// File: /workspace/github_cpp_makefile_star2_O2/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 0x68e87(%rip), %rsi     # 0x99e1f
leaq 0x18(%rsp), %rdi
leaq 0x58(%rsp), %r12
movq %r12, %rdx
callq 0x21904
movq $0x0, 0x10(%rsp)
leaq 0x38(%rsp), %r14
pushq $0x8
popq %r13
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x616be(%rip), %rdx     # 0x92686
leaq 0xa98c1(%rip), %rcx     # 0xda890
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r15d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x31068
movq 0xabfa1(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x68e23(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r14, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r12, %rdi
movq %r14, %rsi
movl %r13d, %edx
callq 0x87e0
movsbl %r15b, %r15d
movq %r14, %rdi
callq 0x8978
cmpl $0x3f, %r15d
je 0x31054
cmpl $0x72, %r15d
je 0x3103e
cmpl $0x68, %r15d
jne 0x3105b
jmp 0x31155
movb $0x1, 0xac9c3(%rip)     # 0xdda08
movq %r12, %rdi
leaq 0x18(%rsp), %rsi
callq 0x8570
jmp 0x3105b
movb $0x1, %al
movq %rax, 0x10(%rsp)
movq %r12, %rdi
callq 0x8220
jmp 0x30fbc
leaq 0x68db0(%rip), %rsi     # 0x99e1f
leaq 0x18(%rsp), %rdi
callq 0x2ea9b
testb %al, %al
je 0x310c6
leaq 0x58(%rsp), %rdi
leaq 0x18(%rsp), %rsi
pushq $0x2c
popq %rdx
callq 0x40349
movq 0x10(%rsp), %r15
movq 0x58(%rsp), %r14
movq 0x60(%rsp), %rax
subq %r14, %rax
cmpq $0x40, %rax
jne 0x310cd
movq (%r14), %rdi
callq 0x86f0
movl %eax, 0xac457(%rip)     # 0xdd50c
movq 0x20(%r14), %rdi
callq 0x86f0
movl %eax, 0xac444(%rip)     # 0xdd508
jmp 0x310e3
movq 0x10(%rsp), %r15
jmp 0x310ed
movb $0x1, %r15b
movq 0xabf11(%rip), %rdi     # 0xdcfe8
leaq 0x679b6(%rip), %rsi     # 0x98a94
callq 0x8480
leaq 0x58(%rsp), %rdi
callq 0x28a08
movq 0xabecc(%rip), %r14     # 0xdcfc0
movslq (%r14), %rax
subl %eax, %ebp
cmpl $0x2, %ebp
jl 0x3116f
jne 0x31178
testb $0x1, %r15b
jne 0x3118b
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0xac8ad(%rip), %rdi     # 0xdd9c8
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0xac8b4(%rip), %rdi     # 0xdd9e8
callq 0x88f0
leaq 0x18(%rsp), %rdi
callq 0x8978
addq $0x1d8, %rsp            # imm = 0x1D8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xabe5c(%rip), %rdi     # 0xdcfb8
leaq 0x6796c(%rip), %rsi     # 0x98acf
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x651ac(%rip), %rsi     # 0x96322
jmp 0x3117f
leaq 0x651b6(%rip), %rsi     # 0x96335
movq 0xabe62(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0xabe26(%rip), %rdi     # 0xdcfb8
leaq 0x627b4(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x6792a(%rip), %rsi     # 0x98acf
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
movq %rax, %rbx
leaq 0x58(%rsp), %rdi
callq 0x28a08
jmp 0x311eb
jmp 0x311d9
jmp 0x311d9
jmp 0x311ca
movq %rax, %rbx
leaq 0x58(%rsp), %rdi
callq 0x8220
jmp 0x311eb
movq %rax, %rbx
jmp 0x311eb
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8978
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870