Struct Reader

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

A BGZF reader.

The reader implements both std::io::Read and std::io::BufRead, consuming compressed data and emitting uncompressed data. It is internally buffered by a single block, and to correctly track (virtual) positions, the reader cannot be double buffered (e.g., using std::io::BufReader).

Examples

use noodles_bgzf as bgzf;
let mut reader = File::open("data.gz").map(bgzf::io::Reader::new)?;
let mut data = Vec::new();
reader.read_to_end(&mut data)?;

Implementations

impl<R> Reader<R>

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

Examples

use noodles_bgzf as bgzf;
let reader = bgzf::io::Reader::new(io::empty());
let _inner = reader.get_ref();

pub fn get_mut(&mut self) -> &mut R

Returns a mutable reference to the underlying reader.

Examples

use noodles_bgzf as bgzf;
let mut reader = bgzf::io::Reader::new(io::empty());
let _inner = reader.get_mut();

pub fn into_inner(self) -> R

Unwraps and returns the underlying writer.

Examples

use noodles_bgzf as bgzf;
let reader = bgzf::io::Reader::new(io::empty());
let _inner = reader.into_inner();

impl<R> Reader<R>

where R: Read,

pub fn new(inner: R) -> Self

Creates a BGZF reader.

Examples

use noodles_bgzf as bgzf;
let reader = bgzf::io::Reader::new(io::empty());

pub fn position(&self) -> u64

Returns the current position of the stream.

Examples

use noodles_bgzf as bgzf;
let reader = bgzf::io::Reader::new(io::empty());
assert_eq!(reader.position(), 0);

pub fn virtual_position(&self) -> VirtualPosition

Returns the current virtual position of the stream.

Examples

use noodles_bgzf as bgzf;
let reader = bgzf::io::Reader::new(io::empty());
assert_eq!(reader.virtual_position(), bgzf::VirtualPosition::from(0));

impl<R> Reader<R>

where R: Read + Seek,

pub fn seek(&mut self, pos: VirtualPosition) -> Result<VirtualPosition>

Seeks the stream to the given virtual position.

The underlying stream’s cursor is first moved the the compressed position. A block is read, decompressed, and has its own cursor moved to the uncompressed position.

Examples

use noodles_bgzf as bgzf;
let mut reader = bgzf::io::Reader::new(io::empty());
reader.seek(bgzf::VirtualPosition::MIN)?;

pub fn seek_by_uncompressed_position( &mut self, index: &Index, pos: u64, ) -> Result<u64>

Seeks the stream to the given uncompressed position.

Examples

use noodles_bgzf::{self as bgzf, gzi};

let mut reader = bgzf::io::Reader::new(io::empty());

let index = gzi::Index::default();
reader.seek_by_uncompressed_position(&index, 0)?;

Trait Implementations

impl<R> BufRead for Reader<R>

where R: Read,

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

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

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 Reader<R>

where R: Read,

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_exact(&mut self, buf: &mut [u8]) -> Result<()>

Reads the exact number of bytes required to fill buf.

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_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” adaptor 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.

impl<R> Read for Reader<R>

where R: Read,

fn virtual_position(&self) -> VirtualPosition

Returns the current virtual position.

impl<R> Seek for Reader<R>

where R: Read + Seek,

fn seek_to_virtual_position( &mut self, pos: VirtualPosition, ) -> Result<VirtualPosition>

Seeks the stream to the given virtual position.

fn seek_with_index(&mut self, index: &Index, pos: SeekFrom) -> Result<u64>

Seeks the stream to the given position using an index.

impl<R> BufRead for Reader<R>

where R: Read,