Struct Fasta 

pub struct Fasta { /* private fields */ }

A loaded FASTA reference with random-access sequence retrieval.

Wraps a noodles IndexedReader for efficient seek-based access. Contig metadata (names, lengths) is pre-computed from the .fai index at construction time.

Implementations

impl Fasta

pub fn from_path(path: &Path) -> Result<Self>

Open a FASTA file and its .fai index.

The .fai file must exist alongside the FASTA (e.g. ref.fa.fai).

Errors

Returns an error if the FASTA or its index cannot be read.

pub fn dict(&self) -> &SequenceDictionary

Return a reference to the underlying sequence dictionary.

pub fn load_contig( &mut self, contig_name: &str, rng: &mut impl Rng, ) -> Result<Vec<u8>>

Load and return the full sequence of contig_name.

Uses seek-based access via the FAI index for efficiency, avoiding the intermediate Record allocation that query() performs.

Bases are normalized during loading:

• A, C, G, T (case-insensitive) are stored as uppercase.
• U (RNA) is converted to T.
• Any other IUPAC ambiguity code (R, Y, S, W, K, M, B, D, H, V, N) is resolved to a uniformly-random base drawn from that code’s ambiguity set and stored in lowercase. The lowercase marker allows downstream sampling to detect and optionally reject reads that contain too many synthesized bases (see crate::fragment::lowercase_fraction).
• Any other byte is rejected with an error.

Passing the same rng state produces a deterministic resolution, so two runs seeded identically produce identical reference buffers.

Errors

Returns an error if the contig is unknown, the FASTA cannot be read, or the contig contains an unrecognized base.

pub fn contig_names(&self) -> Vec<&str>

Return contig names in index order.