// File: /workspace/github_cpp_makefile_star2_O3/millanek[P]evo/process_vcf_variant_sharing.cpp
// Function: parseVariantSharingOptions(int, char**)
void parseVariantSharingOptions(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 OPT_POP: arg >> opt::populationsFile; break;
            case OPT_INDIV: arg >> opt::individualsFile; break;    
            case 'h':
                std::cout << SHARING_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;
    }
    
    // Make sure we have INDIVIDUALS_FILE or POPULATIONS_FILE if calculating statistics
    if (opt::populationsFile.empty() && opt::individualsFile.empty()) {
        std::cerr << "You should provide an INDIVIDUALS_FILE or POPULATIONS_FILE (most likely sample_individuals_All.txt)\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << SHARING_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 0x6693a(%rip), %rdx     # 0xca176
leaq 0x9cd3d(%rip), %rcx     # 0x100580
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 0x63974
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0x9e6f4(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x6a132(%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 0x638e0
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x3e, %r14d
jg 0x6390e
leaq 0x9fa07(%rip), %rsi     # 0x1032f8
cmpl $0x2, %r14d
je 0x63904
cmpl $0x3, %r14d
jne 0x63927
leaq 0x9fa14(%rip), %rsi     # 0x103318
movq %r12, %rdi
callq 0x8560
jmp 0x63927
cmpl $0x3f, %r14d
jne 0x6391d
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x63927
cmpl $0x68, %r14d
je 0x63a19
movq %r12, %rdi
movq 0x9e667(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x66825(%rip), %rdx     # 0xca176
leaq 0x9cc28(%rip), %rcx     # 0x100580
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x63885
movq 0x9e645(%rip), %rbx     # 0x101fc0
subl (%rbx), %ebp
jle 0x6399e
cmpl $0x1, %ebp
movq 0x8(%rsp), %rcx
je 0x639b8
movq 0x9e658(%rip), %rdi     # 0x101fe8
leaq 0x6855e(%rip), %rsi     # 0xcbef5
movl $0x13, %edx
jmp 0x639b1
movq 0x9e643(%rip), %rdi     # 0x101fe8
leaq 0x68536(%rip), %rsi     # 0xcbee2
movl $0x12, %edx
callq 0x84e0
movb $0x1, %cl
movq 0x9f941(%rip), %rax     # 0x103300
orq 0x9f95a(%rip), %rax     # 0x103320
je 0x63a33
testb $0x1, %cl
jne 0x63a4b
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %rcx
movq (%rcx,%rax,8), %rbx
movq 0x9f8fb(%rip), %r14     # 0x1032e0
leaq 0x9f8ec(%rip), %r15     # 0x1032d8
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 0x9e598(%rip), %rdi     # 0x101fb8
leaq 0x70455(%rip), %rsi     # 0xd3e7c
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0x9e5ae(%rip), %rdi     # 0x101fe8
leaq 0x703c0(%rip), %rsi     # 0xd3e01
movl $0x64, %edx
callq 0x84e0
movq 0x9e566(%rip), %rdi     # 0x101fb8
leaq 0x679e4(%rip), %rsi     # 0xcb43d
callq 0x8460
leaq 0x70417(%rip), %rsi     # 0xd3e7c
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x63a79
movq %rax, %r14
movq 0x9e515(%rip), %rsi     # 0x101f98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x63abb
movq %rax, %r14
jmp 0x63abb
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x63abb
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840
nop