cusbf::detail::DensePackedKmerInput< Config > Struct Template Reference

Device-side view of a dense packed symbol sequence. More...

Collaboration diagram for cusbf::detail::DensePackedKmerInput< Config >:

Public Member Functions
constexpr __host__ __device__ uint64_t	kmerCount () const
	Number of k-mer windows in this sequence.

Public Attributes
device_span< const uint64_t >	words {}
	Dense packed words (device memory).
uint64_t	num_symbols {}
	Number of valid encoded symbols represented in words.

Detailed Description

template<typename Config>
struct cusbf::detail::DensePackedKmerInput< Config >

Device-side view of a dense packed symbol sequence.

Layout: word w holds symbols [S*w, S*w + S - 1] where S = dense_packed_symbols_per_word. Symbol i occupies bits [symbolBits*(i % S), symbolBits*(i % S) + symbolBits - 1] of word i/S (LSB = earlier symbol). Values use Config::Alphabet encoding masked with Config::symbolMask. Trailing bits in the final word beyond symbolBits*num_symbols are ignored.

Adjacent k-mers overlap in the same words; kernels decode a per-block symbol tile and slide packed k-mers like the byte SequenceKmerInput path.

Definition at line 44 of file dense_packed.cuh.

Member Function Documentation

kmerCount()

template<typename Config >

constexpr __host__ __device__ uint64_t cusbf::detail::DensePackedKmerInput< Config >::kmerCount ( ) const

inlineconstexpr

Number of k-mer windows in this sequence.

Definition at line 51 of file dense_packed.cuh.

                                                                           {
        return dense_packed_kmer_count<Config>(num_symbols);
    }

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Member Data Documentation

num_symbols

template<typename Config >

uint64_t cusbf::detail::DensePackedKmerInput< Config >::num_symbols {}

Number of valid encoded symbols represented in words.

Definition at line 48 of file dense_packed.cuh.

{};

words

template<typename Config >

device_span<const uint64_t> cusbf::detail::DensePackedKmerInput< Config >::words {}

Dense packed words (device memory).

Definition at line 46 of file dense_packed.cuh.

{};

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The documentation for this struct was generated from the following file:

• dense_packed.cuh