// File: 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
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 0xf788c(%rip), %rdx     # 0x199800
leaq 0xf5625(%rip), %rcx     # 0x1975a0
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x12(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0xa213d
movq 0xf6ff5(%rip), %rax     # 0x198f90
cmpq $0x0, (%rax)
je 0xa1fb4
movq 0xf6fe8(%rip), %rax     # 0x198f90
movq (%rax), %rax
movq %rax, -0x1d8(%rbp)
jmp 0xa1fc4
leaq 0x93f24(%rip), %rax     # 0x135edf
movq %rax, -0x1d8(%rbp)
jmp 0xa1fc4
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 0xa2001
leaq -0x198(%rbp), %rdi
leaq -0x1b8(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0xa201b
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
movsbl -0x12(%rbp), %eax
movl %eax, -0x1ec(%rbp)
subl $0x2, %eax
je 0xa20f9
jmp 0xa2048
movl -0x1ec(%rbp), %eax
subl $0x3, %eax
je 0xa20bf
jmp 0xa2055
movl -0x1ec(%rbp), %eax
subl $0x3f, %eax
je 0xa20b9
jmp 0xa2062
movl -0x1ec(%rbp), %eax
subl $0x68, %eax
je 0xa2110
jmp 0xa212c
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
jmp 0xa20a8
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 0xa2235
movb $0x1, -0x11(%rbp)
jmp 0xa212c
leaq 0xf8732(%rip), %rsi     # 0x19a7f8
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0xa20d4
jmp 0xa212c
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0xa2235
leaq 0xf86d8(%rip), %rsi     # 0x19a7d8
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0xa210e
jmp 0xa212c
movq 0xf76f1(%rip), %rsi     # 0x199808
movq 0xf6e9a(%rip), %rdi     # 0x198fb8
callq 0xa5c0
jmp 0xa2125
xorl %edi, %edi
callq 0xa700
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0xa1f66
movl -0x4(%rbp), %eax
movq 0xf6e79(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x1, %eax
jge 0xa2167
movq 0xf6e9b(%rip), %rdi     # 0x198ff0
leaq 0x902ce(%rip), %rsi     # 0x13242a
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0xa2191
movl -0x4(%rbp), %eax
movq 0xf6e4f(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x1, %eax
jle 0xa218f
movq 0xf6e71(%rip), %rdi     # 0x198ff0
leaq 0x902b7(%rip), %rsi     # 0x13243d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0xa2191
leaq 0xf8660(%rip), %rdi     # 0x19a7f8
callq 0xaa70
testb $0x1, %al
jne 0xa21a3
jmp 0xa21cc
leaq 0xf862e(%rip), %rdi     # 0x19a7d8
callq 0xaa70
testb $0x1, %al
jne 0xa21b5
jmp 0xa21cc
movq 0xf6e34(%rip), %rdi     # 0x198ff0
leaq 0x9c7aa(%rip), %rsi     # 0x13e96d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
testb $0x1, -0x11(%rbp)
je 0xa21fe
movq 0xf6ddf(%rip), %rdi     # 0x198fb8
leaq 0x8d6ad(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, %rdi
movq 0xf7619(%rip), %rsi     # 0x199808
callq 0xa5c0
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0xf6db7(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0xf6da9(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0xf8591(%rip), %rdi     # 0x19a7b8
callq 0xa810
addq $0x1f0, %rsp            # imm = 0x1F0
popq %rbp
retq
movq -0x1c8(%rbp), %rdi
callq 0xab50
nopw %cs:(%rax,%rax)
nopl (%rax,%rax)