// File: /workspace/github_cpp_makefile_star2_O1/millanek[P]evo/evo_abba_baba.cpp
// Function: parseAbbaBabaOptions(int, char**)
void parseAbbaBabaOptions(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 's': arg >> opt::sampleNameFile; break;
            case 'f': opt::bFrequency = true; opt::jackKniveWindowSize = JACKKNIVE_WINDOW_SIZE_FREQUENCY; break;
            case 'w': arg >> opt::windowSize; break;
            case 'n': arg >> opt::runName; break;
            case OPT_AA_EQ_O: opt::bAaEqO = true; break;
            case OPT_NO_AA_O: opt::bNoAaO = true; break;
            case 'h':
                std::cout << ABBA_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (opt::runName == "") {
        if (opt::bFrequency) { opt::runName = "frequency"; }
        if (!opt::bFrequency) { opt::runName = "sequence"; }
    }
    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" << ABBA_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::setsFile = argv[optind++];
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movl %edi, %ebp
leaq 0x961cc(%rip), %rdx     # 0xcf7e0
leaq 0xcf155(%rip), %rcx     # 0x108770
movq $0x0, 0x8(%rsp)
movq %rsi, 0x10(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0x397a8
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0xd191c(%rip), %rax     # 0x10af80
movq (%rax), %r13
testq %r13, %r13
leaq 0x9860e(%rip), %rax     # 0xd1c7f
cmoveq %rax, %r13
movq %rbx, 0x18(%rsp)
movq %r13, %rdi
callq 0x81f0
leaq (%rax,%r13), %rdx
movq %r15, %rdi
movq %r13, %rsi
callq 0x28952
movq %r12, %rdi
movq %r15, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x396b8
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x67, %r14d
jg 0x396e0
cmpl $0x3e, %r14d
jg 0x39703
testl %r14d, %r14d
je 0x3973a
cmpl $0x1, %r14d
jne 0x3975b
movb $0x1, 0xd22a8(%rip)     # 0x10b986
jmp 0x3975b
cmpl $0x72, %r14d
jle 0x39722
cmpl $0x73, %r14d
je 0x3974c
cmpl $0x77, %r14d
jne 0x3975b
movq %r12, %rdi
leaq 0xd1dd8(%rip), %rsi     # 0x10b4d4
callq 0x82b0
jmp 0x3975b
cmpl $0x3f, %r14d
je 0x39743
cmpl $0x66, %r14d
jne 0x3975b
movb $0x1, 0xd226f(%rip)     # 0x10b985
movl $0x1388, 0xd1db0(%rip)  # imm = 0x1388
jmp 0x3975b
leaq 0xd220f(%rip), %rsi     # 0x10b938
cmpl $0x6e, %r14d
je 0x39753
cmpl $0x68, %r14d
jne 0x3975b
jmp 0x398e7
movb $0x1, 0xd2243(%rip)     # 0x10b984
jmp 0x3975b
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x3975b
leaq 0xd21c5(%rip), %rsi     # 0x10b918
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0xd1833(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x9605b(%rip), %rdx     # 0xcf7e0
leaq 0xcefe4(%rip), %rcx     # 0x108770
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x3965d
leaq 0xd2189(%rip), %rdi     # 0x10b938
leaq 0x984c9(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
jne 0x39815
cmpb $0x1, 0xd21bf(%rip)     # 0x10b985
jne 0x397ea
movq 0xd2171(%rip), %rdx     # 0x10b940
leaq 0xd2162(%rip), %rdi     # 0x10b938
leaq 0xa376b(%rip), %rcx     # 0xdcf48
movl $0x9, %r8d
xorl %esi, %esi
callq 0x86c0
cmpb $0x0, 0xd2194(%rip)     # 0x10b985
jne 0x39815
movq 0xd2146(%rip), %rdx     # 0x10b940
leaq 0xd2137(%rip), %rdi     # 0x10b938
leaq 0x95f1e(%rip), %rcx     # 0xcf726
movl $0x8, %r8d
xorl %esi, %esi
callq 0x86c0
movq 0xd17a4(%rip), %rbx     # 0x10afc0
subl (%rbx), %ebp
cmpl $0x1, %ebp
jg 0x39838
movq 0xd17be(%rip), %rdi     # 0x10afe8
leaq 0x94981(%rip), %rsi     # 0xce1b2
movl $0x12, %edx
jmp 0x39855
cmpl $0x2, %ebp
movq 0x8(%rsp), %rax
je 0x3985c
movq 0xd179f(%rip), %rdi     # 0x10afe8
leaq 0x94975(%rip), %rsi     # 0xce1c5
movl $0x13, %edx
callq 0x84e0
movb $0x1, %al
testb $0x1, %al
jne 0x39901
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %r13
movq (%r13,%rax,8), %r14
movq 0xd2063(%rip), %r15     # 0x10b8e0
leaq 0xd2054(%rip), %r12     # 0x10b8d8
movq %r14, %rdi
callq 0x81f0
movq %r12, %rdi
xorl %esi, %esi
movq %r15, %rdx
movq %r14, %rcx
movq %rax, %r8
callq 0x86c0
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %rbx
movq 0xd204d(%rip), %r14     # 0x10b900
leaq 0xd203e(%rip), %r15     # 0x10b8f8
movq %rbx, %rdi
callq 0x81f0
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x86c0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xd16ca(%rip), %rdi     # 0x10afb8
leaq 0x95f18(%rip), %rsi     # 0xcf80d
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0xd16b0(%rip), %rdi     # 0x10afb8
leaq 0x92d6e(%rip), %rsi     # 0xcc67d
callq 0x8460
leaq 0x95ef2(%rip), %rsi     # 0xcf80d
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x3992f
movq %rax, %r14
movq 0xd165f(%rip), %rsi     # 0x10af98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x39971
movq %rax, %r14
jmp 0x39971
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x39971
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840