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//! BGZF reader.
pub(crate) mod block;
mod builder;
pub use self::builder::Builder;
use std::io::{self, BufRead, Read, Seek, SeekFrom};
use super::{gzi, Block, VirtualPosition};
/// 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
///
/// ```no_run
/// # use std::{fs::File, io::{self, Read}};
/// 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)?;
/// # Ok::<(), io::Error>(())
/// ```
pub struct Reader<R> {
inner: block::Inner<R>,
position: u64,
block: Block,
}
impl<R> Reader<R>
where
R: Read,
{
/// Creates a BGZF reader.
///
/// # Examples
///
/// ```
/// use noodles_bgzf as bgzf;
/// let data = [];
/// let reader = bgzf::Reader::new(&data[..]);
/// ```
pub fn new(inner: R) -> Self {
Builder::default().build_from_reader(inner)
}
/// 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_ref(&self) -> &R {
self.inner.get_ref()
}
/// 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 get_mut(&mut self) -> &mut R {
self.inner.get_mut()
}
/// 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());
/// ```
pub fn into_inner(self) -> R {
self.inner.into_inner()
}
/// 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 position(&self) -> u64 {
self.position
}
/// 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));
/// ```
pub fn virtual_position(&self) -> VirtualPosition {
self.block.virtual_position()
}
fn read_block(&mut self) -> io::Result<()> {
while let Some(mut block) = self.inner.next_block()? {
block.set_position(self.position);
self.position += block.size();
self.block = block;
if self.block.data().len() > 0 {
break;
}
}
Ok(())
}
}
impl<R> Reader<R>
where
R: Read + Seek,
{
/// 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
///
/// ```no_run
/// # use std::io::{self, Cursor};
/// 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)?;
/// # Ok::<(), io::Error>(())
/// ```
pub fn seek(&mut self, pos: VirtualPosition) -> io::Result<VirtualPosition> {
let (cpos, upos) = pos.into();
self.inner.get_mut().seek(SeekFrom::Start(cpos))?;
self.position = cpos;
self.read_block()?;
self.block.data_mut().set_position(usize::from(upos));
Ok(pos)
}
/// Seeks the stream to the given uncompressed position.
///
/// # Examples
///
/// ```no_run
/// # use std::io;
/// 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)?;
/// # Ok::<_, io::Error>(())
/// ```
pub fn seek_by_uncompressed_position(
&mut self,
index: &gzi::Index,
pos: u64,
) -> io::Result<u64> {
assert!(!index.is_empty());
let i = index.partition_point(|r| r.1 <= pos);
// SAFETY: `i` is > 0.
let record = index[i - 1];
let cpos = record.0;
self.inner.get_mut().seek(SeekFrom::Start(cpos))?;
self.position = cpos;
self.read_block()?;
let upos = usize::try_from(pos - record.1)
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;
self.block.data_mut().set_position(upos);
Ok(pos)
}
}
impl<R> Read for Reader<R>
where
R: Read,
{
fn read(&mut self, buf: &mut [u8]) -> io::Result<usize> {
let mut src = self.fill_buf()?;
let amt = src.read(buf)?;
self.consume(amt);
Ok(amt)
}
}
impl<R> BufRead for Reader<R>
where
R: Read,
{
fn consume(&mut self, amt: usize) {
self.block.data_mut().consume(amt);
}
fn fill_buf(&mut self) -> io::Result<&[u8]> {
if !self.block.data().has_remaining() {
self.read_block()?;
}
Ok(self.block.data().as_ref())
}
}
#[cfg(feature = "libdeflate")]
pub(crate) fn inflate_data(src: &[u8], dst: &mut [u8]) -> io::Result<()> {
use libdeflater::Decompressor;
let mut decoder = Decompressor::new();
decoder
.deflate_decompress(src, dst)
.map(|_| ())
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
}
#[cfg(not(feature = "libdeflate"))]
pub(crate) fn inflate_data(src: &[u8], dst: &mut [u8]) -> io::Result<()> {
use flate2::bufread::DeflateDecoder;
let mut decoder = DeflateDecoder::new(src);
decoder.read_exact(dst)
}
#[cfg(test)]
mod tests {
use std::io::Cursor;
use super::*;
#[test]
fn test_read_with_empty_block() -> io::Result<()> {
#[rustfmt::skip]
let data = [
// block 0 (b"noodles")
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x22, 0x00, 0xcb, 0xcb, 0xcf, 0x4f, 0xc9, 0x49, 0x2d, 0x06, 0x00, 0xa1,
0x58, 0x2a, 0x80, 0x07, 0x00, 0x00, 0x00,
// block 1 (b"")
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x1b, 0x00, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
// block 2 (b"bgzf")
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x1f, 0x00, 0x4b, 0x4a, 0xaf, 0x4a, 0x03, 0x00, 0x20, 0x68, 0xf2, 0x8c,
0x04, 0x00, 0x00, 0x00,
// EOF block
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x1b, 0x00, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
];
let mut reader = Reader::new(&data[..]);
let mut buf = Vec::new();
reader.read_to_end(&mut buf)?;
assert_eq!(buf, b"noodlesbgzf");
Ok(())
}
#[test]
fn test_seek() -> Result<(), Box<dyn std::error::Error>> {
#[rustfmt::skip]
let data = [
// block 0 (b"noodles")
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x22, 0x00, 0xcb, 0xcb, 0xcf, 0x4f, 0xc9, 0x49, 0x2d, 0x06, 0x00, 0xa1,
0x58, 0x2a, 0x80, 0x07, 0x00, 0x00, 0x00,
// EOF block
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x1b, 0x00, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
];
let eof = VirtualPosition::try_from((63, 0))?;
let mut reader = Reader::new(Cursor::new(&data));
let mut buf = Vec::new();
reader.read_to_end(&mut buf)?;
assert_eq!(reader.virtual_position(), eof);
reader.seek(VirtualPosition::try_from((0, 3))?)?;
buf.clear();
reader.read_to_end(&mut buf)?;
assert_eq!(buf, b"dles");
assert_eq!(reader.virtual_position(), eof);
Ok(())
}
#[test]
fn test_seek_by_uncompressed_position() -> io::Result<()> {
#[rustfmt::skip]
let data = [
// block 0 (b"noodles")
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x22, 0x00, 0xcb, 0xcb, 0xcf, 0x4f, 0xc9, 0x49, 0x2d, 0x06, 0x00, 0xa1,
0x58, 0x2a, 0x80, 0x07, 0x00, 0x00, 0x00,
// block 1 (b"bgzf")
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x1f, 0x00, 0x4b, 0x4a, 0xaf, 0x4a, 0x03, 0x00, 0x20, 0x68, 0xf2, 0x8c,
0x04, 0x00, 0x00, 0x00,
// EOF block
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x1b, 0x00, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
];
let index = vec![(0, 0), (35, 7)];
let mut reader = Reader::new(Cursor::new(&data));
reader.seek_by_uncompressed_position(&index, 3)?;
let mut buf = [0; 4];
reader.read_exact(&mut buf)?;
assert_eq!(&buf, b"dles");
reader.seek_by_uncompressed_position(&index, 8)?;
let mut buf = [0; 2];
reader.read_exact(&mut buf)?;
assert_eq!(&buf, b"gz");
Ok(())
}
}