mem_inl.h File Reference

Go to the source code of this file.

Classes
struct	nvbio::mem::range_size< rank_type >
struct	nvbio::mem::rank_string_id< rank_type >
struct	nvbio::mem::rank_span_size< rank_type >
struct	nvbio::mem::mem_handler< coord_type >
struct	nvbio::mem::mem_functor< index_type, string_set_type >
struct	nvbio::mem::right_mem_functor< index_type, string_set_type >
struct	nvbio::mem::split_mem_functor< index_type, string_set_type >
struct	nvbio::mem::left_mem_functor< index_type, string_set_type >
struct	nvbio::mem::filter_results< coord_type >
struct	nvbio::mem::locate_ssa_results< index_type >
struct	nvbio::mem::lookup_ssa_results< index_type >

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.
	nvbio::mem

Functions
template<typename pattern_type , typename fm_index_type , typename delegate_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::find_kmems (const uint32 pattern_len, const pattern_type pattern, const uint32 x, const fm_index_type f_index, const fm_index_type r_index, delegate_type &handler, const uint32 min_intv=1u, const uint32 min_span=1u)
template<typename pattern_type , typename fm_index_type , typename delegate_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::find_threshold_kmems (const uint32 pattern_len, const pattern_type pattern, const uint32 x, const fm_index_type f_index, const fm_index_type r_index, delegate_type &handler, const uint32 min_intv=1u, const uint32 min_span=1u)
template<typename pattern_type , typename fm_index_type , typename output_vector >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::mem::right_kmems (const uint32 pattern_len, const pattern_type pattern, const uint32 string_id, const uint32 x, const fm_index_type f_index, const fm_index_type r_index, output_vector &output, const uint32 min_intv)
template<typename rank_type >
__global__ void	nvbio::mem::discard_ranges_kernel (const uint32 n_items, VectorArrayView< rank_type > ranges, const uint32 max_intv, const uint32 min_span, const uint32 reverse)
template<typename rank_type >
void	nvbio::mem::discard_ranges (const device_tag system_tag, const uint32 n_items, DeviceVectorArray< rank_type > &ranges, const uint32 max_intv, const uint32 min_span, const bool reverse)
template<typename rank_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::mem::copy_ranges (const uint32 i, const VectorArrayView< rank_type > in_ranges, const uint32 *slots, vector_view< rank_type *, uint64 > out_ranges)
template<typename rank_type >
__global__ void	nvbio::mem::reorder_ranges_kernel (const uint32 n_items, const VectorArrayView< rank_type > in_ranges, const uint32 *slots, vector_view< rank_type *, uint64 > out_ranges)
template<typename rank_type >
void	nvbio::mem::reorder_ranges (const device_tag system_tag, const uint32 n_items, const VectorArrayView< rank_type > in_ranges, const uint32 *slots, vector_view< rank_type *, uint64 > out_ranges)
template<typename rank_type >
void	nvbio::mem::reorder_ranges (const host_tag system_tag, const uint32 n_items, const VectorArrayView< rank_type > in_ranges, const uint32 *slots, vector_view< rank_type *, uint64 > out_ranges)
template<typename system_tag , typename fm_index_type >
uint32	nvbio::string_batch_bound (const MEMFilter< system_tag, fm_index_type > &filter, const uint32 mem_count)