Struct Reader

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

An async BAM reader.

Examples

use futures::TryStreamExt;
use noodles_bam as bam;
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;
let _header = reader.read_header().await?;

let mut records = reader.records();

while let Some(_record) = records.try_next().await? {
    // ...
}

Implementations

impl<R> Reader<R>

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

Examples

use noodles_bam as bam;
use tokio::io;
let reader = bam::r#async::io::Reader::from(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_bam as bam;
use tokio::io;
let mut reader = bam::r#async::io::Reader::from(io::empty());
let _inner = reader.get_mut();

pub fn into_inner(self) -> R

Returns the underlying reader.

Examples

use noodles_bam as bam;
use tokio::io;
let reader = bam::r#async::io::Reader::from(io::empty());
let _inner = reader.into_inner();

impl<R> Reader<R>

where R: AsyncRead + Unpin,

pub async fn read_header(&mut self) -> Result<Header>

Reads the SAM header.

This verifies the BAM magic number, reads and parses the raw SAM header, and reads the binary reference sequences. If the SAM header has a reference sequence dictionary, it must match the binary reference sequences; otherwise, the binary reference sequences are added to the SAM header.

The position of the stream is expected to be at the start.

Examples

use noodles_bam as bam;
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;
let header = reader.read_header().await?;

pub async fn read_record_buf( &mut self, _header: &Header, record: &mut RecordBuf, ) -> Result<usize>

Reads a record into an alignment record buffer.

The record block size (bs) is read from the underlying stream and bs bytes are read into an internal buffer. This buffer is then used to decode fields into the given record.

The stream is expected to be directly after the reference sequences or at the start of another record.

It is more ergonomic to read records using a stream (see Self::records and Self::query), but using this method directly allows the reuse of a RecordBuf.

If successful, the record block size is returned. If a block size of 0 is returned, the stream reached EOF.

Examples

use noodles_bam as bam;
use noodles_sam::alignment::RecordBuf;
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;
let header = reader.read_header().await?;

let mut record = RecordBuf::default();
reader.read_record_buf(&header, &mut record).await?;

pub async fn read_record(&mut self, record: &mut Record) -> Result<usize>

Reads a record.

The record block size (bs) is read from the underlying stream and bs bytes are read into the record’s buffer. No fields are decoded, meaning the record is not necessarily valid. However, the structure of the buffer is guaranteed to be record-like.

The stream is expected to be directly after the reference sequences or at the start of another record.

If successful, the record block size is returned. If a block size of 0 is returned, the stream reached EOF.

Examples

use noodles_bam as bam;
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;
reader.read_header().await?;

let mut record = bam::Record::default();
reader.read_record(&mut record).await?;

pub fn record_bufs<'a>( &'a mut self, _header: &'a Header, ) -> impl Stream<Item = Result<RecordBuf>> + '_

Returns an (async) stream over alignment record buffers starting from the current (input) stream position.

The (input) stream is expected to be directly after the reference sequences or at the start of another record.

Examples

use futures::TryStreamExt;
use noodles_bam as bam;
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;
let header = reader.read_header().await?;

let mut records = reader.record_bufs(&header);

while let Some(record) = records.try_next().await? {
    // ...
}

pub fn records(&mut self) -> impl Stream<Item = Result<Record>> + '_

Returns a stream over records.

The (input) stream is expected to be directly after the reference sequences or at the start of another record.

Examples

use futures::TryStreamExt;
use noodles_bam as bam;
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;
reader.read_header().await?;

let mut records = reader.records();

while let Some(record) = records.try_next().await? {
    // ...
}

impl<R> Reader<AsyncReader<R>>

where R: AsyncRead + Unpin,

pub fn new(reader: R) -> Self

Creates an async BAM reader.

The given reader must be a raw BGZF stream, as the underlying reader wraps it in a decoder.

Examples

use noodles_bam as bam;
let data = [];
let reader = bam::r#async::io::Reader::new(&data[..]);

impl<R> Reader<AsyncReader<R>>

where R: AsyncRead + AsyncSeek + Unpin,

pub fn query<I>( &mut self, header: &Header, index: &I, region: &Region, ) -> Result<impl Stream<Item = Result<Record>> + '_>

where I: BinningIndex,

Returns a stream over records that intersect the given region.

To query for unmapped records, use Self::query_unmapped.

Examples

use futures::TryStreamExt;
use noodles_bam::{self as bam, bai};
use noodles_core::Region;
use noodles_sam as sam;
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;
let header = reader.read_header().await?;

let index = bai::r#async::read("sample.bam.bai").await?;
let region = "sq0:8-13".parse()?;
let mut query = reader.query(&header, &index, &region)?;

while let Some(record) = query.try_next().await? {
    // ...
}

pub async fn query_unmapped<I>( &mut self, index: &I, ) -> Result<impl Stream<Item = Result<Record>> + '_>

where I: BinningIndex,

Returns an iterator of unmapped records after querying for the unmapped region.

Examples

use futures::TryStreamExt;
use noodles_bam::{self as bam, bai};
use tokio::fs::File;

let mut reader = File::open("sample.bam").await.map(bam::r#async::io::Reader::new)?;

let index = bai::r#async::read("sample.bam.bai").await?;
let mut query = reader.query_unmapped(&index).await?;

while let Some(record) = query.try_next().await? {
    // ...
}

Trait Implementations

impl<R> From<R> for Reader<R>

fn from(inner: R) -> Self

Converts to this type from the input type.