// File: /workspace/github_cpp_makefile_star2_O1/millanek[P]evo/process_vcf_linkGeneNames.cpp
// Function: linkGNOptions(int, char**)
void linkGNOptions(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 'o': arg >> opt::out; break;
            case 's': arg >> opt::species; break;
            case OPT_V1: arg >> opt::v1orthologousClustersFile; break;
            case OPT_V2: arg >> opt::v2orthologsFile; break;
            case OPT_NtoN: opt::NtoN = true; break;
            case OPT_SEP_BY_COPY: arg >> opt::sepByCopyNumberPrefix; break;
            case 'h':
                std::cout << LINKGN_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (opt::v1orthologousClustersFile == "" && opt::v2orthologsFile == "") {
        std::cerr << "either --v1 or --v2 ortholog assigment must be supplied\n";
        die = true;
    }
    
    if (argc - optind < 1) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 2)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (opt::out != "") opt::out = "_" + opt::out;
    
    if (die) {
        std::cout << "\n" << LINKGN_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::gpFile = argv[optind++];
    if (argc - optind >= 1) {
        opt::ensGeneFile = argv[optind++];
    }
    
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movq %rsi, %rbp
leaq 0x441ce(%rip), %rdx     # 0xe4c95
leaq 0x696d2(%rip), %rcx     # 0x10a1a0
movq $0x0, 0x10(%rsp)
movl %edi, 0xc(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xa0b18
leaq 0x6c0be(%rip), %rdi     # 0x10cbb8
leaq 0x3117e(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0xa0c81
movq 0x10(%rsp), %r12
jmp 0xa0cb8
leaq 0x28(%rsp), %rbx
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0x6a449(%rip), %rax     # 0x10af80
movq (%rax), %r13
testq %r13, %r13
leaq 0x3113b(%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 0xa0b8b
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x3e, %r14d
jg 0xa0bb7
cmpl $0x3, %r14d
ja 0xa0c0f
movl %r14d, %eax
leaq 0x43e7b(%rip), %rcx     # 0xe4a20
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
jmpq *%rax
leaq 0x6c003(%rip), %rsi     # 0x10cbb8
jmp 0xa0c07
cmpl $0x6e, %r14d
jle 0xa0bd2
cmpl $0x6f, %r14d
je 0xa0bf7
leaq 0x6c08e(%rip), %rsi     # 0x10cc58
cmpl $0x73, %r14d
je 0xa0c07
jmp 0xa0c0f
cmpl $0x3f, %r14d
jne 0xa0c61
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0xa0c0f
movb $0x1, 0x6c0ac(%rip)     # 0x10cc98
jmp 0xa0c0f
leaq 0x6c083(%rip), %rsi     # 0x10cc78
jmp 0xa0c07
leaq 0x6c01a(%rip), %rsi     # 0x10cc18
jmp 0xa0c07
leaq 0x6c031(%rip), %rsi     # 0x10cc38
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0x6a37f(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl 0xc(%rsp), %edi
movq %rbp, %rsi
leaq 0x4405c(%rip), %rdx     # 0xe4c95
leaq 0x69560(%rip), %rcx     # 0x10a1a0
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xa0b30
jmp 0xa0af3
cmpl $0x68, %r14d
jne 0xa0c0f
movq 0x6a34a(%rip), %rdi     # 0x10afb8
leaq 0x4404e(%rip), %rsi     # 0xe4cc3
callq 0x8460
xorl %edi, %edi
callq 0x8530
leaq 0x6bfb0(%rip), %rdi     # 0x10cc38
leaq 0x30ff0(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
movq 0x10(%rsp), %r12
jne 0xa0cb8
movq 0x6a344(%rip), %rdi     # 0x10afe8
leaq 0x43fa8(%rip), %rsi     # 0xe4c53
movl $0x38, %edx
callq 0x84e0
movb $0x1, %r12b
movq 0x6a301(%rip), %rbx     # 0x10afc0
movl 0xc(%rsp), %eax
subl (%rbx), %eax
jle 0xa0ce1
cmpl $0x3, %eax
jl 0xa0cfc
movq 0x6a315(%rip), %rdi     # 0x10afe8
leaq 0x2d4eb(%rip), %rsi     # 0xce1c5
movl $0x13, %edx
jmp 0xa0cf4
movq 0x6a300(%rip), %rdi     # 0x10afe8
leaq 0x2d4c3(%rip), %rsi     # 0xce1b2
movl $0x12, %edx
callq 0x84e0
movb $0x1, %r12b
leaq 0x6bf15(%rip), %rdi     # 0x10cc18
leaq 0x30f75(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0xa0d56
leaq 0x3a822(%rip), %rsi     # 0xdb53c
leaq 0x6bef7(%rip), %r14     # 0x10cc18
leaq 0x38(%rsp), %r15
movq %r15, %rdi
movq %r14, %rdx
callq 0x77abc
movq %r14, %rdi
movq %r15, %rsi
callq 0x8540
movq (%r15), %rdi
leaq 0x48(%rsp), %rax
cmpq %rax, %rdi
je 0xa0d56
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
testb $0x1, %r12b
jne 0xa0de4
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%rbp,%rax,8), %r14
movq 0x6be2c(%rip), %r15     # 0x10cba0
leaq 0x6be1d(%rip), %r12     # 0x10cb98
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
cmpl 0xc(%rsp), %eax
jge 0xa0dd2
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%rbp,%rax,8), %rbx
movq 0x6be30(%rip), %r14     # 0x10cbe0
leaq 0x6be21(%rip), %r15     # 0x10cbd8
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 0x6a1cd(%rip), %rdi     # 0x10afb8
leaq 0x2b88b(%rip), %rsi     # 0xcc67d
callq 0x8460
leaq 0x43ec5(%rip), %rsi     # 0xe4cc3
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0xa0e12
movq %rax, %r14
movq 0x6a17c(%rip), %rsi     # 0x10af98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0xa0e54
movq %rax, %r14
jmp 0xa0e54
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0xa0e54
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840