Struct seqkmer::fasta::BufferFastaReader

pub struct BufferFastaReader<R>
where
    R: Read + Send,
{ /* private fields */ }

BufferFastaReader for reading FASTA format files with buffering.

Examples

use seqkmer::{BufferFastaReader, Reader};
use std::path::Path;

let path = Path::new("tests/data/test.fasta");
let mut reader = BufferFastaReader::from_path(path, 0)?;

while let Some(sequences) = reader.next()? {
    for sequence in sequences {
        println!("Sequence ID: {}", sequence.header.id);
        println!("Sequence length: {}", sequence.body.single().unwrap().len());
    }
}

Implementations

impl<R> BufferFastaReader<R>

where R: Read + Send,

pub fn new(reader: R, file_index: usize) -> Self

Creates a new BufferFastaReader with default capacity and batch size.

Examples

use seqkmer::BufferFastaReader;
use std::fs::File;

let file = File::open("tests/data/test.fasta")?;
let reader = BufferFastaReader::new(file, 0);

pub fn with_capacity( reader: R, file_index: usize, capacity: usize, batch_size: usize, ) -> Self

Creates a new BufferFastaReader with specified capacity and batch size.

Examples

use seqkmer::BufferFastaReader;
use std::fs::File;

let file = File::open("tests/data/test.fasta")?;
let reader = BufferFastaReader::with_capacity(file, 0, 4096, 50);

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

pub fn _next(&mut self) -> Result<Option<Base<Vec<u8>>>>

impl BufferFastaReader<Box<dyn Read + Send>>

pub fn from_path<P: AsRef<Path>>(path: P, file_index: usize) -> Result<Self>

Creates a new BufferFastaReader from a file path.

Examples

use seqkmer::BufferFastaReader;
use std::path::Path;

let path = Path::new("tests/data/test.fasta");
let reader = BufferFastaReader::from_path(path, 0)?;

Trait Implementations

impl<R: Read + Send> Reader for BufferFastaReader<R>

fn next(&mut self) -> Result<Option<Vec<Base<Vec<u8>>>>>