Struct FastaReader 

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

Slab-style streaming FASTA reader over any Read input.

The reader accepts ordinary multiline FASTA. Header lines must begin with >, sequence lines are concatenated without newline bytes, and blank lines before the first record or between records are ignored.

Implementations

impl<R: Read> FastaReader<R>

pub fn new(reader: R) -> Self

Create a reader with FastaConfig::default.

pub fn with_config(reader: R, config: FastaConfig) -> Self

Create a reader with explicit configuration.

pub fn into_inner(self) -> R

Return the wrapped reader.

pub fn next_batch(&mut self) -> Result<Option<FastaBatch<'_>>>

Read the next batch of FASTA records.

Returns Ok(None) at EOF. A malformed non-empty line before the first header is reported as a format error.

pub fn next_owned_batch(&mut self) -> Result<Option<OwnedFastaBatch>>

Read the next FASTA batch into an owned transferable buffer.

pub fn visit_records<F>(&mut self, visit: F) -> Result<()>

where F: FnMut(FastaVisitRecord<'_>) -> Result<()>,

Visit every FASTA record in the stream.

This is a convenience path for single-pass consumers. It avoids the batch record and identifier side tables used by next_batch.

pub fn visit_records_with_sink<S>(&mut self, sink: &mut S) -> Result<()>

where S: FastaRecordSink,

Visit every FASTA record using a sink implementation.

pub fn stats(&mut self) -> Result<FastaStats>

Count all records and bases in an ordinary FASTA stream.

This uses the robust multiline FASTA parser, so it accepts wrapped sequence records and blank lines in the same way as next_batch.

Trait Implementations

impl<R: Debug> Debug for FastaReader<R>

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

Formats the value using the given formatter.