// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/evo_permute_codons.cpp
// Function: parsePermuteCodonsOptions(int, char**)
void parsePermuteCodonsOptions(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 'p': arg >> opt::ploidy; break;
            case 'l': arg >> opt::alignmentListFile; break;
            case 'h':
                std::cout << PERMUTE_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (opt::alignmentListFile == "") {
        std::cerr << "The -l option must be specified\n";
        die = true;
    }
    
    
    if (opt::ploidy != 'h' && opt::ploidy != 'd') {
        std::cerr << "The -p (--ploidy) option can only have the values 'h' or 'd'\n";
        std::cerr << "At the moment I don't support other than haploid and diploid species\n";
        die = true;
    }
    
    if (argc - optind < 0) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 0)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << PERMUTE_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movq %rsi, %r14
movl %edi, %ebx
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r13
leaq 0x38(%rsp), %r15
pushq $0x8
popq %r12
movl %ebx, %edi
movq %r14, %rsi
leaq 0x6a2dc(%rip), %rdx     # 0x967c3
leaq 0xae222(%rip), %rcx     # 0xda710
xorl %r8d, %r8d
callq 0x8790
movl %eax, %ebp
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x2c594
movq 0xb0a83(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x6d905(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r13, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r15, %rdi
movq %r13, %rsi
movl %r12d, %edx
callq 0x87e0
movsbl %bpl, %ebp
movq %r13, %rdi
callq 0x8978
cmpl $0x3f, %ebp
je 0x2c56f
cmpl $0x6c, %ebp
je 0x2c578
cmpl $0x70, %ebp
je 0x2c55e
cmpl $0x68, %ebp
jne 0x2c587
jmp 0x2c621
movq %r15, %rdi
leaq 0xb0f94(%rip), %rsi     # 0xdd4fc
callq 0x85c0
jmp 0x2c587
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x2c587
movq %r15, %rdi
leaq 0xb1366(%rip), %rsi     # 0xdd8e8
callq 0x8570
movq %r15, %rdi
callq 0x8220
jmp 0x2c4db
leaq 0xb134d(%rip), %rdi     # 0xdd8e8
leaq 0x6d87d(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
movq 0x10(%rsp), %rcx
je 0x2c5c5
movq 0xb0a31(%rip), %rdi     # 0xdcfe8
leaq 0x6a158(%rip), %rsi     # 0x96716
callq 0x8480
movb $0x1, %cl
movzbl 0xb0f30(%rip), %eax     # 0xdd4fc
cmpl $0x64, %eax
je 0x2c5fd
cmpl $0x68, %eax
je 0x2c5fd
movq 0xb0a0b(%rip), %r14     # 0xdcfe8
leaq 0x6a153(%rip), %rsi     # 0x96737
movq %r14, %rdi
callq 0x8480
leaq 0x6a182(%rip), %rsi     # 0x96775
movq %r14, %rdi
callq 0x8480
movb $0x1, %cl
movq 0xb09bc(%rip), %rax     # 0xdcfc0
cmpl %ebx, (%rax)
jg 0x2c63b
jne 0x2c644
testb $0x1, %cl
jne 0x2c657
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xb0990(%rip), %rdi     # 0xdcfb8
leaq 0x6a1b2(%rip), %rsi     # 0x967e1
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x69ce0(%rip), %rsi     # 0x96322
jmp 0x2c64b
leaq 0x69cea(%rip), %rsi     # 0x96335
movq 0xb0996(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0xb095a(%rip), %rdi     # 0xdcfb8
leaq 0x672e8(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x6a170(%rip), %rsi     # 0x967e1
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x2c683
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x2c6a4
movq %rax, %rbx
jmp 0x2c6a4
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870