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use std::{
fs::File,
io::{self, BufReader, Read},
path::Path,
};
use noodles_bam as bam;
use noodles_cram::{self as cram, crai};
use noodles_csi::{
self as csi,
binning_index::index::reference_sequence::index::{BinnedIndex, LinearIndex},
BinningIndex,
};
use noodles_fasta as fasta;
use noodles_sam as sam;
use super::IndexedReader;
use crate::alignment::io::{
reader::builder::{detect_compression_method, detect_format},
CompressionMethod, Format,
};
/// An alignment index.
pub enum Index {
/// CSI.
Csi(Box<dyn BinningIndex>),
/// CRAI.
Crai(crai::Index),
}
impl From<csi::binning_index::Index<BinnedIndex>> for Index {
fn from(index: csi::binning_index::Index<BinnedIndex>) -> Self {
Self::Csi(Box::new(index))
}
}
impl From<csi::binning_index::Index<LinearIndex>> for Index {
fn from(index: csi::binning_index::Index<LinearIndex>) -> Self {
Self::Csi(Box::new(index))
}
}
impl From<crai::Index> for Index {
fn from(index: crai::Index) -> Self {
Self::Crai(index)
}
}
/// An indexed alignment reader builder.
#[derive(Default)]
pub struct Builder {
compression_method: Option<Option<CompressionMethod>>,
format: Option<Format>,
reference_sequence_repository: fasta::Repository,
index: Option<Index>,
}
impl Builder {
/// Sets the compression method.
///
/// By default, the compression method is autodetected on build. This can be used to override
/// it, but note that only bgzip-compressed streams can be indexed.
///
/// # Examples
///
/// ```
/// use noodles_util::alignment::{self, io::CompressionMethod};
/// let builder = alignment::io::indexed_reader::Builder::default()
/// .set_compression_method(Some(CompressionMethod::Bgzf));
/// ```
pub fn set_compression_method(mut self, compression_method: Option<CompressionMethod>) -> Self {
self.compression_method = Some(compression_method);
self
}
/// Sets the format of the input.
///
/// By default, the format is autodetected on build. This can be used to override it.
///
/// # Examples
///
/// ```
/// use noodles_util::alignment::{self, io::Format};
/// let builder = alignment::io::indexed_reader::Builder::default()
/// .set_format(Format::Sam);
/// ```
pub fn set_format(mut self, format: Format) -> Self {
self.format = Some(format);
self
}
/// Sets the reference sequence repository.
pub fn set_reference_sequence_repository(
mut self,
reference_sequence_repository: fasta::Repository,
) -> Self {
self.reference_sequence_repository = reference_sequence_repository;
self
}
/// Sets an index.
///
/// When building from a path ([`Self::build_from_path`]), an associated index depending on the
/// format will attempt to be loaded. This can be used to override it if the index cannot be
/// found or when building from a reader ([`Self::build_from_reader`]).
///
/// # Examples
///
/// ```
/// use noodles_bam::bai;
/// use noodles_util::alignment;
///
/// let index = bai::Index::default();
/// let builder = alignment::io::indexed_reader::Builder::default()
/// .set_index(index);
/// ```
pub fn set_index<I>(mut self, index: I) -> Self
where
I: Into<Index>,
{
self.index = Some(index.into());
self
}
/// Builds an indexed alignment reader from a path.
///
/// The compression method and format will be autodetected, if not overridden. If no index is
/// set ([`Self::set_index`]), this will attempt to load an associated index depending on the
/// format.
///
/// # Examples
///
/// ```no_run
/// use noodles_util::alignment;
/// let reader = alignment::io::indexed_reader::Builder::default()
/// .build_from_path("sample.bam")?;
/// # Ok::<_, std::io::Error>(())
/// ```
pub fn build_from_path<P>(self, src: P) -> io::Result<IndexedReader<File>>
where
P: AsRef<Path>,
{
let mut reader = File::open(src.as_ref()).map(BufReader::new)?;
let compression_method = match self.compression_method {
Some(compression_method) => compression_method,
None => detect_compression_method(&mut reader)?,
};
let format = match self.format {
Some(format) => format,
None => detect_format(&mut reader, compression_method)?,
};
match (format, compression_method) {
(Format::Sam | Format::Bam, None) => Err(io::Error::new(
io::ErrorKind::InvalidData,
"source not bgzip-compressed",
)),
(Format::Sam, Some(CompressionMethod::Bgzf)) => {
sam::io::indexed_reader::Builder::default()
.build_from_path(src)
.map(IndexedReader::Sam)
}
(Format::Bam, Some(CompressionMethod::Bgzf)) => {
bam::io::indexed_reader::Builder::default()
.build_from_path(src)
.map(IndexedReader::Bam)
}
(Format::Cram, None) => cram::io::indexed_reader::Builder::default()
.set_reference_sequence_repository(self.reference_sequence_repository)
.build_from_path(src)
.map(IndexedReader::Cram),
(Format::Cram, Some(CompressionMethod::Bgzf)) => Err(io::Error::new(
io::ErrorKind::InvalidData,
"CRAM cannot be bgzip-compressed",
)),
}
}
/// Builds an indexed alignment reader from a reader.
///
/// The compression method and format will be autodetected, if not overridden. An index must be
/// set ([`Self::set_index`]). The reader must be a bgzip-compressed stream.
///
/// # Examples
///
/// ```
/// # use std::io::{self, Write};
/// use noodles_bam::bai;
/// use noodles_bgzf as bgzf;
/// use noodles_util::alignment;
///
/// let mut writer = bgzf::Writer::new(Vec::new());
/// writer.write_all(b"BAM\x01")?;
/// let data = writer.finish()?;
///
/// let index = bai::Index::default();
/// let reader = alignment::io::indexed_reader::Builder::default()
/// .set_index(index)
/// .build_from_reader(&data[..])?;
/// # Ok::<_, std::io::Error>(())
/// ```
pub fn build_from_reader<R>(self, reader: R) -> io::Result<IndexedReader<BufReader<R>>>
where
R: Read,
{
let mut reader = BufReader::new(reader);
let compression_method = match self.compression_method {
Some(compression_method) => compression_method,
None => detect_compression_method(&mut reader)?,
};
let format = match self.format {
Some(format) => format,
None => detect_format(&mut reader, compression_method)?,
};
match (format, compression_method) {
(Format::Sam | Format::Bam, None) => Err(io::Error::new(
io::ErrorKind::InvalidData,
"source not bgzip-compressed",
)),
(Format::Sam, Some(CompressionMethod::Bgzf)) => {
let mut builder = sam::io::indexed_reader::Builder::default();
if let Some(Index::Csi(index)) = self.index {
builder = builder.set_index(index);
}
builder.build_from_reader(reader).map(IndexedReader::Sam)
}
(Format::Bam, Some(CompressionMethod::Bgzf)) => {
let mut builder = bam::io::indexed_reader::Builder::default();
if let Some(Index::Csi(index)) = self.index {
builder = builder.set_index(index);
}
builder.build_from_reader(reader).map(IndexedReader::Bam)
}
(Format::Cram, None) => {
let mut builder = cram::io::indexed_reader::Builder::default()
.set_reference_sequence_repository(self.reference_sequence_repository);
if let Some(Index::Crai(index)) = self.index {
builder = builder.set_index(index);
}
builder.build_from_reader(reader).map(IndexedReader::Cram)
}
(Format::Cram, Some(CompressionMethod::Bgzf)) => Err(io::Error::new(
io::ErrorKind::InvalidData,
"CRAM cannot be bgzip-compressed",
)),
}
}
}