// File: /workspace/github_cpp_makefile_star2_O3/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
movl %edi, %ebp
leaq 0x64d77(%rip), %rdx     # 0xd6745
leaq 0x8efab(%rip), %rcx     # 0x100980
movq $0x0, 0x8(%rsp)
movq %rsi, 0x10(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x71a39
cmpb $0x0, 0x91c1e(%rip)     # 0x103620
je 0x71baa
cmpb $0x1, 0x91c12(%rip)     # 0x103621
movq 0x8(%rsp), %rdx
jne 0x71baf
movq 0x905c7(%rip), %rdi     # 0x101fe8
leaq 0x64a9f(%rip), %rsi     # 0xd64c7
movl $0x29, %edx
callq 0x84e0
movb $0x1, %dl
jmp 0x71baf
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0x90528(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x5bf66(%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 0x71aac
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x67, %r14d
jg 0x71ad0
cmpl $0x3e, %r14d
jg 0x71af3
testl %r14d, %r14d
je 0x71b1f
cmpl $0x1, %r14d
jne 0x71b38
leaq 0x91b12(%rip), %rsi     # 0x1035e0
jmp 0x71ae9
cmpl $0x6f, %r14d
jle 0x71b10
cmpl $0x70, %r14d
je 0x71b31
leaq 0x91b1d(%rip), %rsi     # 0x103600
cmpl $0x73, %r14d
jne 0x71b38
movq %r12, %rdi
callq 0x8560
jmp 0x71b38
cmpl $0x3f, %r14d
je 0x71b28
cmpl $0x48, %r14d
jne 0x71b38
movq %r12, %rdi
leaq 0x90a6f(%rip), %rsi     # 0x102578
callq 0x85a0
jmp 0x71b38
cmpl $0x6e, %r14d
jne 0x71b8a
movb $0x1, 0x91b03(%rip)     # 0x103620
jmp 0x71b38
movb $0x1, 0x91afc(%rip)     # 0x103622
jmp 0x71b38
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x71b38
movb $0x1, 0x91ae9(%rip)     # 0x103621
movq %r12, %rdi
movq 0x90456(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x64be3(%rip), %rdx     # 0xd6745
leaq 0x8ee17(%rip), %rcx     # 0x100980
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x71a51
jmp 0x719fb
cmpl $0x68, %r14d
jne 0x71b38
movq 0x90421(%rip), %rdi     # 0x101fb8
leaq 0x64bc1(%rip), %rsi     # 0xd675f
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0x8(%rsp), %rdx
movzbl 0x909c2(%rip), %eax     # 0x102578
addl $-0x62, %eax
cmpl $0x10, %eax
ja 0x71caa
movl $0x14081, %ecx          # imm = 0x14081
btl %eax, %ecx
jae 0x71caa
movq 0x903e9(%rip), %rbx     # 0x101fc0
movslq (%rbx), %rax
subl %eax, %ebp
cmpl $0x3, %ebp
jl 0x71cc9
jne 0x71cd7
testb $0x1, %dl
jne 0x71cef
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %r13
movq (%r13,%rax,8), %r14
movq 0x9197e(%rip), %r15     # 0x103588
leaq 0x9196f(%rip), %r12     # 0x103580
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 (%r13,%rax,8), %r14
movq 0x91968(%rip), %r15     # 0x1035a8
leaq 0x91959(%rip), %r12     # 0x1035a0
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 (%r13,%rax,8), %rbx
movq 0x91952(%rip), %r14     # 0x1035c8
leaq 0x91943(%rip), %r15     # 0x1035c0
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 0x90337(%rip), %rdi     # 0x101fe8
leaq 0x633c6(%rip), %rsi     # 0xd507e
movl $0x4f, %edx
callq 0x84e0
movb $0x1, %dl
jmp 0x71bd0
leaq 0x5a212(%rip), %rsi     # 0xcbee2
movl $0x12, %edx
jmp 0x71ce3
leaq 0x5a217(%rip), %rsi     # 0xcbef5
movl $0x13, %edx
movq 0x902fe(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0x902c2(%rip), %rdi     # 0x101fb8
leaq 0x59740(%rip), %rsi     # 0xcb43d
callq 0x8460
leaq 0x64a56(%rip), %rsi     # 0xd675f
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x71d1d
movq %rax, %r14
movq 0x90271(%rip), %rsi     # 0x101f98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x71d5f
movq %rax, %r14
jmp 0x71d5f
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x71d5f
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840