip), %r15     # 0x103388
movq %rbx, %rdi
callq 0x81f0
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x86c0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x9b147(%rip), %rdi     # 0x101fb8
leaq 0x6d94a(%rip), %rsi     # 0xd47c2
callq 0x8460
xorl %edi, %edi
callq 0x8530
leaq 0x65057(%rip), %rsi     # 0xcbee2
movl $0x12, %edx
jmp 0x66e9e
leaq 0x6505c(%rip), %rsi     # 0xcbef5
movl $0x13, %edx
movq 0x9b143(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0x9b107(%rip), %rdi     # 0x101fb8
leaq 0x64585(%rip), %rsi     # 0xcb43d
callq 0x8460
leaq 0x6d8fe(%rip), %rsi     # 0xd47c2
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x66ed8
movq %rax, %r14
movq 0x9b0b6(%rip), %rsi     # 0x101f98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x66f1a
movq %rax, %r14
jmp 0x66f1a
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x66f1a
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840