Struct TwoBitExactCodec 

pub struct TwoBitExactCodec;

Exact 2-bit sequence encoding with sparse ambiguity sideband.

Canonical bases (A, C, G, T) are packed into 2 bits each via bitnuc with SIMD acceleration. Non-canonical IUPAC bases are stored in a sparse sideband for exact reconstruction.

On-disk layout per record:

[2-bit packed bases as le u64s]
[ambiguity_count: u32 le]
[positions: u32 le each]
[IUPAC bytes: u8 each]

Lowercase canonical bases are normalized to uppercase during encoding. Ambiguous bases preserve their original byte value.

Trait Implementations

impl Clone for TwoBitExactCodec

fn clone(&self) -> TwoBitExactCodec

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for TwoBitExactCodec

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for TwoBitExactCodec

fn default() -> TwoBitExactCodec

Returns the “default value” for a type.

impl SequenceCodec for TwoBitExactCodec

const TYPE_TAG: [u8; 16]

Stable type tag written into block headers.

const LOSSY: bool = false

Whether this encoding is lossy.

fn encode_into(sequence: &[u8], output: &mut Vec<u8>) -> Result<(), DryIceError>

Encode a raw ASCII nucleotide sequence, appending the encoded bytes directly into the provided output buffer.

fn decode_into( encoded: &[u8], original_len: usize, output: &mut Vec<u8>, ) -> Result<(), DryIceError>

Decode an encoded buffer, appending the decoded ASCII bytes directly into the provided output buffer.

const IS_IDENTITY: bool = false

Whether the encoded form is identical to the raw input bytes. When true, the decoder can skip decoding and return slices directly into the block’s payload buffer.

fn encode(sequence: &[u8]) -> Result<Vec<u8>, DryIceError>

Encode a sequence, returning a new allocated buffer.

fn decode(encoded: &[u8], original_len: usize) -> Result<Vec<u8>, DryIceError>

Decode an encoded buffer, returning a new allocated buffer.

impl Copy for TwoBitExactCodec