Struct noodles_bgzf::Reader
source · [−]pub struct Reader<R> { /* private fields */ }
Expand description
A BGZF reader.
Due to the static structure of a BGZF block, gzip headers are mostly discarded. CRC32 validation is also disabled when decompressing data.
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
sourceimpl<R> Reader<R> where
R: Read,
impl<R> Reader<R> where
R: Read,
sourcepub fn new(inner: R) -> Self
pub fn new(inner: R) -> Self
Creates a BGZF reader.
Examples
use noodles_bgzf as bgzf;
let data = [];
let reader = bgzf::Reader::new(&data[..]);
sourcepub fn get_ref(&self) -> &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());
sourcepub fn get_mut(&mut self) -> &mut R
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());
sourcepub fn into_inner(self) -> R
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());
sourcepub fn position(&self) -> u64
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);
sourcepub fn virtual_position(&self) -> VirtualPosition
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));
sourceimpl<R> Reader<R> where
R: Read + Seek,
impl<R> Reader<R> where
R: Read + Seek,
sourcepub fn seek(&mut self, pos: VirtualPosition) -> Result<VirtualPosition>
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(Cursor::new(Vec::new()));
let virtual_position = bgzf::VirtualPosition::from(102334155);
reader.seek(virtual_position)?;
Trait Implementations
sourceimpl<R> BufRead for Reader<R> where
R: Read,
impl<R> BufRead for Reader<R> where
R: Read,
sourcefn consume(&mut self, amt: usize)
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
. Read more
sourcefn fill_buf(&mut self) -> Result<&[u8]>
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. Read more
sourcefn has_data_left(&mut self) -> Result<bool, Error>
fn has_data_left(&mut self) -> Result<bool, Error>
buf_read_has_data_left
)Check if the underlying Read
has any data left to be read. Read more
1.0.0 · sourcefn read_until(
&mut self,
byte: u8,
buf: &mut Vec<u8, Global>
) -> Result<usize, Error>
fn read_until(
&mut self,
byte: u8,
buf: &mut Vec<u8, Global>
) -> Result<usize, Error>
Read all bytes into buf
until the delimiter byte
or EOF is reached. Read more
1.0.0 · sourcefn read_line(&mut self, buf: &mut String) -> Result<usize, Error>
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 buffer. You do not need to clear the buffer before
appending. Read more
sourceimpl<R> Read for Reader<R> where
R: Read,
impl<R> Read for Reader<R> where
R: Read,
sourcefn read(&mut self, buf: &mut [u8]) -> Result<usize>
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. Read more
sourcefn read_exact(&mut self, buf: &mut [u8]) -> Result<()>
fn read_exact(&mut self, buf: &mut [u8]) -> Result<()>
Read the exact number of bytes required to fill buf
. Read more
1.36.0 · sourcefn read_vectored(&mut self, bufs: &mut [IoSliceMut<'_>]) -> Result<usize, Error>
fn read_vectored(&mut self, bufs: &mut [IoSliceMut<'_>]) -> Result<usize, Error>
Like read
, except that it reads into a slice of buffers. Read more
sourcefn is_read_vectored(&self) -> bool
fn is_read_vectored(&self) -> bool
can_vector
)Determines if this Read
er has an efficient read_vectored
implementation. Read more
1.0.0 · sourcefn read_to_end(&mut self, buf: &mut Vec<u8, Global>) -> Result<usize, Error>
fn read_to_end(&mut self, buf: &mut Vec<u8, Global>) -> Result<usize, Error>
Read all bytes until EOF in this source, placing them into buf
. Read more
1.0.0 · sourcefn read_to_string(&mut self, buf: &mut String) -> Result<usize, Error>
fn read_to_string(&mut self, buf: &mut String) -> Result<usize, Error>
Read all bytes until EOF in this source, appending them to buf
. Read more
sourcefn read_buf(&mut self, buf: &mut ReadBuf<'_>) -> Result<(), Error>
fn read_buf(&mut self, buf: &mut ReadBuf<'_>) -> Result<(), Error>
read_buf
)Pull some bytes from this source into the specified buffer. Read more
sourcefn read_buf_exact(&mut self, buf: &mut ReadBuf<'_>) -> Result<(), Error>
fn read_buf_exact(&mut self, buf: &mut ReadBuf<'_>) -> Result<(), Error>
read_buf
)Read the exact number of bytes required to fill buf
. Read more
1.0.0 · sourcefn by_ref(&mut self) -> &mut Self
fn by_ref(&mut self) -> &mut Self
Creates a “by reference” adaptor for this instance of Read
. Read more
