Struct BgzfChunkReader 

pub struct BgzfChunkReader<R> { /* private fields */ }

A reader that decodes a sequence of virtual position ranges (“chunks”) in a BGZF-encoded file.

The chunks normally come from querying an index file with a genomic range.

Examples

use oxbow::util::query::BgzfChunkReader;
use std::fs::File;
use std::io::{self, BufReader};
use noodles::bgzf::VirtualPosition;

let inner = File::open("sample.bam").unwrap();
let bgzf_reader = noodles::bgzf::io::Reader::new(BufReader::new(inner));
let chunks = vec![
    (VirtualPosition::from(0), VirtualPosition::from(6)),
    (VirtualPosition::from(12), VirtualPosition::from(18)),
];
let mut chunk_reader = BgzfChunkReader::new(bgzf_reader, chunks);

use oxbow::util::query::BgzfChunkReader;
use std::fs::File;
use std::io::{self, BufReader};
use noodles::core::region::Interval;
use noodles::csi::BinningIndex;

let inner = File::open("sample.bam").unwrap();
let index = noodles::bam::bai::fs::read("sample.bam.bai").unwrap();
let chrom_id = 4;
let interval = "101-200".parse::<Interval>().unwrap();
let bgzf_reader = noodles::bgzf::io::Reader::new(BufReader::new(inner));
let chunks: Vec<_> = index.query(chrom_id, interval).unwrap()
    .into_iter().map(|c| (c.start(), c.end())).collect();
let mut chunk_reader = BgzfChunkReader::new(bgzf_reader, chunks);

Implementations

impl<R> BgzfChunkReader<R>

where R: BufRead + Seek,

pub fn new(reader: R, chunks: Vec<VirtualRange>) -> Self

Trait Implementations

impl<R> BufRead for BgzfChunkReader<R>

where R: BufRead + Seek,

fn fill_buf(&mut self) -> Result<&[u8]>

Returns the contents of the internal buffer, filling it with more data, via Read methods, if empty.

fn consume(&mut self, amt: usize)

Marks the given amount of additional bytes from the internal buffer as having been read. Subsequent calls to read only return bytes that have not been marked as read.

fn has_data_left(&mut self) -> Result<bool, Error>

🔬This is a nightly-only experimental API. (buf_read_has_data_left)

Checks if there is any data left to be read.

fn read_until(&mut self, byte: u8, buf: &mut Vec<u8>) -> Result<usize, Error>

Reads all bytes into buf until the delimiter byte or EOF is reached.

fn skip_until(&mut self, byte: u8) -> Result<usize, Error>

Skips all bytes until the delimiter byte or EOF is reached.

fn read_line(&mut self, buf: &mut String) -> Result<usize, Error>

Reads all bytes until a newline (the 0xA byte) is reached, and append them to the provided String buffer.

fn split(self, byte: u8) -> Split<Self>

where Self: Sized,

Returns an iterator over the contents of this reader split on the byte byte.

fn lines(self) -> Lines<Self>

where Self: Sized,

Returns an iterator over the lines of this reader.

impl<R> Read for BgzfChunkReader<R>

where R: BufRead + Seek,

fn read(&mut self, buf: &mut [u8]) -> Result<usize>

Pull some bytes from this source into the specified buffer, returning how many bytes were read.

fn read_vectored(&mut self, bufs: &mut [IoSliceMut<'_>]) -> Result<usize, Error>

Like read, except that it reads into a slice of buffers.

fn is_read_vectored(&self) -> bool

🔬This is a nightly-only experimental API. (can_vector)

Determines if this Reader has an efficient read_vectored implementation.

fn read_to_end(&mut self, buf: &mut Vec<u8>) -> Result<usize, Error>

Reads all bytes until EOF in this source, placing them into buf.

fn read_to_string(&mut self, buf: &mut String) -> Result<usize, Error>

Reads all bytes until EOF in this source, appending them to buf.

fn read_exact(&mut self, buf: &mut [u8]) -> Result<(), Error>

Reads the exact number of bytes required to fill buf.

fn read_buf(&mut self, buf: BorrowedCursor<'_>) -> Result<(), Error>

🔬This is a nightly-only experimental API. (read_buf)

Pull some bytes from this source into the specified buffer.

fn read_buf_exact(&mut self, cursor: BorrowedCursor<'_>) -> Result<(), Error>

🔬This is a nightly-only experimental API. (read_buf)

Reads the exact number of bytes required to fill cursor.

fn by_ref(&mut self) -> &mut Self

where Self: Sized,

Creates a “by reference” adapter for this instance of Read.

fn bytes(self) -> Bytes<Self>

where Self: Sized,

Transforms this Read instance to an Iterator over its bytes.

fn chain<R>(self, next: R) -> Chain<Self, R>

where R: Read, Self: Sized,

Creates an adapter which will chain this stream with another.

fn take(self, limit: u64) -> Take<Self>

where Self: Sized,

Creates an adapter which will read at most limit bytes from it.

fn read_array<const N: usize>(&mut self) -> Result<[u8; N], Error>

where Self: Sized,

🔬This is a nightly-only experimental API. (read_array)

Read and return a fixed array of bytes from this source.