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

Creates a FASTQ scanner.

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.

pub fn scan_byte_ranges<R: BufRead + Seek>( &self, fmt_reader: Reader<R>, byte_ranges: Vec<(u64, u64)>, fields: Option<Vec<String>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches from specified byte ranges.

This operation requires a seekable (typically uncompressed) source.

The scan will traverse the specified byte ranges without filtering by genomic coordinates. This is useful when you have pre-computed file offsets from a custom index. The byte ranges must align with record boundaries.

pub fn scan_virtual_ranges<R: Read + Seek>( &self, fmt_reader: Reader<Reader<R>>, vpos_ranges: Vec<(VirtualPosition, VirtualPosition)>, fields: Option<Vec<String>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches from specified virtual position ranges.

This operation requires a BGZF-compressed source.

The scan will traverse the specified virtual position ranges without filtering by genomic coordinates. This is useful when you have pre-computed virtual offsets from a custom index.

Trait Implementations

impl Default for Scanner

fn default() -> Self

Returns the “default value” for a type.