Auto Trait Implementations
impl<R> RefUnwindSafe for Reader<R> where
R: RefUnwindSafe,
impl<R> Send for Reader<R> where
R: Send,
impl<R> Sync for Reader<R> where
R: Sync,
impl<R> Unpin for Reader<R> where
R: Unpin,
impl<R> UnwindSafe for Reader<R> where
R: UnwindSafe,
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
sourceimpl<T> Instrument for T
impl<T> Instrument for T
sourcefn instrument(self, span: Span) -> Instrumented<Self>
fn instrument(self, span: Span) -> Instrumented<Self>
sourcefn in_current_span(self) -> Instrumented<Self>
fn in_current_span(self) -> Instrumented<Self>
sourceimpl<R> ReadBytesExt for R where
R: Read + ?Sized,
impl<R> ReadBytesExt for R where
R: Read + ?Sized,
sourcefn read_u8(&mut self) -> Result<u8, Error>
fn read_u8(&mut self) -> Result<u8, Error>
Reads an unsigned 8 bit integer from the underlying reader. Read more
sourcefn read_i8(&mut self) -> Result<i8, Error>
fn read_i8(&mut self) -> Result<i8, Error>
Reads a signed 8 bit integer from the underlying reader. Read more
sourcefn read_u16<T>(&mut self) -> Result<u16, Error> where
T: ByteOrder,
fn read_u16<T>(&mut self) -> Result<u16, Error> where
T: ByteOrder,
Reads an unsigned 16 bit integer from the underlying reader. Read more
sourcefn read_i16<T>(&mut self) -> Result<i16, Error> where
T: ByteOrder,
fn read_i16<T>(&mut self) -> Result<i16, Error> where
T: ByteOrder,
Reads a signed 16 bit integer from the underlying reader. Read more
sourcefn read_u24<T>(&mut self) -> Result<u32, Error> where
T: ByteOrder,
fn read_u24<T>(&mut self) -> Result<u32, Error> where
T: ByteOrder,
Reads an unsigned 24 bit integer from the underlying reader. Read more
sourcefn read_i24<T>(&mut self) -> Result<i32, Error> where
T: ByteOrder,
fn read_i24<T>(&mut self) -> Result<i32, Error> where
T: ByteOrder,
Reads a signed 24 bit integer from the underlying reader. Read more
sourcefn read_u32<T>(&mut self) -> Result<u32, Error> where
T: ByteOrder,
fn read_u32<T>(&mut self) -> Result<u32, Error> where
T: ByteOrder,
Reads an unsigned 32 bit integer from the underlying reader. Read more
sourcefn read_i32<T>(&mut self) -> Result<i32, Error> where
T: ByteOrder,
fn read_i32<T>(&mut self) -> Result<i32, Error> where
T: ByteOrder,
Reads a signed 32 bit integer from the underlying reader. Read more
sourcefn read_u48<T>(&mut self) -> Result<u64, Error> where
T: ByteOrder,
fn read_u48<T>(&mut self) -> Result<u64, Error> where
T: ByteOrder,
Reads an unsigned 48 bit integer from the underlying reader. Read more
sourcefn read_i48<T>(&mut self) -> Result<i64, Error> where
T: ByteOrder,
fn read_i48<T>(&mut self) -> Result<i64, Error> where
T: ByteOrder,
Reads a signed 48 bit integer from the underlying reader. Read more
sourcefn read_u64<T>(&mut self) -> Result<u64, Error> where
T: ByteOrder,
fn read_u64<T>(&mut self) -> Result<u64, Error> where
T: ByteOrder,
Reads an unsigned 64 bit integer from the underlying reader. Read more
sourcefn read_i64<T>(&mut self) -> Result<i64, Error> where
T: ByteOrder,
fn read_i64<T>(&mut self) -> Result<i64, Error> where
T: ByteOrder,
Reads a signed 64 bit integer from the underlying reader. Read more
sourcefn read_u128<T>(&mut self) -> Result<u128, Error> where
T: ByteOrder,
fn read_u128<T>(&mut self) -> Result<u128, Error> where
T: ByteOrder,
Reads an unsigned 128 bit integer from the underlying reader. Read more
sourcefn read_i128<T>(&mut self) -> Result<i128, Error> where
T: ByteOrder,
fn read_i128<T>(&mut self) -> Result<i128, Error> where
T: ByteOrder,
Reads a signed 128 bit integer from the underlying reader. Read more
sourcefn read_uint<T>(&mut self, nbytes: usize) -> Result<u64, Error> where
T: ByteOrder,
fn read_uint<T>(&mut self, nbytes: usize) -> Result<u64, Error> where
T: ByteOrder,
Reads an unsigned n-bytes integer from the underlying reader. Read more
sourcefn read_int<T>(&mut self, nbytes: usize) -> Result<i64, Error> where
T: ByteOrder,
fn read_int<T>(&mut self, nbytes: usize) -> Result<i64, Error> where
T: ByteOrder,
Reads a signed n-bytes integer from the underlying reader. Read more
sourcefn read_uint128<T>(&mut self, nbytes: usize) -> Result<u128, Error> where
T: ByteOrder,
fn read_uint128<T>(&mut self, nbytes: usize) -> Result<u128, Error> where
T: ByteOrder,
Reads an unsigned n-bytes integer from the underlying reader.
