// File: /workspace/github_cpp_makefile_star2_O2/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
movl %edi, %ebx
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r13
leaq 0x38(%rsp), %r15
pushq $0x8
popq %rbp
movl %ebx, %edi
movq %r14, %rsi
leaq 0x65811(%rip), %rdx     # 0x99e7a
leaq 0xa6360(%rip), %rcx     # 0xda9d0
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r12d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x3472d
movq 0xa8900(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x65782(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r13, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r15, %rdi
movq %r13, %rsi
movl %ebp, %edx
callq 0x87e0
movsbl %r12b, %r12d
movq %r13, %rdi
callq 0x8978
testl %r12d, %r12d
je 0x34711
cmpl $0x1, %r12d
je 0x346f6
cmpl $0x3f, %r12d
je 0x346ff
cmpl $0x61, %r12d
je 0x34708
leaq 0xa95db(%rip), %rsi     # 0xddcc0
cmpl $0x6c, %r12d
je 0x34718
cmpl $0x68, %r12d
jne 0x34720
jmp 0x347e6
leaq 0xa9603(%rip), %rsi     # 0xddd00
jmp 0x34718
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x34720
leaq 0xa9591(%rip), %rsi     # 0xddca0
jmp 0x34718
leaq 0xa95c8(%rip), %rsi     # 0xddce0
movq %r15, %rdi
callq 0x8570
movq %r15, %rdi
callq 0x8220
jmp 0x3465d
leaq 0xa956c(%rip), %rdi     # 0xddca0
leaq 0x656e4(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
je 0x34778
leaq 0xa9575(%rip), %rdi     # 0xddcc0
leaq 0x656cd(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
movq 0x10(%rsp), %r14
je 0x3477d
movq 0xa8881(%rip), %rdi     # 0xdcfe8
leaq 0x656b2(%rip), %rsi     # 0x99e20
callq 0x8480
movb $0x1, %r14b
jmp 0x3477d
movq 0x10(%rsp), %r14
leaq 0xa951c(%rip), %rdi     # 0xddca0
leaq 0x65694(%rip), %rsi     # 0x99e1f
callq 0x2ea9b
testb %al, %al
je 0x347c1
leaq 0xa9525(%rip), %rdi     # 0xddcc0
leaq 0x6567d(%rip), %rsi     # 0x99e1f
callq 0x2ea9b
testb %al, %al
je 0x347c1
movq 0xa8836(%rip), %rdi     # 0xdcfe8
leaq 0x65692(%rip), %rsi     # 0x99e4b
callq 0x8480
movb $0x1, %r14b
movq 0xa87f8(%rip), %rax     # 0xdcfc0
cmpl %ebx, (%rax)
jg 0x34800
jne 0x34809
testb $0x1, %r14b
jne 0x3481c
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xa87cb(%rip), %rdi     # 0xdcfb8
leaq 0x65696(%rip), %rsi     # 0x99e8a
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x61b1b(%rip), %rsi     # 0x96322
jmp 0x34810
leaq 0x61b25(%rip), %rsi     # 0x96335
movq 0xa87d1(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0xa8795(%rip), %rdi     # 0xdcfb8
leaq 0x5f123(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x65654(%rip), %rsi     # 0x99e8a
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x34848
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x34869
movq %rax, %rbx
jmp 0x34869
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870
nop