 
     const uint32 batch_size = 16*1024*1024;
 
-    typedef QGramFilter<system_tag,qgram_index_type,const uint64*,const uint32*> qgram_filter_type;
-
     typedef typename qgram_filter_type::hit_type        hit_type;
     typedef typename qgram_filter_type::diagonal_type   diagonal_type;
 

    const genome_string         genome,
          Stats&                stats)
{
    const uint32 Q = qgram_index.Q;

    typedef typename qgram_index_type::system_tag system_tag;

    // prepare some vectors to store the query qgrams
    nvbio::vector<system_tag,uint64>  qgrams( n_queries );
    nvbio::vector<system_tag,uint64>  sorted_qgrams( n_queries );
    nvbio::vector<system_tag,uint32>  sorted_indices( n_queries );

    Timer timer;
    timer.start();

        occurrences(0),
        merged(0) {}

    float   time;
    float   build_time;
    float   extract_time;
    float   rank_time;
