Struct noodles_bam::reader::Reader

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

A BAM reader.

A BAM file is an encoded and compressed version of a SAM file. While a SAM file has a header and a list of records, a BAM is comprised of three parts:

1. a SAM header,
2. a list of reference sequences, and
3. a list of encoded SAM records.

The reader reads records sequentially but can use virtual positions to seek to offsets from the start of a seekable stream.

Examples

use noodles_bam as bam;

let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
reader.read_header()?;
reader.read_reference_sequences()?;

for result in reader.records() {
    let record = result?;
    println!("{:?}", record);
}

Implementations

impl<R> Reader<R> where
    R: Read, 

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

Examples

use noodles_bam as bam;
let data = [];
let reader = bam::Reader::from(&data[..]);
assert!(reader.get_ref().is_empty());

pub fn get_mut(&mut self) -> &mut R

Returns a mutable reference to the underlying reader.

Examples

use noodles_bam as bam;
let data = [];
let mut reader = bam::Reader::from(&data[..]);
assert!(reader.get_mut().is_empty());

pub fn into_inner(self) -> R

Returns the underlying reader.

Examples

use noodles_bam as bam;
let data = [];
let reader = bam::Reader::from(&data[..]);
assert!(reader.into_inner().is_empty());

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

Reads the raw SAM header.

The BAM magic number is also checked.

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

This returns the raw SAM header as a String. It can subsequently be parsed as a noodles_sam::Header.

Examples

use noodles_bam as bam;
let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
let header = reader.read_header()?;

pub fn read_reference_sequences(&mut self) -> Result<ReferenceSequences>

Reads the binary reference sequences after the SAM header.

This is not the same as the @SQ records in the SAM header. A BAM has a list of reference sequences containing name and length tuples after the SAM header and before the list of records.

The position of the stream is expected to be directly after the header.

This returns a reference sequence dictionary (noodles_sam::header::ReferenceSequences), which can be used to build a minimal noodles_sam::Header if the SAM header is empty.

Examples

use noodles_bam as bam;
let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
reader.read_header()?;
let reference_sequences = reader.read_reference_sequences()?;

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

Reads a single record.

The record block size (bs) is read from the underlying stream and bs bytes are read into an internal buffer. This buffer is used to populate 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 an iterator (see Self::records and Self::query), but using this method directly allows the reuse of a single Record buffer.

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::Record;

let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
reader.read_header()?;
reader.read_reference_sequences()?;

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

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

Reads a single record without eagerly decoding its fields.

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

let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
reader.read_header()?;
reader.read_reference_sequences()?;

let mut record = bam::lazy::Record::default();
reader.read_lazy_record(&mut record)?;

pub fn records(&mut self) -> Records<'_, R>

Returns an iterator over records starting from the current stream position.

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

Examples

use noodles_bam as bam;

let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
reader.read_header()?;
reader.read_reference_sequences()?;

for result in reader.records() {
    let record = result?;
    println!("{:?}", record);
}

pub fn lazy_records(&mut self) -> LazyRecords<'_, R>

Returns an iterator over lazy records.

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

Examples

use noodles_bam as bam;

let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
reader.read_header()?;
reader.read_reference_sequences()?;

for result in reader.lazy_records() {
    let record = result?;
    // ...
}

impl<R> Reader<Reader<R>> where
    R: Read, 

pub fn new(reader: R) -> Self

Creates a 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::Reader::new(&data[..]);

pub fn virtual_position(&self) -> VirtualPosition

Returns the current virtual position of the underlying BGZF reader.

Examples

use noodles_bam as bam;

let data = Vec::new();
let reader = bam::Reader::new(&data[..]);
let virtual_position = reader.virtual_position();

assert_eq!(virtual_position.compressed(), 0);
assert_eq!(virtual_position.uncompressed(), 0);

impl<R> Reader<Reader<R>> where
    R: Read + Seek, 

pub fn seek(&mut self, pos: VirtualPosition) -> Result<VirtualPosition>

Seeks the underlying BGZF reader to the given virtual position.

Virtual positions typically come from the associated BAM index file.

Examples

use noodles_bam as bam;
use noodles_bgzf as bgzf;
let mut reader = bam::Reader::new(Cursor::new(Vec::new()));
let virtual_position = bgzf::VirtualPosition::default();
reader.seek(virtual_position)?;

pub fn query<I>(
    &mut self,
    reference_sequences: &ReferenceSequences,
    index: &I,
    region: &Region
) -> Result<Query<'_, R>> where
    I: BinningIndex, 

Returns an iterator over records that intersect the given region.

Examples

use noodles_bam::{self as bam, bai};
use noodles_core::Region;
use noodles_sam as sam;

let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
let header: sam::Header = reader.read_header()?.parse()?;

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

for result in query {
    let record = result?;
    println!("{:?}", record);
}

pub fn query_unmapped(
    &mut self,
    index: &Index
) -> Result<UnmappedRecords<'_, R>>

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

Examples

use noodles_bam::{self as bam, bai};

let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
let index = bai::read("sample.bam.bai")?;
let query = reader.query_unmapped(&index)?;

for result in query {
    let record = result?;
    println!("{:?}", record);
}

Trait Implementations

impl<R> AlignmentReader for Reader<R> where
    R: Read, 

fn read_alignment_header(&mut self) -> Result<Header>

Reads a SAM header.

fn alignment_records<'a>(
    &'a mut self,
    _: &'a Repository,
    _: &'a Header
) -> Box<dyn Iterator<Item = Result<Record>> + 'a>

Returns an iterator over records.

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

fn from(inner: R) -> Self

Converts to this type from the input type.