// File: /workspace/github_cpp_makefile_star2_O3/millanek[P]evo/evo_fullAnnotationExtract.cpp
// Function: parseAnnotExtractOptions(int, char**)
void parseAnnotExtractOptions(int argc, char** argv) {
    bool die = false;
    std::string regulString = "";
    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 'r': opt::regulatory = true; arg >> regulString;
                break;
            case 'h':
                std::cout << ANNOTEXTRACT_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (regulString != "") {
        std::vector<string> upDown = split(regulString, ',');
        if (upDown.size() != 2) {
            std::cerr << "Check the format of your --regulatory argument\n";
            die = true;
        } else {
            opt::bp_5prime = atoi(upDown[0].c_str()); opt::bp_3prime = atoi(upDown[1].c_str());
        }
    }
    
    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" << ANNOTEXTRACT_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    opt::gpFile = argv[optind++];
    opt::annotationFile = argv[optind++];
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1d8, %rsp            # imm = 0x1D8
movq %rsi, %rbx
movl %edi, %ebp
leaq 0x28(%rsp), %rax
movq %rax, -0x10(%rax)
leaq 0x93e4e(%rip), %rdx     # 0xcd9cb
leaq 0x18(%rsp), %rdi
movq %rdx, %rsi
callq 0x28a52
leaq 0x905e5(%rip), %rdx     # 0xca176
leaq 0xc5bd8(%rip), %rcx     # 0xff770
movq $0x0, 0x8(%rsp)
movl %ebp, %edi
movq %rbx, 0x10(%rsp)
movq %rbx, %rsi
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r15d
shll $0x18, %r15d
cmpl $0xff000000, %r15d      # imm = 0xFF000000
je 0x39cbf
leaq 0x48(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x38(%rsp), %r12
leaq 0x58(%rsp), %r13
movq 0xc839a(%rip), %rax     # 0x101f80
movq (%rax), %r14
testq %r14, %r14
leaq 0x93dd8(%rip), %rax     # 0xcd9cb
cmoveq %rax, %r14
movq %rbx, 0x38(%rsp)
movq %r14, %rdi
callq 0x81f0
leaq (%rax,%r14), %rdx
movq %r12, %rdi
movq %r14, %rsi
callq 0x28a52
movq %r13, %rdi
movq %r12, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x38(%rsp), %rdi
cmpq %rbx, %rdi
je 0x39c3a
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r15d
cmpl $0x3f, %r15d
je 0x39c6b
cmpl $0x72, %r15d
je 0x39c55
cmpl $0x68, %r15d
jne 0x39c72
jmp 0x39e0c
movb $0x1, 0xc8d7c(%rip)     # 0x1029d8
movq %r13, %rdi
leaq 0x18(%rsp), %rsi
callq 0x8560
jmp 0x39c72
movb $0x1, %al
movq %rax, 0x8(%rsp)
movq %r13, %rdi
movq 0xc831c(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xd0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x904da(%rip), %rdx     # 0xca176
leaq 0xc5acd(%rip), %rcx     # 0xff770
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r15d
shll $0x18, %r15d
cmpl $0xff000000, %r15d      # imm = 0xFF000000
jne 0x39bdf
leaq 0x93d05(%rip), %rsi     # 0xcd9cb
leaq 0x18(%rsp), %rdi
callq 0x8160
testl %eax, %eax
je 0x39d1f
leaq 0x58(%rsp), %rdi
leaq 0x18(%rsp), %rsi
movl $0x2c, %edx
callq 0x4d650
movq 0x8(%rsp), %r14
movq 0x58(%rsp), %rbx
movq 0x60(%rsp), %rax
subq %rbx, %rax
cmpq $0x40, %rax
jne 0x39d26
movq (%rbx), %rdi
callq 0x86e0
movl %eax, 0xc87ae(%rip)     # 0x1024bc
movq 0x20(%rbx), %rdi
callq 0x86e0
movl %eax, 0xc879b(%rip)     # 0x1024b8
jmp 0x39d41
movq 0x8(%rsp), %r14
jmp 0x39d4b
movb $0x1, %r14b
movq 0xc82b8(%rip), %rdi     # 0x101fe8
leaq 0x933c5(%rip), %rsi     # 0xcd0fc
movl $0x2f, %edx
callq 0x84e0
leaq 0x58(%rsp), %rdi
callq 0x2e784
movq 0xc826e(%rip), %rbx     # 0x101fc0
movslq (%rbx), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0x39e26
movq 0x10(%rsp), %r13
jne 0x39e34
testb $0x1, %r14b
jne 0x39e4c
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %r14
movq 0xc8c1a(%rip), %r15     # 0x1029a0
leaq 0xc8c0b(%rip), %r12     # 0x102998
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 0xc8c04(%rip), %r14     # 0x1029c0
leaq 0xc8bf5(%rip), %r15     # 0x1029b8
movq %rbx, %rdi
callq 0x81f0
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x86c0
movq 0x18(%rsp), %rdi
leaq 0x28(%rsp), %rax
cmpq %rax, %rdi
je 0x39dfa
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
addq $0x1d8, %rsp            # imm = 0x1D8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xc81a5(%rip), %rdi     # 0x101fb8
leaq 0x9331d(%rip), %rsi     # 0xcd137
callq 0x8460
xorl %edi, %edi
callq 0x8530
movl $0x12, %edx
leaq 0x920b0(%rip), %rsi     # 0xcbee2
jmp 0x39e40
movl $0x13, %edx
leaq 0x920b5(%rip), %rsi     # 0xcbef5
movq 0xc81a1(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0xc8165(%rip), %rdi     # 0x101fb8
leaq 0x915e3(%rip), %rsi     # 0xcb43d
movl $0x1, %edx
callq 0x84e0
movq 0xc814d(%rip), %rdi     # 0x101fb8
leaq 0x932c5(%rip), %rsi     # 0xcd137
callq 0x8460
movl $0x1, %edi
callq 0x8530
movq %rax, %r14
leaq 0x58(%rsp), %rdi
callq 0x2e784
jmp 0x39ed8
jmp 0x39eb9
jmp 0x39e96
jmp 0x39eb9
movq %rax, %r14
movq 0xc80f8(%rip), %rsi     # 0x101f98
leaq 0x58(%rsp), %rdi
callq 0x8620
leaq 0xd0(%rsp), %rdi
callq 0x8190
jmp 0x39ed8
movq %rax, %r14
jmp 0x39ed8
movq %rax, %r14
movq 0x38(%rsp), %rdi
cmpq %rbx, %rdi
je 0x39ed8
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
movq 0x18(%rsp), %rdi
leaq 0x28(%rsp), %rax
cmpq %rax, %rdi
je 0x39ef4
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840