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//! BAM reader and iterators.
mod query;
pub mod record;
mod records;
mod unmapped_records;
pub use self::{query::Query, records::Records, unmapped_records::UnmappedRecords};
use std::{
convert::TryFrom,
ffi::CStr,
io::{self, Read, Seek},
};
use byteorder::{LittleEndian, ReadBytesExt};
use noodles_bgzf as bgzf;
use noodles_core::{region::Interval, Region};
use noodles_csi::{BinningIndex, BinningIndexReferenceSequence};
use noodles_sam::header::{ReferenceSequence, ReferenceSequences};
use super::{bai, Record, MAGIC_NUMBER};
/// 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
///
/// ```no_run
/// # use std::{fs::File, io};
/// 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);
/// }
///
/// # Ok::<(), io::Error>(())
/// ```
pub struct Reader<R>
where
R: Read,
{
inner: bgzf::Reader<R>,
}
impl<R> Reader<R>
where
R: Read,
{
/// Creates a BAM reader.
///
/// The given reader must be a raw BGZF stream, as the underlying reader wraps it in a decoder.
///
/// # Examples
///
/// ```no_run
/// # use std::{fs::File, io};
/// use noodles_bam as bam;
/// let mut _reader = File::open("sample.bam").map(bam::Reader::new)?;
/// # Ok::<(), io::Error>(())
/// ```
pub fn new(reader: R) -> Self {
Self {
inner: bgzf::Reader::new(reader),
}
}
/// 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
///
/// ```no_run
/// # use std::{fs::File, io};
/// use noodles_bam as bam;
/// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
/// let header = reader.read_header()?;
/// # Ok::<(), io::Error>(())
/// ```
pub fn read_header(&mut self) -> io::Result<String> {
read_magic(&mut self.inner)?;
read_header(&mut self.inner)
}
/// 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
///
/// ```no_run
/// # use std::{fs::File, io};
/// 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()?;
/// # Ok::<(), io::Error>(())
/// ```
pub fn read_reference_sequences(&mut self) -> io::Result<ReferenceSequences> {
read_reference_sequences(&mut self.inner)
}
/// Reads a single record.
///
/// The record block size (`bs`) is read from the underlying stream, and `bs` additional bytes
/// are read 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 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
///
/// ```no_run
/// # use std::{fs::File, io};
/// 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::Record::default();
/// reader.read_record(&mut record)?;
///
/// # Ok::<(), io::Error>(())
/// ```
pub fn read_record(&mut self, record: &mut Record) -> io::Result<usize> {
read_record(&mut self.inner, record)
}
/// 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
///
/// ```no_run
/// # use std::{fs::File, io};
/// 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);
/// }
/// # Ok::<(), io::Error>(())
/// ```
pub fn records(&mut self) -> Records<'_, R> {
Records::new(self)
}
/// Returns the current virtual position of the underlying BGZF reader.
///
/// # Examples
///
/// ```
/// # use std::io;
/// 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);
/// # Ok::<(), io::Error>(())
/// ```
pub fn virtual_position(&self) -> bgzf::VirtualPosition {
self.inner.virtual_position()
}
}
impl<R> Reader<R>
where
R: Read + Seek,
{
/// Seeks the underlying BGZF reader to the given virtual position.
///
/// Virtual positions typically come from the associated BAM index file.
///
/// # Examples
///
/// ```
/// # use std::io::{self, Cursor};
/// 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)?;
/// # Ok::<(), io::Error>(())
/// ```
pub fn seek(&mut self, pos: bgzf::VirtualPosition) -> io::Result<bgzf::VirtualPosition> {
self.inner.seek(pos)
}
// Seeks to the first record by setting the cursor to the beginning of the stream and
// (re)reading the header and binary reference sequences.
fn seek_to_first_record(&mut self) -> io::Result<bgzf::VirtualPosition> {
self.seek(bgzf::VirtualPosition::default())?;
self.read_header()?;
self.read_reference_sequences()?;
Ok(self.virtual_position())
}
/// Returns an iterator over records that intersect the given region.
///
/// # Examples
///
/// ```no_run
/// # use std::fs::File;
/// 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 = Region::mapped("sq0", 17711..=28657);
/// let query = reader.query(reference_sequences, &index, ®ion)?;
///
/// for result in query {
/// let record = result?;
/// println!("{:?}", record);
/// }
/// # Ok::<(), Box<dyn std::error::Error>>(())
/// ```
pub fn query<I, IRS>(
&mut self,
reference_sequences: &ReferenceSequences,
index: &I,
region: &Region,
) -> io::Result<Query<'_, R>>
where
I: BinningIndex<IRS>,
IRS: BinningIndexReferenceSequence,
{
let (reference_sequence_id, interval) = resolve_region(reference_sequences, region)?;
let chunks = index.query(reference_sequence_id, interval)?;
Ok(Query::new(self, chunks, reference_sequence_id, interval))
}
/// Returns an iterator of unmapped records after querying for the unmapped region.
