Struct Reader

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

A BAM index (BAI) reader.

A BAM index has three top-level fields:

1. a magic number,
2. a list of reference sequences,
3. and optionally, the number of unmapped reads in the associated BAM.

While these fields can be read individually, consider using [super::read] to read the entire index at once.

Examples

use noodles_bam::bai;
let mut reader = File::open("sample.bam.bai").map(bai::io::Reader::new)?;
let index = reader.read_index()?;

Implementations

impl<R> Reader<R>

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

Examples

use noodles_bam::bai;
let reader = bai::io::Reader::new(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::bai;
let mut reader = bai::io::Reader::new(io::empty());
let _inner = reader.get_mut();

pub fn into_inner(self) -> R

Returns the underlying reader.

Examples

use noodles_bam::bai;
let reader = bai::io::Reader::new(io::empty());
let _inner = reader.into_inner();

impl<R> Reader<R>

where R: Read,

pub fn new(inner: R) -> Self

Creates a BAM index reader.

Examples

use noodles_bam::bai;
let reader = File::open("sample.bam.bai").map(bai::io::Reader::new)?;

pub fn read_index(&mut self) -> Result<Index>

Reads the BAM index.

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

Examples

use noodles_bam::bai;
let mut reader = File::open("sample.bam.bai").map(bai::io::Reader::new)?;
let index = reader.read_index()?;