Struct ConsensusSequence 

pub struct ConsensusSequence { /* private fields */ }

Consensus sequence with per-base annotations.

This struct maintains parallel vectors for bases, quality scores, depths, and errors. All vectors are guaranteed to have the same length through the API.

Layout

Uses a Structure-of-Arrays layout for cache-friendly access:

• Sequential access to all bases is cache-efficient
• Sequential access to all qualities is cache-efficient
• etc.

Example

use fgumi_lib::consensus::ConsensusSequence;

let mut seq = ConsensusSequence::new();
seq.push(b'A', 30, 10, 0);
seq.push(b'C', 25, 8, 1);

assert_eq!(seq.len(), 2);
assert_eq!(seq.bases(), &[b'A', b'C']);
assert_eq!(seq.quals(), &[30, 25]);

Implementations

impl ConsensusSequence

pub fn new() -> ConsensusSequence

Creates a new empty consensus sequence.

pub fn with_capacity(capacity: usize) -> ConsensusSequence

Creates a new consensus sequence with the given capacity.

pub fn from_vecs( bases: Vec<u8>, quals: Vec<u8>, depths: Vec<u16>, errors: Vec<u16>, ) -> ConsensusSequence

Creates a consensus sequence from parallel vectors.

Panics

Panics if the vectors have different lengths.

pub fn len(&self) -> usize

Returns the length of the consensus sequence.

pub fn is_empty(&self) -> bool

Returns true if the consensus sequence is empty.

pub fn push(&mut self, base: u8, qual: u8, depth: u16, error: u16)

Appends a single base with its annotations.

pub fn extend(&mut self, other: &ConsensusSequence)

Extends this sequence with another.

pub fn clear(&mut self)

Clears all vectors.

pub fn bases(&self) -> &[u8]

Returns the consensus bases.

pub fn bases_mut(&mut self) -> &mut [u8]

Returns mutable access to the consensus bases.

Note

The caller should not change the length (slices prevent this anyway).

pub fn quals(&self) -> &[u8]

Returns the quality scores.

pub fn quals_mut(&mut self) -> &mut [u8]

Returns mutable access to the quality scores.

Note

The caller should not change the length (slices prevent this anyway).

pub fn depths(&self) -> &[u16]

Returns the per-base depths.

pub fn depths_mut(&mut self) -> &mut [u16]

Returns mutable access to the per-base depths.

Note

The caller should not change the length (slices prevent this anyway).

pub fn errors(&self) -> &[u16]

Returns the per-base error counts.

pub fn errors_mut(&mut self) -> &mut [u16]

Returns mutable access to the per-base error counts.

Note

The caller should not change the length (slices prevent this anyway).

pub fn max_depth(&self) -> u16

Returns the maximum depth across all positions.

pub fn min_depth(&self) -> u16

Returns the minimum depth across all positions.

pub fn error_rate(&self) -> f32

Returns the error rate (total errors / total depth).

pub fn into_vecs(self) -> (Vec<u8>, Vec<u8>, Vec<u16>, Vec<u16>)

Decomposes this sequence into its component vectors.

This is useful when the caller needs ownership of the vectors.

pub fn padded( &self, new_length: usize, left: bool, base: u8, qual: u8, ) -> ConsensusSequence

Pads the sequence to a new length by adding values to the left or right.

Arguments

• new_length - Target length (must be >= current length)
• left - If true, pad on the left side; otherwise pad on the right
• base - Base to use for padding (default: ‘n’)
• qual - Quality to use for padding (default: 2)

Panics

Panics if new_length < current length

Trait Implementations

impl Clone for ConsensusSequence

fn clone(&self) -> ConsensusSequence

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ConsensusSequence

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

Formats the value using the given formatter.

impl Default for ConsensusSequence

fn default() -> ConsensusSequence

Returns the “default value” for a type.