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)
	Maps three DNA bytes to a 6-bit triplet index, or invalidSymbol.

Static Public Attributes
static constexpr uint64_t	symbolWidth = 3
	Input bytes per encoded symbol (one DNA triplet).
static constexpr uint64_t	symbolCount = 64
	Number of packed triplet symbols.
static constexpr uint8_t	invalidSymbol = 0xFFu
	Sentinel returned by encode for invalid triplets.
static constexpr uint8_t	separator = 'N'
	Separator byte between concatenated records.
static constexpr char	validBytes [] = "ACGT"
	Representative valid bytes for compile-time separator checks.

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 150 of file Alphabet.cuh.

Member Function Documentation

encode()

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

inlinestaticconstexpr

Maps three DNA bytes to a 6-bit triplet index, or invalidSymbol.

Parameters

input

Pointer to three raw bytes.

Definition at line 167 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

Sentinel returned by encode for invalid triplets.

Definition at line 156 of file Alphabet.cuh.

separator

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

staticconstexpr

Separator byte between concatenated records.

Definition at line 158 of file Alphabet.cuh.

symbolCount

constexpr uint64_t cusbf::DnaTripletAlphabet::symbolCount = 64

staticconstexpr

Number of packed triplet symbols.

Definition at line 154 of file Alphabet.cuh.

symbolWidth

constexpr uint64_t cusbf::DnaTripletAlphabet::symbolWidth = 3

staticconstexpr

Input bytes per encoded symbol (one DNA triplet).

Definition at line 152 of file Alphabet.cuh.

validBytes

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

staticconstexpr

Representative valid bytes for compile-time separator checks.

Definition at line 160 of file Alphabet.cuh.

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

• Alphabet.cuh