nvbio::mem Namespace Reference

Classes
struct	range_size
struct	rank_string_id
struct	rank_span_size
struct	mem_handler
struct	mem_functor
struct	right_mem_functor
struct	split_mem_functor
struct	left_mem_functor
struct	filter_results
struct	locate_ssa_results
struct	lookup_ssa_results

Functions
template<typename pattern_type , typename fm_index_type , typename output_vector >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	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	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	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	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	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	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	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)

Function Documentation

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
	)

Definition at line 1092 of file mem_inl.h.

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
	)

Definition at line 1053 of file mem_inl.h.

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
	)

Definition at line 981 of file mem_inl.h.

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
	)

Definition at line 1126 of file mem_inl.h.

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
	)

Definition at line 1144 of file mem_inl.h.

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
	)

Definition at line 1111 of file mem_inl.h.

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
	)

Definition at line 483 of file mem_inl.h.