Struct TwoBitSequence 

pub struct TwoBitSequence { /* private fields */ }

A DNA sequence stored in 2-bit packed representation.

Each byte holds 4 bases. The encoding is:

• A = 0b00
• C = 0b01
• G = 0b10
• T = 0b11

Bases are packed from the most significant bits: the first base occupies bits 7..6, the second bits 5..4, and so on.

Implementations

impl TwoBitSequence

pub fn encode(seq: &[u8]) -> Result<Self>

Encode an ASCII DNA sequence into 2-bit packed representation.

Only unambiguous bases (A, C, G, T) are supported. Case-insensitive.

Errors

Returns CyaneaError::InvalidInput if any base is not A, C, G, or T.

Example

use cyanea_seq::twobit::TwoBitSequence;

let seq = TwoBitSequence::encode(b"ACGT").unwrap();
assert_eq!(seq.len(), 4);
assert_eq!(seq.decode(), b"ACGT");

pub fn decode(&self) -> Vec<u8>

Decode back to ASCII DNA bytes.

Always produces uppercase A, C, G, T.

pub fn get(&self, index: usize) -> Option<u8>

Get the base at a specific position.

Returns None if index >= len.

pub fn len(&self) -> usize

Number of bases in the sequence.

pub fn is_empty(&self) -> bool

Whether the sequence is empty.

pub fn kmer(&self, pos: usize, k: usize) -> Option<u64>

Extract a k-mer starting at pos as an integer encoding.

Each base occupies 2 bits in the returned u64, with the first base in the most significant position. Maximum k is 32 (64 bits / 2 bits per base).

Returns None if pos + k > len or k > 32 or k == 0.

pub fn complement(&self) -> Self

Compute the bitwise complement (A<->T, C<->G).

In 2-bit encoding, complement is a simple XOR with 0b11:

• A (00) -> T (11)
• C (01) -> G (10)
• G (10) -> C (01)
• T (11) -> A (00)

Trait Implementations

impl Clone for TwoBitSequence

fn clone(&self) -> TwoBitSequence

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for TwoBitSequence

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

Formats the value using the given formatter.

impl PartialEq for TwoBitSequence

fn eq(&self, other: &TwoBitSequence) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Eq for TwoBitSequence

impl StructuralPartialEq for TwoBitSequence