cusbf::DnaTripletAlphabet Struct Reference

An alphabet that encodes non-overlapping DNA triplets as single symbols. More...

Static Public Member Functions
constexpr __host__ __device__ static __forceinline__ uint8_t	encode (const char *input)

Static Public Attributes
static constexpr uint64_t	symbolWidth = 3
static constexpr uint64_t	symbolCount = 64
static constexpr uint8_t	invalidSymbol = 0xFFu
static constexpr uint8_t	separator = 'N'
static constexpr char	validBytes [] = "ACGT"

Detailed Description

An alphabet that encodes non-overlapping DNA triplets as single symbols.

Each triplet is encoded as a 6-bit value. Invalid bytes in any triplet position produce invalidSymbol.

Definition at line 138 of file Alphabet.cuh.

Member Function Documentation

encode()

constexpr __host__ __device__ static __forceinline__ uint8_t cusbf::DnaTripletAlphabet::encode ( const char *  input )

inlinestaticconstexpr

Definition at line 145 of file Alphabet.cuh.

      {
        const uint8_t a = DnaAlphabet::encode(input + 0);
        const uint8_t b = DnaAlphabet::encode(input + 1);
        const uint8_t c = DnaAlphabet::encode(input + 2);
        const uint8_t valid = (a != invalidSymbol) & (b != invalidSymbol) & (c != invalidSymbol);
        const uint8_t packed = (a << 4u) | (b << 2u) | c;
        const uint8_t mask = -valid;
        return (packed & mask) | (invalidSymbol & ~mask);
    }

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Member Data Documentation

invalidSymbol

constexpr uint8_t cusbf::DnaTripletAlphabet::invalidSymbol = 0xFFu

staticconstexpr

Definition at line 141 of file Alphabet.cuh.

separator

constexpr uint8_t cusbf::DnaTripletAlphabet::separator = 'N'

staticconstexpr

Definition at line 142 of file Alphabet.cuh.

symbolCount

constexpr uint64_t cusbf::DnaTripletAlphabet::symbolCount = 64

staticconstexpr

Definition at line 140 of file Alphabet.cuh.

symbolWidth

constexpr uint64_t cusbf::DnaTripletAlphabet::symbolWidth = 3

staticconstexpr

Definition at line 139 of file Alphabet.cuh.

validBytes

constexpr char cusbf::DnaTripletAlphabet::validBytes[] = "ACGT"

staticconstexpr

Definition at line 143 of file Alphabet.cuh.

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

• Alphabet.cuh