// File: /workspace/github_cpp_makefile_star2_O3/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 0x3d2c1(%rip), %rdx     # 0xdd285
leaq 0x611d5(%rip), %rcx     # 0x1011a0
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 0xa0015
leaq 0x63bd1(%rip), %rdi     # 0x103bc8
leaq 0x2d9cd(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0xa017e
movq 0x10(%rsp), %r12
jmp 0xa01b5
leaq 0x28(%rsp), %rbx
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0x61f4c(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x2d98a(%rip), %rax     # 0xcd9cb
cmoveq %rax, %r13
movq %rbx, 0x18(%rsp)
movq %r13, %rdi
callq 0x81f0
leaq (%rax,%r13), %rdx
movq %r15, %rdi
movq %r13, %rsi
callq 0x28a52
movq %r12, %rdi
movq %r15, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0xa0088
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x3e, %r14d
jg 0xa00b4
cmpl $0x3, %r14d
ja 0xa010c
movl %r14d, %eax
leaq 0x3cf6e(%rip), %rcx     # 0xdd010
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
jmpq *%rax
leaq 0x63b16(%rip), %rsi     # 0x103bc8
jmp 0xa0104
cmpl $0x6e, %r14d
jle 0xa00cf
cmpl $0x6f, %r14d
je 0xa00f4
leaq 0x63ba1(%rip), %rsi     # 0x103c68
cmpl $0x73, %r14d
je 0xa0104
jmp 0xa010c
cmpl $0x3f, %r14d
jne 0xa015e
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0xa010c
movb $0x1, 0x63bbf(%rip)     # 0x103ca8
jmp 0xa010c
leaq 0x63b96(%rip), %rsi     # 0x103c88
jmp 0xa0104
leaq 0x63b2d(%rip), %rsi     # 0x103c28
jmp 0xa0104
leaq 0x63b44(%rip), %rsi     # 0x103c48
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0x61e82(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl 0xc(%rsp), %edi
movq %rbp, %rsi
leaq 0x3d14f(%rip), %rdx     # 0xdd285
leaq 0x61063(%rip), %rcx     # 0x1011a0
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xa002d
jmp 0x9fff0
cmpl $0x68, %r14d
jne 0xa010c
movq 0x61e4d(%rip), %rdi     # 0x101fb8
leaq 0x3d141(%rip), %rsi     # 0xdd2b3
callq 0x8460
xorl %edi, %edi
callq 0x8530
leaq 0x63ac3(%rip), %rdi     # 0x103c48
leaq 0x2d83f(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
movq 0x10(%rsp), %r12
jne 0xa01b5
movq 0x61e47(%rip), %rdi     # 0x101fe8
leaq 0x3d09b(%rip), %rsi     # 0xdd243
movl $0x38, %edx
callq 0x84e0
movb $0x1, %r12b
movq 0x61e04(%rip), %rbx     # 0x101fc0
movl 0xc(%rsp), %eax
subl (%rbx), %eax
jle 0xa01de
cmpl $0x3, %eax
jb 0xa01f9
movq 0x61e18(%rip), %rdi     # 0x101fe8
leaq 0x2bd1e(%rip), %rsi     # 0xcbef5
movl $0x13, %edx
jmp 0xa01f1
movq 0x61e03(%rip), %rdi     # 0x101fe8
leaq 0x2bcf6(%rip), %rsi     # 0xcbee2
movl $0x12, %edx
callq 0x84e0
movb $0x1, %r12b
leaq 0x63a28(%rip), %rdi     # 0x103c28
leaq 0x2d7c4(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0xa0253
leaq 0x34e65(%rip), %rsi     # 0xd507c
leaq 0x63a0a(%rip), %r14     # 0x103c28
leaq 0x38(%rsp), %r15
movq %r15, %rdi
movq %r14, %rdx
callq 0x77736
movq %r14, %rdi
movq %r15, %rsi
callq 0x8540
movq (%r15), %rdi
leaq 0x48(%rsp), %rax
cmpq %rax, %rdi
je 0xa0253
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
testb $0x1, %r12b
jne 0xa02e1
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%rbp,%rax,8), %r14
movq 0x6393f(%rip), %r15     # 0x103bb0
leaq 0x63930(%rip), %r12     # 0x103ba8
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 0xa02cf
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%rbp,%rax,8), %rbx
movq 0x63943(%rip), %r14     # 0x103bf0
leaq 0x63934(%rip), %r15     # 0x103be8
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 0x61cd0(%rip), %rdi     # 0x101fb8
leaq 0x2b14e(%rip), %rsi     # 0xcb43d
callq 0x8460
leaq 0x3cfb8(%rip), %rsi     # 0xdd2b3
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0xa030f
movq %rax, %r14
movq 0x61c7f(%rip), %rsi     # 0x101f98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0xa0351
movq %rax, %r14
jmp 0xa0351
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0xa0351
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840