Struct Scanner 

pub struct Scanner {}

A FASTQ scanner.

Examples

use oxbow::sequence::format::fastq::Scanner;
use std::fs::File;
use std::io::BufReader;

let inner = File::open("sample.R1.fastq").map(BufReader::new).unwrap();
let fmt_reader = noodles::fastq::io::Reader::new(inner);

let scanner = Scanner::default();
let batches = scanner.scan(fmt_reader, None, None, Some(1000));

Implementations

impl Scanner

pub fn new() -> Self

pub fn field_names(&self) -> Vec<String>

Returns the FASTQ field names.

pub fn schema(&self, fields: Option<Vec<String>>) -> Result<Schema>

Returns the Arrow schema.

impl Scanner

pub fn scan<R: BufRead>( &self, fmt_reader: Reader<R>, fields: Option<Vec<String>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches.

The scan will begin at the current position of the reader and will move the cursor to the end of the last record scanned.

Trait Implementations

impl Default for Scanner

fn default() -> Self

Returns the “default value” for a type.