// File: millanek[P]evo/evo_agpToNewFasta.cpp
// Function: parseAgpFastaOptions(int, char**)
void parseAgpFastaOptions(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 'h':
                std::cout << AGPTOFASTA_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    if (argc - optind < 1) {
        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" << AGPTOFASTA_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::agpFile = argv[optind++];
    opt::genomeFile = 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 0x86bec(%rip), %rdx     # 0x199a50
leaq 0x85a55(%rip), %rcx     # 0x1988c0
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x12(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0x112fdd
movq 0x86105(%rip), %rax     # 0x198f90
cmpq $0x0, (%rax)
je 0x112ea4
movq 0x860f8(%rip), %rax     # 0x198f90
movq (%rax), %rax
movq %rax, -0x1d8(%rbp)
jmp 0x112eb4
leaq 0x23034(%rip), %rax     # 0x135edf
movq %rax, -0x1d8(%rbp)
jmp 0x112eb4
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 0x112ef1
leaq -0x198(%rbp), %rdi
leaq -0x1b8(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0x112f0b
leaq -0x1b8(%rbp), %rdi
callq 0xac88
leaq -0x1b9(%rbp), %rdi
callq 0xa640
movsbl -0x12(%rbp), %eax
movl %eax, -0x1ec(%rbp)
subl $0x3f, %eax
je 0x112f87
jmp 0x112f34
movl -0x1ec(%rbp), %eax
subl $0x68, %eax
je 0x112f8d
jmp 0x112fcc
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
jmp 0x112f76
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 0x1130c8
movb $0x1, -0x11(%rbp)
jmp 0x112fcc
movq 0x86ac4(%rip), %rsi     # 0x199a58
movq 0x8601d(%rip), %rdi     # 0x198fb8
callq 0xa5c0
jmp 0x112fa2
xorl %edi, %edi
callq 0xa700
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x1c8(%rbp)
movl %eax, -0x1cc(%rbp)
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x1130c8
leaq -0x198(%rbp), %rdi
callq 0xa290
jmp 0x112e56
movl -0x4(%rbp), %eax
movq 0x85fd9(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x1, %eax
jge 0x113007
movq 0x85ffb(%rip), %rdi     # 0x198ff0
leaq 0x1f42e(%rip), %rsi     # 0x13242a
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x113031
movl -0x4(%rbp), %eax
movq 0x85faf(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x2, %eax
jle 0x11302f
movq 0x85fd1(%rip), %rdi     # 0x198ff0
leaq 0x1f417(%rip), %rsi     # 0x13243d
callq 0xa5c0
movb $0x1, -0x11(%rbp)
jmp 0x113031
testb $0x1, -0x11(%rbp)
je 0x113063
movq 0x85f7a(%rip), %rdi     # 0x198fb8
leaq 0x1c848(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, %rdi
movq 0x86a04(%rip), %rsi     # 0x199a58
callq 0xa5c0
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0x85f52(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x85f44(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x8853c(%rip), %rdi     # 0x19b5c8
callq 0xa810
movq -0x10(%rbp), %rax
movq 0x85f24(%rip), %rcx     # 0x198fc0
movl (%rcx), %ecx
movl %ecx, %esi
addl $0x1, %esi
movq 0x85f16(%rip), %rdx     # 0x198fc0
movl %esi, (%rdx)
movslq %ecx, %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x8852e(%rip), %rdi     # 0x19b5e8
callq 0xa810
addq $0x1f0, %rsp            # imm = 0x1F0
popq %rbp
retq
movq -0x1c8(%rbp), %rdi
callq 0xab50
nopw %cs:(%rax,%rax)
nop