Struct noodles_bgzf::reader::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::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 data = [];
let reader = bgzf::Reader::new(&data[..]);
assert!(reader.get_ref().is_empty());

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

Returns a mutable reference to the underlying reader.

Examples

use noodles_bgzf as bgzf;
let data = [];
let mut reader = bgzf::Reader::new(&data[..]);
assert!(reader.get_mut().is_empty());

pub fn into_inner(self) -> R

Unwraps and returns the underlying writer.

Examples

use noodles_bgzf as bgzf;
let data = [];
let reader = bgzf::Reader::new(&data[..]);
assert!(reader.into_inner().is_empty());

impl<R> Reader<R>

where R: Read,

pub fn new(inner: R) -> Self

Creates a BGZF reader.

Examples

use noodles_bgzf as bgzf;
let data = [];
let reader = bgzf::Reader::new(&data[..]);

pub fn position(&self) -> u64

Returns the current position of the stream.

Examples

use noodles_bgzf as bgzf;
let data = [];
let reader = bgzf::Reader::new(&data[..]);
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 data = [];
let reader = bgzf::Reader::new(&data[..]);
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::Reader::new(io::empty());
let virtual_position = bgzf::VirtualPosition::MIN;
reader.seek(virtual_position)?;

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 as bgzf;
let mut reader = bgzf::Reader::new(io::empty());
let index = vec![(0, 0)];
reader.seek_by_uncompressed_position(&index, 0)?;

Trait Implementations

impl<R> BufRead for Reader<R>

where R: Read,

fn consume(&mut self, amt: usize)

Tells this buffer that amt bytes have been consumed from the buffer, so they should no longer be returned in calls to read.

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

Returns the contents of the internal buffer, filling it with more data from the inner reader if it is empty.

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

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

Check if the underlying Read has any data left to be read.

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

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

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

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

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

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

Read 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<()>

Read 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>

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

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

Read 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)

Read 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,