 typedef nvbio::lmem_cache_tag<CACHE_SIZE>                                       lmem_cache_tag_type;
 typedef nvbio::uncached_tag                                                     uncached_tag_type;
 
+enum { REF_BITS       = 2 };
+enum { REF_BIG_ENDIAN = false };
+
 //
 // An alignment stream class to be used in conjunction with the BatchAlignmentScore class
 //

    typedef nvbio::vector_view<pattern_iterator>                                                pattern_string;

    typedef nvbio::PackedStringLoader<base_iterator,
        io::FMIndexData::GENOME_BITS,
        io::FMIndexData::GENOME_BIG_ENDIAN,uncached_tag_type>                                   text_loader_type;
    typedef typename text_loader_type::iterator                                                 text_iterator;
    typedef nvbio::vector_view<text_iterator>                                                   text_string;


    typedef nvbio::vector_view<pattern_iterator>                                                pattern_string;

    typedef nvbio::PackedStringLoader<base_iterator,
        REF_BITS,
        REF_BIG_ENDIAN,uncached_tag_type>                                                       text_loader_type;
    typedef typename text_loader_type::iterator                                                 text_iterator;
    typedef nvbio::vector_view<text_iterator>                                                   text_string;

