// File: millanek[P]evo/evo_combineVCFs.cpp
// Function: parseVCFcombOptions(int, char**)
void parseVCFcombOptions(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 'o': arg >> opt::out; break;
            case 'h':
                std::cout << VCF_COMB_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    if (argc - optind < 5) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 5)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << VCF_COMB_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile1 = argv[optind++];
    opt::vcfFile2 = argv[optind++];
    opt::refFile1 = argv[optind++];
    opt::refFile2 = argv[optind++];
    opt::mappabilityFile = 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 0x897dc(%rip), %rdx     # 0x199a30
leaq 0x88585(%rip), %rcx     # 0x1987e0
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x12(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0x1103f5
movq 0x88d15(%rip), %rax     # 0x198f90
cmpq $0x0, (%rax)
je 0x110294
movq 0x88d08(%rip), %rax     # 0x198f90
movq (%rax), %rax
movq %rax, -0x1d8(%rbp)
jmp 0x1102a4
leaq 0x25c44(%rip), %rax     # 0x135edf
movq %rax, -0x1d8(%rbp)
jmp 0x1102a4
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 0x1102e1
leaq -0x198(%rbp), %rdi
leaq -0x1b8(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0x1102fb
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
movsbl -0x12(%rbp), %eax
movl %eax, -0x1ec(%rbp)
subl $0x3f, %eax
je 0x110388
jmp 0x110324
movl -0x1ec(%rbp), %eax
subl $0x68, %eax
je 0x1103c8
jmp 0x110335
movl -0x1ec(%rbp), %eax
subl $0x6f, %eax
je 0x11038e
jmp 0x1103e4
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
jmp 0x110377
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 0x11056a
movb $0x1, -0x11(%rbp)
jmp 0x1103e4
leaq 0x8b19b(%rip), %rsi     # 0x19b530
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0x1103a3
jmp 0x1103e4
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x11056a
movq 0x89669(%rip), %rsi     # 0x199a38
movq 0x88be2(%rip), %rdi     # 0x198fb8
callq 0xa5c0
jmp 0x1103dd
xorl %edi, %edi
callq 0xa700
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x110246
movl -0x4(%rbp), %eax
movq 0x88bc1(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x5, %eax
jge 0x11041f
movq 0x88be3(%rip), %rdi     # 0x198ff0
leaq 0x22016(%rip), %rsi     # 0x13242a
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x110449
movl -0x4(%rbp), %eax
movq 0x88b97(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x5, %eax
jle 0x110447
movq 0x88bb9(%rip), %rdi     # 0x198ff0
leaq 0x21fff(%rip), %rsi     # 0x13243d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x110449
testb $0x1, -0x11(%rbp)
je 0x11047b
movq 0x88b62(%rip), %rdi     # 0x198fb8
leaq 0x1f430(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, %rdi
movq 0x895cc(%rip), %rsi     # 0x199a38
callq 0xa5c0
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0x88b3a(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x88b2c(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x8afec(%rip), %rdi     # 0x19b490
callq 0xa810
movq -0x10(%rbp), %rax
movq 0x88b0c(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x88afe(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x8afde(%rip), %rdi     # 0x19b4b0
callq 0xa810
movq -0x10(%rbp), %rax
movq 0x88ade(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x88ad0(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x8afd0(%rip), %rdi     # 0x19b4d0
callq 0xa810
movq -0x10(%rbp), %rax
movq 0x88ab0(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x88aa2(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x8afc2(%rip), %rdi     # 0x19b4f0
callq 0xa810
movq -0x10(%rbp), %rax
movq 0x88a82(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x88a74(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x8afb4(%rip), %rdi     # 0x19b510
callq 0xa810
addq $0x1f0, %rsp            # imm = 0x1F0
popq %rbp
retq
movq -0x1c8(%rbp), %rdi
callq 0xab50
nopw %cs:(%rax,%rax)