// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/evo_ABS.cpp
// Function: parseABSoptions(int, char**)
void parseABSoptions(int argc, char** argv) {
    bool die = false; string regionArgString; std::vector<string> regionArgs;
    std::vector<string> windowSizeStep;
    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 'w':
                windowSizeStep = split(arg.str(), ',');
                opt::windowSize = atoi(windowSizeStep[0].c_str());
                opt::windowStep = atoi(windowSizeStep[1].c_str());
                break;
            case 'n': arg >> opt::runName; break;
            case OPT_ANNOT: arg >> opt::annotFile; break;
            case 'h':
                std::cout << ABS_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (argc - optind < 3) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 3)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << ABS_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::setsFile = argv[optind++];
    opt::ABSquartetFile = argv[optind++];
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x228, %rsp            # imm = 0x228
movq %rsi, %rbx
movl %edi, %ebp
leaq 0x80(%rsp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb $0x0, (%rax)
andq $0x0, 0x40(%rsp)
xorps %xmm0, %xmm0
movaps %xmm0, 0x30(%rsp)
leaq 0x10(%rsp), %rax
movaps %xmm0, (%rax)
andq $0x0, 0x10(%rax)
movq $0x0, 0x8(%rsp)
leaq 0x50(%rsp), %r15
leaq 0x90(%rsp), %r14
leaq 0xa8(%rsp), %r12
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x2bc30(%rip), %rdx     # 0xb01cb
leaq 0x5819e(%rip), %rcx     # 0xdc740
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r13d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x846a6
movq 0x589ce(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x15850(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r15, %rdi
movq %r14, %rdx
callq 0x21904
movq %r12, %rdi
movq %r15, %rsi
pushq $0x8
popq %rdx
callq 0x87e0
movsbl %r13b, %r13d
movq %r15, %rdi
callq 0x8978
leaq 0x5a989(%rip), %rsi     # 0xdef88
testl %r13d, %r13d
je 0x84631
cmpl $0x3f, %r13d
je 0x84621
cmpl $0x6e, %r13d
je 0x8462a
cmpl $0x77, %r13d
je 0x8463b
cmpl $0x68, %r13d
jne 0x84699
jmp 0x84744
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x84699
leaq 0x5a977(%rip), %rsi     # 0xdefa8
movq %r12, %rdi
callq 0x8570
jmp 0x84699
movq %r15, %rdi
leaq 0xb8(%rsp), %rsi
callq 0x8710
movq %r14, %rdi
movq %r15, %rsi
pushq $0x2c
popq %rdx
callq 0x40349
leaq 0x10(%rsp), %rdi
movq %r14, %rsi
callq 0x2f6c0
movq %r14, %rdi
callq 0x28a08
movq %r15, %rdi
callq 0x8978
movq 0x10(%rsp), %r13
movq (%r13), %rdi
callq 0x86f0
movl %eax, 0x58f86(%rip)     # 0xdd610
movq 0x20(%r13), %rdi
callq 0x86f0
movl %eax, 0x58f7b(%rip)     # 0xdd614
movq %r12, %rdi
callq 0x8220
jmp 0x8458f
movq 0x58913(%rip), %r14     # 0xdcfc0
movslq (%r14), %rax
subl %eax, %ebp
cmpl $0x3, %ebp
jl 0x8475e
jne 0x84767
testb $0x1, 0x8(%rsp)
jne 0x8477a
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x5a84b(%rip), %rdi     # 0xdef28
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x5a852(%rip), %rdi     # 0xdef48
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x5a859(%rip), %rdi     # 0xdef68
callq 0x88f0
leaq 0x10(%rsp), %rdi
callq 0x28a08
leaq 0x30(%rsp), %rdi
callq 0x28a08
leaq 0x70(%rsp), %rdi
callq 0x8978
addq $0x228, %rsp            # imm = 0x228
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x5886d(%rip), %rdi     # 0xdcfb8
leaq 0x2ba7f(%rip), %rsi     # 0xb01d1
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x11bbd(%rip), %rsi     # 0x96322
jmp 0x8476e
leaq 0x11bc7(%rip), %rsi     # 0x96335
movq 0x58873(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0x58837(%rip), %rdi     # 0xdcfb8
leaq 0xf1c5(%rip), %rsi      # 0x9394d
callq 0x8480
leaq 0x2ba3d(%rip), %rsi     # 0xb01d1
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x847b9
jmp 0x847cb
movq %rax, %rbx
leaq 0x50(%rsp), %rdi
callq 0x8978
jmp 0x847bc
jmp 0x847b9
movq %rax, %rbx
leaq 0xa8(%rsp), %rdi
callq 0x8220
jmp 0x847dd
movq %rax, %rbx
jmp 0x847dd
movq %rax, %rbx
leaq 0x50(%rsp), %rdi
callq 0x8978
leaq 0x10(%rsp), %rdi
callq 0x28a08
leaq 0x30(%rsp), %rdi
callq 0x28a08
leaq 0x70(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870