Struct ReaderBuilder 

pub struct ReaderBuilder { /* private fields */ }

Configuration for a FastxReader.

use fastx::{Format, ReaderBuilder};

let data = b">a\nACGT\n";
let mut reader = ReaderBuilder::new()
    .format(Format::Fasta)
    .buffer_size(64 * 1024)
    .build(&data[..]);
assert_eq!(reader.next().unwrap()?.id, "a");

Implementations

impl ReaderBuilder

pub fn new() -> ReaderBuilder

A builder with default settings.

pub fn format(self, format: Format) -> Self

Force a format instead of detecting it.

pub fn buffer_size(self, bytes: usize) -> Self

Size of the internal read buffer, in bytes.

pub fn quality_encoding(self, encoding: QualityEncoding) -> Self

The quality encoding of the input.

Old Illumina 1.3–1.7 files are Phred+64. Set this and the reader will convert quality strings to Phred+33 as it parses, so every Sequence this crate produces uses one encoding.

use fastx::{qual::QualityEncoding, ReaderBuilder};

// 'h' is Q40 in Phred+64.
let data = b"@old\nACGT\n+\nhhhh\n";
let record = ReaderBuilder::new()
    .quality_encoding(QualityEncoding::Phred64)
    .build(&data[..])
    .read_record()?
    .unwrap();

assert_eq!(record.quality.as_deref(), Some(&b"IIII"[..])); // now Phred+33
assert_eq!(record.mean_quality(), Some(40.0));

pub fn max_line_length(self, bytes: usize) -> Self

Refuse lines longer than bytes instead of growing the buffer.

Unlimited by default, because a chromosome legitimately arrives on a single line. Set it when reading files you do not control: without a limit, one unterminated line can grow the buffer until the process is killed.

pub fn max_record_length(self, bytes: usize) -> Self

Refuse records whose sequence exceeds bytes.

Unlimited by default. This bounds a record assembled from many short lines, which max_line_length alone does not catch.

pub fn build<R: Read>(&self, inner: R) -> FastxReader<R>

Build a reader around any Read.

pub fn open<P: AsRef<Path>>( &self, path: P, ) -> Result<FastxReader<Box<dyn Read + Send>>>

Open a path, transparently decompressing gzip and inferring the format.

Trait Implementations

impl Clone for ReaderBuilder

fn clone(&self) -> ReaderBuilder

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ReaderBuilder

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

Formats the value using the given formatter.

impl Default for ReaderBuilder

fn default() -> Self

Returns the “default value” for a type.