sourcefn read_int128<T>(&mut self, nbytes: usize) -> Result<i128, Error> where
T: ByteOrder,
fn read_int128<T>(&mut self, nbytes: usize) -> Result<i128, Error> where
T: ByteOrder,
Reads a signed n-bytes integer from the underlying reader.
sourcefn read_f32<T>(&mut self) -> Result<f32, Error> where
T: ByteOrder,
fn read_f32<T>(&mut self) -> Result<f32, Error> where
T: ByteOrder,
Reads a IEEE754 single-precision (4 bytes) floating point number from the underlying reader. Read more
sourcefn read_f64<T>(&mut self) -> Result<f64, Error> where
T: ByteOrder,
fn read_f64<T>(&mut self) -> Result<f64, Error> where
T: ByteOrder,
Reads a IEEE754 double-precision (8 bytes) floating point number from the underlying reader. Read more
sourcefn read_u16_into<T>(&mut self, dst: &mut [u16]) -> Result<(), Error> where
T: ByteOrder,
fn read_u16_into<T>(&mut self, dst: &mut [u16]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of unsigned 16 bit integers from the underlying reader. Read more
sourcefn read_u32_into<T>(&mut self, dst: &mut [u32]) -> Result<(), Error> where
T: ByteOrder,
fn read_u32_into<T>(&mut self, dst: &mut [u32]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of unsigned 32 bit integers from the underlying reader. Read more
sourcefn read_u64_into<T>(&mut self, dst: &mut [u64]) -> Result<(), Error> where
T: ByteOrder,
fn read_u64_into<T>(&mut self, dst: &mut [u64]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of unsigned 64 bit integers from the underlying reader. Read more
sourcefn read_u128_into<T>(&mut self, dst: &mut [u128]) -> Result<(), Error> where
T: ByteOrder,
fn read_u128_into<T>(&mut self, dst: &mut [u128]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of unsigned 128 bit integers from the underlying reader. Read more
sourcefn read_i8_into(&mut self, dst: &mut [i8]) -> Result<(), Error>
fn read_i8_into(&mut self, dst: &mut [i8]) -> Result<(), Error>
Reads a sequence of signed 8 bit integers from the underlying reader. Read more
sourcefn read_i16_into<T>(&mut self, dst: &mut [i16]) -> Result<(), Error> where
T: ByteOrder,
fn read_i16_into<T>(&mut self, dst: &mut [i16]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of signed 16 bit integers from the underlying reader. Read more
sourcefn read_i32_into<T>(&mut self, dst: &mut [i32]) -> Result<(), Error> where
T: ByteOrder,
fn read_i32_into<T>(&mut self, dst: &mut [i32]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of signed 32 bit integers from the underlying reader. Read more
sourcefn read_i64_into<T>(&mut self, dst: &mut [i64]) -> Result<(), Error> where
T: ByteOrder,
fn read_i64_into<T>(&mut self, dst: &mut [i64]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of signed 64 bit integers from the underlying reader. Read more
sourcefn read_i128_into<T>(&mut self, dst: &mut [i128]) -> Result<(), Error> where
T: ByteOrder,
fn read_i128_into<T>(&mut self, dst: &mut [i128]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of signed 128 bit integers from the underlying reader. Read more
sourcefn read_f32_into<T>(&mut self, dst: &mut [f32]) -> Result<(), Error> where
T: ByteOrder,
fn read_f32_into<T>(&mut self, dst: &mut [f32]) -> Result<(), Error> where
T: ByteOrder,
Reads a sequence of IEEE754 single-precision (4 bytes) floating point numbers from the underlying reader. Read more
sourcefn read_f32_into_unchecked<T>(&mut self, dst: &mut [f32]) -> Result<(), Error> where
T: ByteOrder,
fn read_f32_into_unchecked<T>(&mut self, dst: &mut [f32]) -> Result<(), Error> where
T: ByteOrder,
please use read_f32_into
instead
DEPRECATED. Read more
sourceimpl<T> WithSubscriber for T
impl<T> WithSubscriber for T
sourcefn with_subscriber<S>(self, subscriber: S) -> WithDispatch<Self> where
S: Into<Dispatch>,
fn with_subscriber<S>(self, subscriber: S) -> WithDispatch<Self> where
S: Into<Dispatch>,
Attaches the provided Subscriber
to this type, returning a
WithDispatch
wrapper. Read more
sourcefn with_current_subscriber(self) -> WithDispatch<Self>
fn with_current_subscriber(self) -> WithDispatch<Self>
Attaches the current default Subscriber
to this type, returning a
WithDispatch
wrapper. Read more