// File: /workspace/github_cpp_makefile_star2_O3/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, %r15
leaq 0x8f653(%rip), %rdx     # 0xcda26
leaq 0xc14d6(%rip), %rcx     # 0xff8b0
movq $0x0, 0x10(%rsp)
movl %edi, 0xc(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0x3e526
leaq 0x28(%rsp), %rbx
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r12
leaq 0x38(%rsp), %r13
movq 0xc3b5e(%rip), %rax     # 0x101f80
movq (%rax), %rbp
testq %rbp, %rbp
leaq 0x8f59c(%rip), %rax     # 0xcd9cb
cmoveq %rax, %rbp
movq %rbx, 0x18(%rsp)
movq %rbp, %rdi
callq 0x81f0
leaq (%rax,%rbp), %rdx
movq %r12, %rdi
movq %rbp, %rsi
callq 0x28a52
movq %r13, %rdi
movq %r12, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3e476
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x60, %r14d
jg 0x3e49a
testl %r14d, %r14d
je 0x3e4b8
cmpl $0x1, %r14d
je 0x3e4ca
cmpl $0x3f, %r14d
jne 0x3e4d9
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x3e4d9
cmpl $0x61, %r14d
je 0x3e4c1
leaq 0xc47e9(%rip), %rsi     # 0x102c90
cmpl $0x6c, %r14d
je 0x3e4d1
cmpl $0x68, %r14d
jne 0x3e4d9
jmp 0x3e5ea
leaq 0xc47f1(%rip), %rsi     # 0x102cb0
jmp 0x3e4d1
leaq 0xc47a8(%rip), %rsi     # 0x102c70
jmp 0x3e4d1
leaq 0xc47ff(%rip), %rsi     # 0x102cd0
movq %r13, %rdi
callq 0x8560
movq %r13, %rdi
movq 0xc3ab5(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl 0xc(%rsp), %edi
movq %r15, %rsi
leaq 0x8f523(%rip), %rdx     # 0xcda26
leaq 0xc13a6(%rip), %rcx     # 0xff8b0
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x3e41b
leaq 0xc4743(%rip), %rdi     # 0x102c70
leaq 0x8f497(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0x3e544
movq 0x10(%rsp), %rbx
jmp 0x3e57a
leaq 0xc4745(%rip), %rdi     # 0x102c90
leaq 0x8f479(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
movq 0x10(%rsp), %rbx
jne 0x3e57a
movq 0xc3a81(%rip), %rdi     # 0x101fe8
leaq 0x8f45e(%rip), %rsi     # 0xcd9cc
movl $0x2a, %edx
callq 0x84e0
movb $0x1, %bl
leaq 0xc46ef(%rip), %rdi     # 0x102c70
leaq 0x8f443(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0x3e5c2
leaq 0xc46f8(%rip), %rdi     # 0x102c90
leaq 0x8f42c(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0x3e5c2
movq 0xc3a39(%rip), %rdi     # 0x101fe8
leaq 0x8f441(%rip), %rsi     # 0xcd9f7
movl $0x2e, %edx
callq 0x84e0
movb $0x1, %bl
movq 0xc39f7(%rip), %rax     # 0x101fc0
movl 0xc(%rsp), %ecx
cmpl %ecx, (%rax)
jg 0x3e604
jne 0x3e612
testb $0x1, %bl
jne 0x3e62a
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xc39c7(%rip), %rdi     # 0x101fb8
leaq 0x8f43e(%rip), %rsi     # 0xcda36
callq 0x8460
xorl %edi, %edi
callq 0x8530
leaq 0x8d8d7(%rip), %rsi     # 0xcbee2
movl $0x12, %edx
jmp 0x3e61e
leaq 0x8d8dc(%rip), %rsi     # 0xcbef5
movl $0x13, %edx
movq 0xc39c3(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0xc3987(%rip), %rdi     # 0x101fb8
leaq 0x8ce05(%rip), %rsi     # 0xcb43d
callq 0x8460
leaq 0x8f3f2(%rip), %rsi     # 0xcda36
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x3e658
movq %rax, %r14
movq 0xc3936(%rip), %rsi     # 0x101f98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x3e69a
movq %rax, %r14
jmp 0x3e69a
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3e69a
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840