Struct noodles_bgzf::indexed_reader::IndexedReader

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

An indexed BGZF reader.

Implementations

impl<R> IndexedReader<R>

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

Examples

use noodles_bgzf::{self as bgzf, gzi};
let reader = bgzf::IndexedReader::new(io::empty(), gzi::Index::default());
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::{self as bgzf, gzi};
let mut reader = bgzf::IndexedReader::new(io::empty(), gzi::Index::default());
let inner = reader.get_mut();

pub fn into_inner(self) -> R

Unwraps and returns the underlying writer.

Examples

use noodles_bgzf::{self as bgzf, gzi};
let reader = bgzf::IndexedReader::new(io::empty(), gzi::Index::default());
let inner = reader.into_inner();

impl<R> IndexedReader<R>

where R: Read,

pub fn new(inner: R, index: Index) -> Self

Creates an indexed BGZF reader.

Examples

use noodles_bgzf::{self as bgzf, gzi};
let reader = bgzf::IndexedReader::new(io::empty(), gzi::Index::default());

pub fn position(&self) -> u64

Returns the current position of the stream.

Examples

use noodles_bgzf::{self as bgzf, gzi};
let reader = bgzf::IndexedReader::new(io::empty(), gzi::Index::default());
assert_eq!(reader.position(), 0);

pub fn virtual_position(&self) -> VirtualPosition

Returns the current virtual position of the stream.

Examples

use noodles_bgzf::{self as bgzf, gzi};
let reader = bgzf::IndexedReader::new(io::empty(), gzi::Index::default());
assert_eq!(reader.virtual_position(), bgzf::VirtualPosition::from(0));

pub fn index(&self) -> &Index

Returns the associated index.

Examples

use noodles_bgzf::{self as bgzf, gzi};
let index = gzi::Index::default();
let reader = bgzf::IndexedReader::new(io::empty(), index.clone());
assert_eq!(reader.index(), &index);

Trait Implementations

impl<R> BufRead for IndexedReader<R>

where R: 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 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 has_data_left(&mut self) -> Result<bool, Error>

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

Checks 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>

Reads 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)

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 IndexedReader<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_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” 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> Seek for IndexedReader<R>

where R: Read + Seek,

fn seek(&mut self, pos: SeekFrom) -> Result<u64>

Seek to an offset, in bytes, in a stream.

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

Rewind to the beginning of a stream.

fn stream_len(&mut self) -> Result<u64, Error>

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

Returns the length of this stream (in bytes).

fn stream_position(&mut self) -> Result<u64, Error>

Returns the current seek position from the start of the stream.

fn seek_relative(&mut self, offset: i64) -> Result<(), Error>

Seeks relative to the current position.