// File: /workspace/github_cpp_makefile_star2_O2/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, %rbx
movl %edi, %ebp
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r12
leaq 0x38(%rsp), %r14
leaq 0x36972(%rip), %r13     # 0xaccf0
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x36bdb(%rip), %rdx     # 0xacf65
leaq 0x65e2f(%rip), %rcx     # 0xdc1c0
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r15d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x76469
movq 0x66bdf(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x23a61(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r14, %rdi
movq %r12, %rsi
pushq $0x8
popq %rdx
callq 0x87e0
movsbl %r15b, %r15d
movq %r12, %rdi
callq 0x8978
cmpl $0x3, %r15d
jbe 0x76413
cmpl $0x3f, %r15d
je 0x7643b
cmpl $0x6f, %r15d
je 0x76444
leaq 0x6888e(%rip), %rsi     # 0xdec90
cmpl $0x73, %r15d
je 0x76454
cmpl $0x68, %r15d
jne 0x7645c
jmp 0x76586
movl %r15d, %eax
movslq (%r13,%rax,4), %rax
addq %r13, %rax
jmpq *%rax
leaq 0x687c9(%rip), %rsi     # 0xdebf0
jmp 0x76454
movb $0x1, 0x688a0(%rip)     # 0xdecd0
jmp 0x7645c
leaq 0x68877(%rip), %rsi     # 0xdecb0
jmp 0x76454
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x7645c
leaq 0x68805(%rip), %rsi     # 0xdec50
jmp 0x76454
leaq 0x6881c(%rip), %rsi     # 0xdec70
movq %r14, %rdi
callq 0x8570
movq %r14, %rdi
callq 0x8220
jmp 0x7637e
leaq 0x68780(%rip), %rdi     # 0xdebf0
leaq 0x239a8(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
je 0x764b4
leaq 0x687e9(%rip), %rdi     # 0xdec70
leaq 0x23991(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
movq 0x10(%rsp), %r13
je 0x764b9
movq 0x66b45(%rip), %rdi     # 0xdcfe8
leaq 0x36a79(%rip), %rsi     # 0xacf23
callq 0x8480
movb $0x1, %r13b
jmp 0x764b9
movq 0x10(%rsp), %r13
movq 0x66b00(%rip), %r12     # 0xdcfc0
movl %ebp, %eax
subl (%r12), %eax
jle 0x764d6
cmpl $0x3, %eax
jb 0x764ec
leaq 0x1fe61(%rip), %rsi     # 0x96335
jmp 0x764dd
leaq 0x1fe45(%rip), %rsi     # 0x96322
movq 0x66b04(%rip), %rdi     # 0xdcfe8
callq 0x8480
movb $0x1, %r13b
leaq 0x6875d(%rip), %rdi     # 0xdec50
leaq 0x23925(%rip), %rsi     # 0x99e1f
callq 0x2ea9b
testb %al, %al
je 0x76534
leaq 0x2d2b2(%rip), %rsi     # 0xa37bc
leaq 0x6873f(%rip), %r14     # 0xdec50
leaq 0x38(%rsp), %r15
movq %r15, %rdi
movq %r14, %rdx
callq 0x5b784
movq %r14, %rdi
movq %r15, %rsi
callq 0x8550
movq %r15, %rdi
callq 0x8978
testb $0x1, %r13b
jne 0x765a0
movslq (%r12), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r12)
movq (%rbx,%rax,8), %rsi
leaq 0x68680(%rip), %rdi     # 0xdebd0
callq 0x88f0
movslq (%r12), %rax
cmpl %ebp, %eax
jge 0x76574
leal 0x1(%rax), %ecx
movl %ecx, (%r12)
movq (%rbx,%rax,8), %rsi
leaq 0x686a1(%rip), %rdi     # 0xdec10
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x66a2b(%rip), %rdi     # 0xdcfb8
leaq 0x369ff(%rip), %rsi     # 0xacf93
callq 0x8480
xorl %edi, %edi
callq 0x8540
movq 0x66a11(%rip), %rdi     # 0xdcfb8
leaq 0x1d39f(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x369d9(%rip), %rsi     # 0xacf93
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x765cc
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x765ed
movq %rax, %rbx
jmp 0x765ed
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870