///
/// # Examples
///
/// ```no_run
/// # use std::{fs::File, io};
/// 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);
/// }
/// # Ok::<(), io::Error>(())
/// ```
pub fn query_unmapped(&mut self, index: &bai::Index) -> io::Result<UnmappedRecords<'_, R>> {
if let Some(pos) = index.first_record_in_last_linear_bin_start_position() {
self.seek(pos)?;
} else {
self.seek_to_first_record()?;
}
Ok(UnmappedRecords::new(self))
}
}
fn read_magic<R>(reader: &mut R) -> io::Result<()>
where
R: Read,
{
let mut magic = [0; 4];
reader.read_exact(&mut magic)?;
if magic == MAGIC_NUMBER {
Ok(())
} else {
Err(io::Error::new(
io::ErrorKind::InvalidData,
"invalid BAM header",
))
}
}
fn read_header<R>(reader: &mut R) -> io::Result<String>
where
R: Read,
{
let l_text = reader.read_u32::<LittleEndian>().and_then(|n| {
usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
})?;
let mut text = vec![0; l_text];
reader.read_exact(&mut text)?;
// § 4.2 The BAM format (2021-06-03): "Plain header text in SAM; not necessarily
// NUL-terminated".
bytes_with_nul_to_string(&text).or_else(|_| {
String::from_utf8(text).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
})
}
fn read_reference_sequences<R>(reader: &mut R) -> io::Result<ReferenceSequences>
where
R: Read,
{
let n_ref = reader.read_u32::<LittleEndian>().and_then(|n| {
usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
})?;
let mut reference_sequences = ReferenceSequences::with_capacity(n_ref);
for _ in 0..n_ref {
let reference_sequence = read_reference_sequence(reader)?;
reference_sequences.insert(reference_sequence.name().into(), reference_sequence);
}
Ok(reference_sequences)
}
fn read_reference_sequence<R>(reader: &mut R) -> io::Result<ReferenceSequence>
where
R: Read,
{
let l_name = reader.read_u32::<LittleEndian>().and_then(|n| {
usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
})?;
let mut c_name = vec![0; l_name];
reader.read_exact(&mut c_name)?;
let name = bytes_with_nul_to_string(&c_name)?;
let l_ref = reader.read_u32::<LittleEndian>().and_then(|len| {
i32::try_from(len).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
})?;
ReferenceSequence::new(name, l_ref).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
}
fn read_record<R>(reader: &mut R, record: &mut Record) -> io::Result<usize>
where
R: Read,
{
let block_size = match reader.read_u32::<LittleEndian>() {
Ok(bs) => usize::try_from(bs).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?,
Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof => return Ok(0),
Err(e) => return Err(e),
};
record.resize(block_size);
reader.read_exact(record)?;
Ok(block_size)
}
pub(crate) fn bytes_with_nul_to_string(buf: &[u8]) -> io::Result<String> {
CStr::from_bytes_with_nul(buf)
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
.and_then(|c_str| {
c_str
.to_str()
.map(|s| s.to_string())
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
})
}
pub(crate) fn resolve_region(
reference_sequences: &ReferenceSequences,
region: &Region,
) -> io::Result<(usize, Interval)> {
if let Some(r) = region.as_mapped() {
let i = reference_sequences.get_index_of(r.name()).ok_or_else(|| {
io::Error::new(
io::ErrorKind::InvalidInput,
format!(
"region reference sequence does not exist in reference sequences: {:?}",
region
),
)
})?;
Ok((i, r.interval()))
} else {
Err(io::Error::new(
io::ErrorKind::InvalidData,
"region is not mapped",
))
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_read_magic() -> io::Result<()> {
let data = b"BAM\x01";
let mut reader = &data[..];
assert!(read_magic(&mut reader).is_ok());
let data = [];
let mut reader = &data[..];
assert!(matches!(
read_magic(&mut reader),
Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof
));
let data = b"MThd";
let mut reader = &data[..];
assert!(matches!(
read_magic(&mut reader),
Err(ref e) if e.kind() == io::ErrorKind::InvalidData
));
Ok(())
}
#[test]
fn test_read_header() -> io::Result<()> {
let expected = "@HD\tVN:1.6\n";
let data_len = expected.len() as u32;
let mut data = data_len.to_le_bytes().to_vec();
data.extend(expected.as_bytes());
let mut reader = &data[..];
let actual = read_header(&mut reader)?;
assert_eq!(actual, expected);
Ok(())
}
#[test]
fn test_read_reference_sequences() -> Result<(), Box<dyn std::error::Error>> {
let data = [
0x01, 0x00, 0x00, 0x00, // n_ref = 1
0x04, 0x00, 0x00, 0x00, // ref[0].l_name = 4
0x73, 0x71, 0x30, 0x00, // ref[0].name = "sq0\x00"
0x08, 0x00, 0x00, 0x00, // ref[0].l_ref = 8
];
let mut reader = &data[..];
let actual = read_reference_sequences(&mut reader)?;
let expected: ReferenceSequences = vec![("sq0", 8)]
.into_iter()
.map(|(name, len)| ReferenceSequence::new(name, len).map(|rs| (name.into(), rs)))
.collect::<Result<_, _>>()?;
assert_eq!(actual, expected);
Ok(())
}
#[test]
fn test_read_record() -> io::Result<()> {
let data = [
0x04, 0x00, 0x00, 0x00, // block_size = 4
0x6e, 0x64, 0x6c, 0x73, // ...
];
let mut reader = &data[..];
let mut record = Record::default();
let block_size = read_record(&mut reader, &mut record)?;
assert_eq!(block_size, 4);
assert_eq!(&record[..], &data[4..]);
Ok(())
}
}