cusbf::DnaAlphabet Struct Reference

An alphabet for encoding DNA sequences, consisting of the symbols A, C, G, and T. More...

Static Public Member Functions
constexpr __host__ __device__ static __forceinline__ uint8_t	encode (const char *input)
	Maps one byte to a 2-bit symbol index, or invalidSymbol.

Static Public Attributes
static constexpr uint64_t	symbolWidth = 1
	Input bytes per encoded symbol.
static constexpr uint64_t	symbolCount = 4
	Number of valid symbols (A, C, G, T).
static constexpr uint8_t	invalidSymbol = 0xFFu
	Sentinel returned by encode for invalid input bytes.
static constexpr uint8_t	separator = 'N'
	Byte value used between concatenated records (must not encode as a valid symbol).
static constexpr char	validBytes [] = "ACGT"
	Representative valid bytes for compile-time separator checks.

Detailed Description

An alphabet for encoding DNA sequences, consisting of the symbols A, C, G, and T.

Each symbol is encoded as a 2-bit value: A=0, C=1, T=2, G=3. Invalid bytes are encoded as 0xFF.

Definition at line 113 of file Alphabet.cuh.

Member Function Documentation

encode()

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

inlinestaticconstexpr

Maps one byte to a 2-bit symbol index, or invalidSymbol.

Accepts A/C/G/T in either case.

Parameters

input

Pointer to one raw byte.

Definition at line 132 of file Alphabet.cuh.

      {
        const auto byte = static_cast<uint8_t>(input[0]);
        const uint8_t upper = byte & 0xDFu;   // force upper for validation only
        const uint8_t x = (byte >> 1u) & 3u;  // A=0, C=1, T=2, G=3
        const uint8_t valid = (upper == 'A') | (upper == 'C') | (upper == 'G') | (upper == 'T');
        const uint8_t mask = -valid;
        return (x & mask) | (invalidSymbol & ~mask);
    }

Here is the caller graph for this function:

Member Data Documentation

invalidSymbol

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

staticconstexpr

Sentinel returned by encode for invalid input bytes.

Definition at line 119 of file Alphabet.cuh.

separator

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

staticconstexpr

Byte value used between concatenated records (must not encode as a valid symbol).

Definition at line 121 of file Alphabet.cuh.

symbolCount

constexpr uint64_t cusbf::DnaAlphabet::symbolCount = 4

staticconstexpr

Number of valid symbols (A, C, G, T).

Definition at line 117 of file Alphabet.cuh.

symbolWidth

constexpr uint64_t cusbf::DnaAlphabet::symbolWidth = 1

staticconstexpr

Input bytes per encoded symbol.

Definition at line 115 of file Alphabet.cuh.

validBytes

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

staticconstexpr

Representative valid bytes for compile-time separator checks.

Definition at line 123 of file Alphabet.cuh.

---

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

• Alphabet.cuh