// File: /workspace/github_cpp_makefile_star2_O1/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 0x95225(%rip), %rdx     # 0xd1c7f
leaq 0x18(%rsp), %rdi
movq %rdx, %rsi
callq 0x28952
leaq 0x8e948(%rip), %rdx     # 0xcb3b6
leaq 0xcbdfb(%rip), %rcx     # 0x108870
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 0x3cb9c
leaq 0x48(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x38(%rsp), %r12
leaq 0x58(%rsp), %r13
movq 0xce4bd(%rip), %rax     # 0x10af80
movq (%rax), %r14
testq %r14, %r14
leaq 0x951af(%rip), %rax     # 0xd1c7f
cmoveq %rax, %r14
movq %rbx, 0x38(%rsp)
movq %r14, %rdi
callq 0x81f0
leaq (%rax,%r14), %rdx
movq %r12, %rdi
movq %r14, %rsi
callq 0x28952
movq %r13, %rdi
movq %r12, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x38(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3cb17
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r15d
cmpl $0x3f, %r15d
je 0x3cb48
cmpl $0x72, %r15d
je 0x3cb32
cmpl $0x68, %r15d
jne 0x3cb4f
jmp 0x3cd0a
movb $0x1, 0xcee97(%rip)     # 0x10b9d0
movq %r13, %rdi
leaq 0x18(%rsp), %rsi
callq 0x8560
jmp 0x3cb4f
movb $0x1, %al
movq %rax, 0x8(%rsp)
movq %r13, %rdi
movq 0xce43f(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0xd0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x8e83d(%rip), %rdx     # 0xcb3b6
leaq 0xcbcf0(%rip), %rcx     # 0x108870
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r15d
shll $0x18, %r15d
cmpl $0xff000000, %r15d      # imm = 0xFF000000
jne 0x3cabc
leaq 0x950dc(%rip), %rsi     # 0xd1c7f
leaq 0x18(%rsp), %rdi
callq 0x8160
testl %eax, %eax
je 0x3cc20
leaq 0x58(%rsp), %rdi
leaq 0x18(%rsp), %rsi
movl $0x2c, %edx
callq 0x50624
movq 0x58(%rsp), %rbx
movq 0x60(%rsp), %rax
subq %rbx, %rax
cmpq $0x40, %rax
jne 0x3cbf7
movq (%rbx), %rdi
callq 0x86e0
movl %eax, 0xce8f6(%rip)     # 0x10b4dc
movq 0x20(%rbx), %rdi
callq 0x86e0
movl %eax, 0xce8e3(%rip)     # 0x10b4d8
jmp 0x3cc16
movb $0x1, %al
movq %rax, 0x8(%rsp)
movq 0xce3e3(%rip), %rdi     # 0x10afe8
leaq 0x93ce8(%rip), %rsi     # 0xd08f4
movl $0x2f, %edx
callq 0x84e0
leaq 0x58(%rsp), %rdi
callq 0x3123c
movq 0xce399(%rip), %rbx     # 0x10afc0
subl (%rbx), %ebp
cmpl $0x2, %ebp
jge 0x3cc3c
movl $0x12, %edx
leaq 0x91578(%rip), %rsi     # 0xce1b2
jmp 0x3cc4f
movq 0x8(%rsp), %r14
je 0x3cc5e
movl $0x13, %edx
leaq 0x91576(%rip), %rsi     # 0xce1c5
movb $0x1, %r14b
movq 0xce38f(%rip), %rdi     # 0x10afe8
callq 0x84e0
testb $0x1, %r14b
jne 0x3cd24
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %rcx
movq (%rcx,%rax,8), %r14
movq 0xced18(%rip), %r15     # 0x10b998
leaq 0xced09(%rip), %r12     # 0x10b990
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 0x10(%rsp), %rcx
movq (%rcx,%rax,8), %rbx
movq 0xcecfe(%rip), %r14     # 0x10b9b8
leaq 0xcecef(%rip), %r15     # 0x10b9b0
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 0x3ccf8
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 0xce2a7(%rip), %rdi     # 0x10afb8
leaq 0x93c17(%rip), %rsi     # 0xd092f
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0xce28d(%rip), %rdi     # 0x10afb8
leaq 0x8f94b(%rip), %rsi     # 0xcc67d
movl $0x1, %edx
callq 0x84e0
movq 0xce275(%rip), %rdi     # 0x10afb8
leaq 0x93be5(%rip), %rsi     # 0xd092f
callq 0x8460
movl $0x1, %edi
callq 0x8530
movq %rax, %r14
leaq 0x58(%rsp), %rdi
callq 0x3123c
jmp 0x3cdb0
jmp 0x3cd91
jmp 0x3cd6e
jmp 0x3cd91
movq %rax, %r14
movq 0xce220(%rip), %rsi     # 0x10af98
leaq 0x58(%rsp), %rdi
callq 0x8620
leaq 0xd0(%rsp), %rdi
callq 0x8190
jmp 0x3cdb0
movq %rax, %r14
jmp 0x3cdb0
movq %rax, %r14
movq 0x38(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3cdb0
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
movq 0x18(%rsp), %rdi
leaq 0x28(%rsp), %rax
cmpq %rax, %rdi
je 0x3cdcc
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840