khmer-core-design-kibbitzing.cpp

template<typename HasherType, typename StorageType>
class Sketch
{
protected:
    StorageType storage;

public:
    Sketch(size_t Wordsize, size_t table_size, size_t num_tables = 4);
    add(std::string& kmer);
    get(std::string& kmer);
    save(std::string& filename);
    load(std::string& filename);
};

template<typename HasherType, typename StorageType>
void consume_string(std::string& sequence, Sketch<HasherType, StorageType> sketch);

template<typename HasherType, typename StorageType, typename Parser>
void consume_seqfile(std::string& filename, Sketch<HasherType, StorageType> sketch);


template class Sketch<MurmurHasher, BitStorage>;
template class Sketch<MurmurHasher, ByteStorage>;
template class Sketch<MurmurHasher, NibbleStorage>;
template class Sketch<TwoBitHasher, BitStorage>;
template class Sketch<TwoBitHasher, ByteStorage>;
template class Sketch<TwoBitHasher, NibbleStorage>;

template void consume_string<MurmurHasher, BitStorage>;
template void consume_string<MurmurHasher, ByteStorage>;
template void consume_string<MurmurHasher, NibbleStorage>;
template void consume_string<TwoBitHasher, BitStorage>;
template void consume_string<TwoBitHasher, ByteStorage>;
template void consume_string<TwoBitHasher, NibbleStorage>;

template void consume_seqfile<MurmurHasher, BitStorage, FastxReader>;
template void consume_seqfile<MurmurHasher, ByteStorage, FastxReader>;
template void consume_seqfile<MurmurHasher, NibbleStorage, FastxReader>;
template void consume_seqfile<TwoBitHasher, BitStorage, FastxReader>;
template void consume_seqfile<TwoBitHasher, ByteStorage, FastxReader>;
template void consume_seqfile<TwoBitHasher, NibbleStorage, FastxReader>;
template void consume_seqfile<MurmurHasher, BitStorage, BamReader>;
template void consume_seqfile<MurmurHasher, ByteStorage, BamReader>;
template void consume_seqfile<MurmurHasher, NibbleStorage, BamReader>;
template void consume_seqfile<TwoBitHasher, BitStorage, BamReader>;
template void consume_seqfile<TwoBitHasher, ByteStorage, BamReader>;
template void consume_seqfile<TwoBitHasher, NibbleStorage, BamReader>;