cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ > Struct Template Reference

Compile-time configuration for a cusbf::Filter. More...

Public Types
using	Alphabet = Alphabet_

Static Public Attributes
static constexpr uint16_t	k = K_
static constexpr uint16_t	m = M_
static constexpr uint16_t	s = S_
static constexpr uint64_t	hashCount = HashCount_
static constexpr uint64_t	alphabetSize = Alphabet::symbolCount
static constexpr uint64_t	symbolWidth = Alphabet::symbolWidth
static constexpr uint64_t	symbolBits = cuda::std::bit_width(alphabetSize - 1)
static constexpr uint64_t	symbolMask = (uint64_t{1} << symbolBits) - 1
static constexpr uint64_t	filterBlockBits = 256
static constexpr uint64_t	cudaBlockSize = CudaBlockSize_
static constexpr uint64_t	wordBits = 64
static constexpr uint64_t	blockWordCount = filterBlockBits / wordBits
static constexpr uint64_t	minimizerSpan = k - m + 1
static constexpr uint64_t	findereSpan = k - s + 1
static constexpr uint64_t	insertGroupSize = blockWordCount
static constexpr uint64_t	queryGroupSize = 1
static constexpr uint64_t	maxRunKmers = cudaBlockSize

Detailed Description

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>
struct cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >

Compile-time configuration for a cusbf::Filter.

All filter behaviour (k-mer length, minimizer width, s-mer width, hash count, CUDA block size, and alphabet) is encoded in this struct so that separate configurations produce completely independent Filter types with zero run-time overhead.

Template Parameters

K_	k-mer length (1-32).
S_	s-mer width used as the Bloom hash seed (1-k).
M_	minimizer width used for shard selection (1-k).
HashCount_	number of independent Bloom hash functions (1-16, default 4).
CudaBlockSize_	CUDA threads per block (multiple of 32, default 256).
Alphabet_	byte-to-symbol alphabet encoding.

Definition at line 60 of file BloomFilter.cuh.

Member Typedef Documentation

Alphabet

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

using cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::Alphabet = Alphabet_

Definition at line 61 of file BloomFilter.cuh.

Member Data Documentation

alphabetSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::alphabetSize = Alphabet::symbolCount

staticconstexpr

Definition at line 67 of file BloomFilter.cuh.

blockWordCount

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::blockWordCount = filterBlockBits / wordBits

staticconstexpr

Definition at line 75 of file BloomFilter.cuh.

cudaBlockSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::cudaBlockSize = CudaBlockSize_

staticconstexpr

Definition at line 72 of file BloomFilter.cuh.

filterBlockBits

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::filterBlockBits = 256

staticconstexpr

Definition at line 71 of file BloomFilter.cuh.

findereSpan

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::findereSpan = k - s + 1

staticconstexpr

Definition at line 77 of file BloomFilter.cuh.

hashCount

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::hashCount = HashCount_

staticconstexpr

Definition at line 66 of file BloomFilter.cuh.

insertGroupSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::insertGroupSize = blockWordCount

staticconstexpr

Definition at line 78 of file BloomFilter.cuh.

k

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint16_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::k = K_

staticconstexpr

Definition at line 63 of file BloomFilter.cuh.

m

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint16_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::m = M_

staticconstexpr

Definition at line 64 of file BloomFilter.cuh.

maxRunKmers

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::maxRunKmers = cudaBlockSize

staticconstexpr

Definition at line 80 of file BloomFilter.cuh.

minimizerSpan

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::minimizerSpan = k - m + 1

staticconstexpr

Definition at line 76 of file BloomFilter.cuh.

queryGroupSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::queryGroupSize = 1

staticconstexpr

Definition at line 79 of file BloomFilter.cuh.

s

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint16_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::s = S_

staticconstexpr

Definition at line 65 of file BloomFilter.cuh.

symbolBits

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::symbolBits = cuda::std::bit_width(alphabetSize - 1)

staticconstexpr

Definition at line 69 of file BloomFilter.cuh.

symbolMask

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::symbolMask = (uint64_t{1} << symbolBits) - 1

staticconstexpr

Definition at line 70 of file BloomFilter.cuh.

symbolWidth

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::symbolWidth = Alphabet::symbolWidth

staticconstexpr

Definition at line 68 of file BloomFilter.cuh.

wordBits

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::wordBits = 64

staticconstexpr

Definition at line 74 of file BloomFilter.cuh.

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

• BloomFilter.cuh