noodles_util/alignment/async/io/
reader.rs

1//! Async alignment reader.
2
3mod builder;
4mod inner;
5
6use futures::Stream;
7use noodles_sam as sam;
8use tokio::io::{self, AsyncRead};
9
10pub use self::builder::Builder;
11use self::inner::Inner;
12
13/// An async alignment reader.
14pub struct Reader<R>(Inner<R>)
15where
16    R: AsyncRead + Unpin;
17
18impl<R> Reader<R>
19where
20    R: AsyncRead + Unpin,
21{
22    /// Creates an async alignment reader.
23    ///
24    /// This attempts to autodetect the compression method and format of the input.
25    ///
26    /// # Examples
27    ///
28    /// ```
29    /// # #[tokio::main]
30    /// # async fn main() -> tokio::io::Result<()> {
31    /// use noodles_util::alignment;
32    /// use tokio::io;
33    /// let reader = alignment::r#async::io::Reader::new(io::empty()).await?;
34    /// # Ok(())
35    /// # }
36    /// ```
37    pub async fn new(reader: R) -> io::Result<Self> {
38        Builder::default().build_from_reader(reader).await
39    }
40
41    /// Reads the SAM header.
42    ///
43    /// # Examples
44    ///
45    /// ```
46    /// # #[tokio::main]
47    /// # async fn main() -> tokio::io::Result<()> {
48    /// use noodles_util::alignment;
49    /// use tokio::io;
50    /// let mut reader = alignment::r#async::io::Reader::new(io::empty()).await?;
51    /// let header = reader.read_header().await?;
52    /// # Ok(())
53    /// # }
54    /// ```
55    pub async fn read_header(&mut self) -> io::Result<sam::Header> {
56        self.0.read_header().await
57    }
58
59    /// Returns an iterator over records starting from the current stream position.
60    ///
61    /// # Examples
62    ///
63    /// ```
64    /// # #[tokio::main]
65    /// # async fn main() -> tokio::io::Result<()> {
66    /// use futures::TryStreamExt;
67    /// use noodles_util::alignment;
68    /// use tokio::io;
69    ///
70    /// let mut reader = alignment::r#async::io::Reader::new(io::empty()).await?;
71    /// let header = reader.read_header().await?;
72    ///
73    /// let mut records = reader.records(&header);
74    ///
75    /// while let Some(record) = records.try_next().await? {
76    ///     // ...
77    /// }
78    /// # Ok(())
79    /// # }
80    /// ```
81    pub fn records<'r, 'h: 'r>(
82        &'r mut self,
83        header: &'h sam::Header,
84    ) -> impl Stream<Item = io::Result<Box<dyn sam::alignment::Record>>> + 'r {
85        self.0.records(header)
86    }
87}
noodles_util/alignment/async/io/reader.rs

noodles_util/alignment/async/io/
reader.rs
