Struct IndexedFastaReader 

pub struct IndexedFastaReader<R> { /* private fields */ }

Seekable FASTA reader backed by a .fai index.

Implementations

impl<R: Read + Seek> IndexedFastaReader<R>

pub fn new(inner: R, index: FastaIndex) -> Self

Create a seekable FASTA reader from an input stream and index.

pub fn index(&self) -> &FastaIndex

Return the loaded FASTA index.

pub fn fetch_into( &mut self, name: &[u8], range: Range<u64>, out: &mut Vec<u8>, ) -> Result<()>

Fetch a zero-based half-open sequence range into out.

pub fn fetch(&mut self, name: &[u8], range: Range<u64>) -> Result<Vec<u8>>

Fetch a zero-based half-open sequence range into an owned buffer.

pub fn reference_chunks( &mut self, name: &[u8], range: Range<u64>, chunk_bases: u64, ) -> Result<FastaReferenceChunks<'_, R>>

Stream owned sequence chunks for one reference range.

chunk_bases values below 1 are raised to 1. Chunks are yielded as owned buffers so callers can move them to worker threads after each iterator step.

pub fn reference_chunks_into<S>( &mut self, name: &[u8], range: Range<u64>, chunk_bases: u64, out: &mut Vec<u8>, sink: &mut S, ) -> Result<()>

where S: FastaReferenceChunkSink,

Stream borrowed sequence chunks into a sink using caller-owned storage.

chunk_bases values below 1 are raised to 1. out is cleared and reused for each chunk, and the borrowed chunk passed to sink is valid only until the next sink call or until this method returns.

pub fn fetch_partition( &mut self, partition: &FastaPartition, ) -> Result<FastaReferenceChunk>

Fetch a planned partition into an owned reference chunk.

pub fn into_inner(self) -> (R, FastaIndex)

Return the wrapped reader and index.