Struct MmapSequenceStore 

pub struct MmapSequenceStore { /* private fields */ }

A sequence store backed by memory-mapped FASTA files.

Only the digest index and metadata are held in RAM. Sequence bytes are read from the memory-mapped file on each request, with the OS managing page caching.

Requires a .refget.json digest cache for each FASTA file. Use refget-tools cache to generate them.

Implementations

impl MmapSequenceStore

pub fn new() -> Self

Create an empty store.

pub fn mark_circular(&mut self, circular_names: &[String])

Mark sequences with matching names as circular.

pub fn add_fasta<P: AsRef<Path>>( &mut self, path: P, ) -> StoreResult<Vec<FastaSequenceSummary>>

Add a FASTA file to the store via memory mapping.

Requires a fresh .refget.json digest cache. Returns an error if the cache is missing or stale.

Trait Implementations

impl Default for MmapSequenceStore

fn default() -> Self

Returns the “default value” for a type.

impl SequenceStore for MmapSequenceStore

fn get_sequence( &self, digest: &str, start: Option<u64>, end: Option<u64>, ) -> StoreResult<Option<Vec<u8>>>

Retrieve sequence bases by digest (MD5 or sha512t24u). Supports optional start/end for subsequence retrieval (0-based, half-open).

fn get_metadata(&self, digest: &str) -> StoreResult<Option<SequenceMetadata>>

Retrieve metadata for a sequence by digest.

fn get_length(&self, digest: &str) -> StoreResult<Option<u64>>

Retrieve the length of a sequence by digest.