dense_packed.cuh File Reference

#include <cuda/__cmath/ceil_div.h>
#include <cstdint>
#include <cusbf/config.cuh>
#include <cusbf/device_span.cuh>

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Classes
struct	cusbf::detail::DensePackedKmerInput< Config >
	Device-side view of a dense packed symbol sequence. More...

Namespaces
namespace	cusbf
namespace	cusbf::detail

Functions
template<typename Config >
constexpr uint64_t	cusbf::detail::dense_packed_symbols_per_word ()
	Encoded symbols stored in each uint64_t word for Config.
template<typename Config >
constexpr uint64_t	cusbf::detail::dense_packed_word_count (uint64_t num_symbols)
	Returns the number of uint64_t words required for num_symbols encoded symbols.
template<typename Config >
constexpr uint64_t	cusbf::detail::dense_packed_kmer_count (uint64_t num_symbols)
	Returns the number of k-mer windows in a dense packed symbol sequence.
template<typename Config >
__device__ __forceinline__ uint8_t	cusbf::detail::dense_packed_symbol_at (const uint64_t *words, uint64_t symbol_index)
	Decodes one packed symbol at global index symbol_index.
template<typename Config >
__device__ __forceinline__ uint8_t	cusbf::detail::dense_packed_symbol_at_local (const uint64_t *word_tile, uint64_t first_word_index, uint64_t symbol_index)
	Decodes one packed symbol from a block-local word tile.
template<typename Config >
__device__ __forceinline__ bool	cusbf::detail::prepare_dense_packed_tiles (const uint64_t *words, uint64_t block_start_kmer, uint64_t block_kmers, uint64_t *word_tile, uint8_t *sequence_tile)
	Fills sequence_tile with encoded symbols for k-mers starting at block_start_kmer.
template<typename Config >
__global__ void	cusbf::detail::pack_dense_sequence_kernel (const char *sequence, uint64_t num_symbols, uint64_t *words)
	Packs an encoded byte sequence into dense symbolBits-wide uint64_t words.