// File: millanek[P]evo/process_vcf_reorder.cpp
// Function: parseReorderOptions(int, char**)
void parseReorderOptions(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 'n': arg >> opt::runName; break;
            case 's': arg >> opt::sampleNameFile; break;
            case '?': die = true; break;
            case 'h': std::cout << REORDER_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    if (argc - optind < 2) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 2)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << REORDER_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::newOrderFile = 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 0xc595c(%rip), %rdx     # 0x199910
leaq 0xc3da5(%rip), %rcx     # 0x197d60
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x12(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0xd4181
movq 0xc4fb5(%rip), %rax     # 0x198f90
cmpq $0x0, (%rax)
je 0xd3ff4
movq 0xc4fa8(%rip), %rax     # 0x198f90
movq (%rax), %rax
movq %rax, -0x1d8(%rbp)
jmp 0xd4004
leaq 0x61ee4(%rip), %rax     # 0x135edf
movq %rax, -0x1d8(%rbp)
jmp 0xd4004
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 0xd4041
leaq -0x198(%rbp), %rdi
leaq -0x1b8(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0xd405b
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
movsbl -0x12(%rbp), %eax
movl %eax, -0x1ec(%rbp)
subl $0x3f, %eax
je 0xd414e
jmp 0xd4088
movl -0x1ec(%rbp), %eax
subl $0x68, %eax
je 0xd4154
jmp 0xd4099
movl -0x1ec(%rbp), %eax
subl $0x6e, %eax
je 0xd40fd
jmp 0xd40a6
movl -0x1ec(%rbp), %eax
subl $0x73, %eax
je 0xd4137
jmp 0xd4170
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
jmp 0xd40ec
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 0xd426c
leaq 0xc6cf4(%rip), %rsi     # 0x19adf8
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0xd4112
jmp 0xd4170
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0xd426c
leaq 0xc6c9a(%rip), %rsi     # 0x19add8
leaq -0x198(%rbp), %rdi
callq 0xa750
jmp 0xd414c
jmp 0xd4170
movb $0x1, -0x11(%rbp)
jmp 0xd4170
movq 0xc57bd(%rip), %rsi     # 0x199918
movq 0xc4e56(%rip), %rdi     # 0x198fb8
callq 0xa5c0
jmp 0xd4169
xorl %edi, %edi
callq 0xa700
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0xd3fa6
movl -0x4(%rbp), %eax
movq 0xc4e35(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jge 0xd41ab
movq 0xc4e57(%rip), %rdi     # 0x198ff0
leaq 0x5e28a(%rip), %rsi     # 0x13242a
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0xd41d5
movl -0x4(%rbp), %eax
movq 0xc4e0b(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jle 0xd41d3
movq 0xc4e2d(%rip), %rdi     # 0x198ff0
leaq 0x5e273(%rip), %rsi     # 0x13243d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0xd41d5
testb $0x1, -0x11(%rbp)
je 0xd4207
movq 0xc4dd6(%rip), %rdi     # 0x198fb8
leaq 0x5b6a4(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, %rdi
movq 0xc5720(%rip), %rsi     # 0x199918
callq 0xa5c0
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0xc4dae(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0xc4da0(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0xc6b68(%rip), %rdi     # 0x19ad98
callq 0xa810
movq -0x10(%rbp), %rax
movq 0xc4d80(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0xc4d72(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0xc6b5a(%rip), %rdi     # 0x19adb8
callq 0xa810
addq $0x1f0, %rsp            # imm = 0x1F0
popq %rbp
retq
movq -0x1c8(%rbp), %rdi
callq 0xab50
nopl (%rax,%rax)