// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_coding_sequences.cpp
// Function: parseGetCodingSeqOptions(int, char**)
void parseGetCodingSeqOptions(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 'n': opt::bIsCoding = false; break;
            case 'p': opt::bUsePartial = true; break;
            case 'H': arg >> opt::hetTreatment; break;
            case 's': arg >> opt::sampleNameFile; break;
            case OPT_ONLY_STATS: opt::bNoStats = true; break;
            case OPT_NONDIV_THREE: arg >> opt::nonDivPrefix; break;
            case 'h':
                std::cout << CODINGSEQ_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (!opt::bIsCoding && opt::bUsePartial) {
        std::cerr << "The -n and -p options are not compatible\n";
        die = true;
    }
    
    if (opt::hetTreatment != 'r' && opt::hetTreatment != 'p' && opt::hetTreatment != 'b' && opt::hetTreatment != 'i') {
        std::cerr << "The -H (--het-treatment) option can only have the values 'r', 'p', 'b', or 'i'\n";
        die = true;
    }
    
    if (argc - optind < 3) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 3)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << CODINGSEQ_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::genomeFile = argv[optind++];
    opt::geneFile = 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), %r13
pushq $0x8
popq %r14
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x4d6b4(%rip), %rdx     # 0xa4c81
leaq 0x843cc(%rip), %rcx     # 0xdb9a0
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r15d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x576b8
movq 0x8599c(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x4281e(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r13, %rdi
movq %r12, %rsi
movl %r14d, %edx
callq 0x87e0
movsbl %r15b, %r15d
movq %r12, %rdi
callq 0x8978
testl %r15d, %r15d
je 0x5768a
cmpl $0x1, %r15d
je 0x5769c
cmpl $0x3f, %r15d
je 0x57693
cmpl $0x48, %r15d
je 0x57667
cmpl $0x6e, %r15d
je 0x57678
cmpl $0x70, %r15d
je 0x57681
leaq 0x86fda(%rip), %rsi     # 0xde630
cmpl $0x73, %r15d
je 0x576a3
cmpl $0x68, %r15d
jne 0x576ab
jmp 0x577a0
movq %r13, %rdi
leaq 0x85f37(%rip), %rsi     # 0xdd5a8
callq 0x85c0
jmp 0x576ab
movb $0x1, 0x86fd1(%rip)     # 0xde650
jmp 0x576ab
movb $0x1, 0x86fc9(%rip)     # 0xde651
jmp 0x576ab
movb $0x1, 0x86fc1(%rip)     # 0xde652
jmp 0x576ab
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x576ab
leaq 0x86f6d(%rip), %rsi     # 0xde610
movq %r13, %rdi
callq 0x8570
movq %r13, %rdi
callq 0x8220
jmp 0x575c1
cmpb $0x0, 0x86f91(%rip)     # 0xde650
je 0x576e6
cmpb $0x1, 0x86f89(%rip)     # 0xde651
movq 0x10(%rsp), %rdx
jne 0x576eb
movq 0x85912(%rip), %rdi     # 0xdcfe8
leaq 0x4d326(%rip), %rsi     # 0xa4a03
callq 0x8480
movb $0x1, %dl
jmp 0x576eb
movq 0x10(%rsp), %rdx
movzbl 0x85eb6(%rip), %eax     # 0xdd5a8
addl $-0x62, %eax
cmpl $0x10, %eax
ja 0x57786
movl $0x14081, %ecx          # imm = 0x14081
btl %eax, %ecx
jae 0x57786
movq 0x858b1(%rip), %r14     # 0xdcfc0
movslq (%r14), %rax
subl %eax, %ebp
cmpl $0x3, %ebp
jl 0x577ba
jne 0x577c3
testb $0x1, %dl
jne 0x577d6
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x86e73(%rip), %rdi     # 0xde5b0
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x86e7a(%rip), %rdi     # 0xde5d0
callq 0x88f0
movslq (%r14), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%r14)
movq (%rbx,%rax,8), %rsi
leaq 0x86e81(%rip), %rdi     # 0xde5f0
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x8585b(%rip), %rdi     # 0xdcfe8
leaq 0x4c02a(%rip), %rsi     # 0xa37be
callq 0x8480
movb $0x1, %dl
jmp 0x57708
movq 0x85811(%rip), %rdi     # 0xdcfb8
leaq 0x4d4ed(%rip), %rsi     # 0xa4c9b
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x3eb61(%rip), %rsi     # 0x96322
jmp 0x577ca
leaq 0x3eb6b(%rip), %rsi     # 0x96335
movq 0x85817(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0x857db(%rip), %rdi     # 0xdcfb8
leaq 0x3c169(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x4d4ab(%rip), %rsi     # 0xa4c9b
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x57802
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x57823
movq %rax, %rbx
jmp 0x57823
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870