// File: /workspace/github_cpp_makefile_star2_O3/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 $0x248, %rsp            # imm = 0x248
movl %edi, %ebp
leaq 0x60(%rsp), %rax
movq %rax, -0x10(%rax)
xorl %ecx, %ecx
movq %rcx, -0x8(%rax)
movb $0x0, (%rax)
movq %rcx, 0xa0(%rsp)
xorps %xmm0, %xmm0
movaps %xmm0, 0x90(%rsp)
movq $0x0, 0x8(%rsp)
movq %rcx, 0x20(%rsp)
movaps %xmm0, 0x10(%rsp)
leaq 0x296e5(%rip), %rdx     # 0xdef73
leaq 0x4be8b(%rip), %rcx     # 0x101720
movq %rsi, 0x28(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0xb5a8b
leaq 0x40(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x30(%rsp), %r12
leaq 0xc8(%rsp), %r13
movq 0x4c6a8(%rip), %rax     # 0x101f80
movq (%rax), %r15
testq %r15, %r15
leaq 0x180e6(%rip), %rax     # 0xcd9cb
cmoveq %rax, %r15
movq %rbx, 0x30(%rsp)
movq %r15, %rdi
callq 0x81f0
leaq (%rax,%r15), %rdx
movq %r12, %rdi
movq %r15, %rsi
callq 0x28a52
movq %r13, %rdi
movq %r12, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x30(%rsp), %rdi
cmpq %rbx, %rdi
je 0xb592c
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x67, %r14d
jle 0xb5a08
cmpl $0x6e, %r14d
je 0xb5a23
cmpl $0x77, %r14d
jne 0xb5a34
movq %r12, %rdi
leaq 0xd8(%rsp), %rsi
callq 0x8700
leaq 0x70(%rsp), %r14
movq %r14, %rdi
movq %r12, %rsi
movl $0x2c, %edx
callq 0x4d650
movq 0x20(%rsp), %rax
movaps 0x70(%rsp), %xmm0
movq 0x80(%rsp), %rcx
movq %rcx, 0x20(%rsp)
movaps 0x10(%rsp), %xmm1
movaps %xmm0, 0x10(%rsp)
movaps %xmm1, 0xb0(%rsp)
movq %rax, 0xc0(%rsp)
xorps %xmm0, %xmm0
movaps %xmm0, 0x70(%rsp)
movq $0x0, 0x80(%rsp)
leaq 0xb0(%rsp), %rdi
callq 0x2e784
movq %r14, %rdi
callq 0x2e784
movq 0x30(%rsp), %rdi
cmpq %rbx, %rdi
je 0xb59e4
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
movq 0x10(%rsp), %r14
movq (%r14), %rdi
callq 0x86e0
movl %eax, 0x4cbe1(%rip)     # 0x1025d8
movq 0x20(%r14), %rdi
callq 0x86e0
movl %eax, 0x4cbd6(%rip)     # 0x1025dc
jmp 0xb5a3e
leaq 0x4e551(%rip), %rsi     # 0x103f60
testl %r14d, %r14d
je 0xb5a2a
cmpl $0x3f, %r14d
jne 0xb5a3e
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0xb5a3e
leaq 0x4e556(%rip), %rsi     # 0x103f80
movq %r13, %rdi
callq 0x8560
jmp 0xb5a3e
cmpl $0x68, %r14d
je 0xb5b9a
movq %r13, %rdi
movq 0x4c550(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0x140(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x28(%rsp), %rsi
leaq 0x2950b(%rip), %rdx     # 0xdef73
leaq 0x4bcb1(%rip), %rcx     # 0x101720
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xb58d1
movq 0x4c52e(%rip), %rbx     # 0x101fc0
movslq (%rbx), %rax
subl %eax, %ebp
cmpl $0x3, %ebp
jl 0xb5bb4
movq 0x28(%rsp), %r13
jne 0xb5bc2
testb $0x1, 0x8(%rsp)
jne 0xb5bda
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %r14
movq 0x4e441(%rip), %r15     # 0x103f08
leaq 0x4e432(%rip), %r12     # 0x103f00
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), %r14
movq 0x4e42b(%rip), %r15     # 0x103f28
leaq 0x4e41c(%rip), %r12     # 0x103f20
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 0x4e415(%rip), %r14     # 0x103f48
leaq 0x4e406(%rip), %r15     # 0x103f40
movq %rbx, %rdi
callq 0x81f0
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x86c0
leaq 0x10(%rsp), %rdi
callq 0x2e784
leaq 0x90(%rsp), %rdi
callq 0x2e784
movq 0x50(%rsp), %rdi
leaq 0x60(%rsp), %rax
cmpq %rax, %rdi
je 0xb5b88
movq 0x60(%rsp), %rsi
incq %rsi
callq 0x8480
addq $0x248, %rsp            # imm = 0x248
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x4c417(%rip), %rdi     # 0x101fb8
leaq 0x293d1(%rip), %rsi     # 0xdef79
callq 0x8460
xorl %edi, %edi
callq 0x8530
movl $0x12, %edx
leaq 0x16322(%rip), %rsi     # 0xcbee2
jmp 0xb5bce
movl $0x13, %edx
leaq 0x16327(%rip), %rsi     # 0xcbef5
movq 0x4c413(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0x4c3d7(%rip), %rdi     # 0x101fb8
leaq 0x15855(%rip), %rsi     # 0xcb43d
movl $0x1, %edx
callq 0x84e0
movq 0x4c3bf(%rip), %rdi     # 0x101fb8
leaq 0x29379(%rip), %rsi     # 0xdef79
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0xb5c31
movq %rax, %r14
movq 0x30(%rsp), %rdi
cmpq %rbx, %rdi
je 0xb5c34
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
jmp 0xb5c34
jmp 0xb5c31
jmp 0xb5c57
movq %rax, %r14
movq 0x4c35d(%rip), %rsi     # 0x101f98
leaq 0xc8(%rsp), %rdi
callq 0x8620
leaq 0x140(%rsp), %rdi
callq 0x8190
jmp 0xb5c76
movq %rax, %r14
jmp 0xb5c76
movq %rax, %r14
movq 0x30(%rsp), %rdi
cmpq %rbx, %rdi
je 0xb5c76
movq 0x40(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x10(%rsp), %rdi
callq 0x2e784
leaq 0x90(%rsp), %rdi
callq 0x2e784
movq 0x50(%rsp), %rdi
leaq 0x60(%rsp), %rax
cmpq %rax, %rdi
je 0xb5ca9
movq 0x60(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840