Struct FastqReader 

pub struct FastqReader { /* private fields */ }

FASTQ file reader (streaming, memory-efficient)

Create using FastqReader::from_path() or FastqReader::from_buffer().

FASTQ format:

• Line 1: @ID description
• Line 2: Sequence
• Line 3: + (optional ID)
• Line 4: Quality

Implementations

impl FastqReader

pub fn from_buffer<R: BufRead + 'static>(reader: R) -> Self

Create a FASTQ reader from a buffered reader

This is the low-level constructor that accepts any buffered reader. Use this when you already have a BufRead source (e.g., from seeking to a specific position in a file for parallel processing).

Example

use genomicframe_core::formats::fastq::FastqReader;
use std::io::BufReader;
use std::fs::File;

let file = File::open("reads.fastq")?;
let buf_reader = BufReader::new(file);
let mut reader = FastqReader::from_buffer(buf_reader);

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

Open a FASTQ file - handles .fastq, .fq, .fastq.gz, .fq.gz automatically

Memory Behavior

• Opens file handle (~8KB buffer)
• Does NOT load reads into memory
• Records are parsed on-demand as you iterate

Example

use genomicframe_core::formats::fastq::FastqReader;
use genomicframe_core::core::GenomicRecordIterator;

// Works with multi-GB files using only ~10KB RAM
let mut reader = FastqReader::from_path("reads.fastq.gz")?;

while let Some(record) = reader.next_record()? {
    if record.mean_quality() >= 30.0 {
        println!("High quality: {}", record.id);
    }
}

pub fn header(&self) -> &FastqHeader

Get the FASTQ header metadata

Trait Implementations

impl GenomicReader for FastqReader

type Metadata = FastqHeader

Metadata type for this reader

fn metadata(&self) -> &Self::Metadata

Get metadata about the genomic data (headers, contigs, etc.)

impl GenomicRecordIterator for FastqReader

type Record = FastqRecord

The record type yielded by this iterator

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

Advance to the next raw record

fn next_record(&mut self) -> Result<Option<Self::Record>>

Advance to the next record

fn collect_all(self) -> Result<Vec<Self::Record>>

where Self: Sized,

Consume the iterator and collect all records into a vector

fn chunks(self, chunk_size: usize) -> ChunkedIterator<Self>

where Self: Sized,

Process records in chunks for memory-efficient batch operations