// File: /workspace/github_cpp_makefile_star2_O1/millanek[P]evo/evo_protein_SegregatingSites.cpp
// Function: parseProteinSsOptions(int, char**)
void parseProteinSsOptions(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 'a': arg >> opt::alignmentFile; break;
            case 'l': arg >> opt::alignmentListFile; break;
            case OPT_NEW_LABELS: arg >> opt::newLabelFile; break;
            case OPT_FOLDER: arg >> opt::outFolder; break;
            case 'h':
                std::cout << DNATOPROTEIN_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (opt::alignmentFile == "" && opt::alignmentListFile == "") {
        std::cerr << "Either -a or -l options must be specified\n";
        die = true;
    }
    
    if (opt::alignmentFile != "" && opt::alignmentListFile != "") {
        std::cerr << "The -a and -l options can't both be specified\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" << DNATOPROTEIN_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
leaq 0x909ef(%rip), %rdx     # 0xd1cda
leaq 0xc76be(%rip), %rcx     # 0x1089b0
movq $0x0, 0x10(%rsp)
movl %edi, 0xc(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r15d
shll $0x18, %r15d
cmpl $0xff000000, %r15d      # imm = 0xFF000000
je 0x4143e
leaq 0x28(%rsp), %rbx
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r12
leaq 0x38(%rsp), %r13
movq 0xc9c46(%rip), %rax     # 0x10af80
movq (%rax), %rbp
testq %rbp, %rbp
leaq 0x90938(%rip), %rax     # 0xd1c7f
cmoveq %rax, %rbp
movq %rbx, 0x18(%rsp)
movq %rbp, %rdi
callq 0x81f0
leaq (%rax,%rbp), %rdx
movq %r12, %rdi
movq %rbp, %rsi
callq 0x28952
movq %r13, %rdi
movq %r12, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x4138e
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r15d
cmpl $0x60, %r15d
jg 0x413b2
testl %r15d, %r15d
je 0x413d0
cmpl $0x1, %r15d
je 0x413e2
cmpl $0x3f, %r15d
jne 0x413f1
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x413f1
cmpl $0x61, %r15d
je 0x413d9
leaq 0xca8c9(%rip), %rsi     # 0x10bc88
cmpl $0x6c, %r15d
je 0x413e9
cmpl $0x68, %r15d
jne 0x413f1
jmp 0x41531
leaq 0xca8d1(%rip), %rsi     # 0x10bca8
jmp 0x413e9
leaq 0xca888(%rip), %rsi     # 0x10bc68
jmp 0x413e9
leaq 0xca8df(%rip), %rsi     # 0x10bcc8
movq %r13, %rdi
callq 0x8560
movq %r13, %rdi
movq 0xc9b9d(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl 0xc(%rsp), %edi
movq %r14, %rsi
leaq 0x908bf(%rip), %rdx     # 0xd1cda
leaq 0xc758e(%rip), %rcx     # 0x1089b0
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r15d
shll $0x18, %r15d
cmpl $0xff000000, %r15d      # imm = 0xFF000000
jne 0x41333
leaq 0xca823(%rip), %rdi     # 0x10bc68
leaq 0x90833(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0x4145c
movq 0x10(%rsp), %rbx
jmp 0x41492
leaq 0xca825(%rip), %rdi     # 0x10bc88
leaq 0x90815(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
movq 0x10(%rsp), %rbx
jne 0x41492
movq 0xc9b69(%rip), %rdi     # 0x10afe8
leaq 0x907fa(%rip), %rsi     # 0xd1c80
movl $0x2a, %edx
callq 0x84e0
movb $0x1, %bl
leaq 0xca7cf(%rip), %rdi     # 0x10bc68
leaq 0x907df(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0x414da
leaq 0xca7d8(%rip), %rdi     # 0x10bc88
leaq 0x907c8(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0x414da
movq 0xc9b21(%rip), %rdi     # 0x10afe8
leaq 0x907dd(%rip), %rsi     # 0xd1cab
movl $0x2e, %edx
callq 0x84e0
movb $0x1, %bl
movq 0xc9adf(%rip), %rax     # 0x10afc0
movl 0xc(%rsp), %ecx
cmpl %ecx, (%rax)
jle 0x414fe
movq 0xc9af8(%rip), %rdi     # 0x10afe8
leaq 0x8ccbb(%rip), %rsi     # 0xce1b2
movl $0x12, %edx
jmp 0x41513
je 0x4151a
movq 0xc9ae1(%rip), %rdi     # 0x10afe8
leaq 0x8ccb7(%rip), %rsi     # 0xce1c5
movl $0x13, %edx
callq 0x84e0
movb $0x1, %bl
testb $0x1, %bl
jne 0x4154b
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xc9a80(%rip), %rdi     # 0x10afb8
leaq 0x907ab(%rip), %rsi     # 0xd1cea
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0xc9a66(%rip), %rdi     # 0x10afb8
leaq 0x8b124(%rip), %rsi     # 0xcc67d
callq 0x8460
leaq 0x90785(%rip), %rsi     # 0xd1cea
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x41579
movq %rax, %r14
movq 0xc9a15(%rip), %rsi     # 0x10af98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x415bb
movq %rax, %r14
jmp 0x415bb
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x415bb
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840
nop