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//! Indexed alignment reader.
mod builder;
pub use self::builder::Builder;
use std::io::{self, Read, Seek};
use noodles_bam as bam;
use noodles_bgzf as bgzf;
use noodles_core::Region;
use noodles_cram as cram;
use noodles_sam::{self as sam, alignment::Record};
/// An indexed alignment reader.
pub enum IndexedReader<R> {
/// SAM.
Sam(sam::io::IndexedReader<R>),
/// BAM.
Bam(bam::io::IndexedReader<bgzf::Reader<R>>),
/// CRAM.
Cram(cram::io::IndexedReader<R>),
}
impl<R> IndexedReader<R>
where
R: Read,
{
/// Reads the SAM header.
///
/// # Examples
///
/// ```no_run
/// use noodles_util::alignment;
///
/// let mut reader = alignment::io::indexed_reader::Builder::default()
/// .build_from_path("sample.bam")?;
///
/// let _header = reader.read_header()?;
/// # Ok::<_, std::io::Error>(())
/// ```
pub fn read_header(&mut self) -> io::Result<sam::Header> {
match self {
Self::Sam(reader) => reader.read_header(),
Self::Bam(reader) => reader.read_header(),
Self::Cram(reader) => reader.read_header(),
}
}
/// Returns an iterator over records starting from the current stream position.
///
/// # Examples
///
/// ```no_run
/// use noodles_util::alignment;
///
/// let mut reader = alignment::io::indexed_reader::Builder::default()
/// .build_from_path("sample.bam")?;
///
/// let header = reader.read_header()?;
///
/// for result in reader.records(&header) {
/// let record = result?;
/// // ...
/// }
/// # Ok::<_, std::io::Error>(())
/// ```
pub fn records<'r, 'h: 'r>(
&'r mut self,
header: &'h sam::Header,
) -> impl Iterator<Item = io::Result<Box<dyn Record>>> + 'r {
let records: Box<dyn Iterator<Item = io::Result<Box<dyn Record>>>> = match self {
Self::Sam(reader) => Box::new(
reader
.records()
.map(|result| result.map(|record| Box::new(record) as Box<dyn Record>)),
),
Self::Bam(reader) => Box::new(
reader
.records()
.map(|result| result.map(|record| Box::new(record) as Box<dyn Record>)),
),
Self::Cram(reader) => Box::new(reader.records(header).map(|result| {
result.and_then(|record| {
record
.try_into_alignment_record(header)
.map(|alignment_record| {
Box::new(alignment_record) as Box<dyn sam::alignment::Record>
})
})
})),
};
records
}
}
impl<R> IndexedReader<R>
where
R: Read + Seek,
{
/// Returns an iterator over records that intersects the given region.
///
/// # Examples
///
/// ```no_run
/// use noodles_util::alignment;
///
/// let mut reader = alignment::io::indexed_reader::Builder::default()
/// .build_from_path("sample.bam")?;
///
/// let header = reader.read_header()?;
///
/// let region = "sq0:8-13".parse()?;
/// let query = reader.query(&header, ®ion)?;
///
/// for result in query {
/// let record = result?;
/// // ...
/// }
/// # Ok::<_, Box<dyn std::error::Error>>(())
/// ```
pub fn query<'r, 'h: 'r>(
&'r mut self,
header: &'h sam::Header,
region: &Region,
) -> io::Result<impl Iterator<Item = io::Result<Box<dyn Record>>> + 'r> {
let records: Box<dyn Iterator<Item = io::Result<Box<dyn Record>>>> = match self {
Self::Sam(reader) => {
let query = reader.query(header, region)?;
Box::new(
query.map(|result| result.map(|record| Box::new(record) as Box<dyn Record>)),
)
}
Self::Bam(reader) => {
let query = reader.query(header, region)?;
Box::new(
query.map(|result| result.map(|record| Box::new(record) as Box<dyn Record>)),
)
}
Self::Cram(reader) => {
let query = reader.query(header, region)?;
Box::new(query.map(|result| {
result.and_then(|record| {
record
.try_into_alignment_record(header)
.map(|alignment_record| {
Box::new(alignment_record) as Box<dyn sam::alignment::Record>
})
})
}))
}
};
Ok(records)
}
}