noodles_sam/io/reader/
builder.rs

1use std::{
2    fs::File,
3    io::{self, BufRead, BufReader, Read},
4    path::Path,
5};
6
7use noodles_bgzf as bgzf;
8
9use super::Reader;
10use crate::io::CompressionMethod;
11
12/// A SAM reader builder.
13#[derive(Debug, Default)]
14pub struct Builder {
15    compression_method: Option<CompressionMethod>,
16}
17
18impl Builder {
19    /// Sets the compression method.
20    ///
21    /// # Examples
22    ///
23    /// ```
24    /// use noodles_sam::io::{reader::Builder, CompressionMethod};
25    /// let builder = Builder::default().set_compression_method(CompressionMethod::Bgzf);
26    /// ```
27    pub fn set_compression_method(mut self, compression_method: CompressionMethod) -> Self {
28        self.compression_method = Some(compression_method);
29        self
30    }
31
32    /// Builds a SAM reader from a path.
33    ///
34    /// By default, the compression method will be autodetected. This can be overridden by using
35    /// [`Self::set_compression_method`].
36    ///
37    /// # Examples
38    ///
39    /// ```no_run
40    /// # use std::io;
41    /// use noodles_sam::io::reader::Builder;
42    /// let reader = Builder::default().build_from_path("sample.sam")?;
43    /// # Ok::<_, std::io::Error>(())
44    /// ```
45    pub fn build_from_path<P>(mut self, src: P) -> io::Result<Reader<Box<dyn BufRead>>>
46    where
47        P: AsRef<Path>,
48    {
49        let src = src.as_ref();
50
51        if self.compression_method.is_none() {
52            self.compression_method = match src.extension().and_then(|ext| ext.to_str()) {
53                Some("gz" | "bgz") => Some(CompressionMethod::Bgzf),
54                _ => Some(CompressionMethod::None),
55            };
56        }
57
58        let reader = File::open(src)?;
59        self.build_from_reader(reader)
60    }
61
62    /// Builds a SAM reader from a reader.
63    ///
64    /// # Examples
65    ///
66    /// ```
67    /// # use std::io;
68    /// use noodles_sam::io::reader::Builder;
69    /// let reader = Builder::default().build_from_reader(io::empty());
70    /// ```
71    pub fn build_from_reader<'r, R>(self, reader: R) -> io::Result<Reader<Box<dyn BufRead + 'r>>>
72    where
73        R: Read + 'r,
74    {
75        let inner: Box<dyn BufRead> = match self.compression_method {
76            Some(CompressionMethod::Bgzf) => Box::new(bgzf::Reader::new(reader)),
77            Some(CompressionMethod::None) | None => Box::new(BufReader::new(reader)),
78        };
79
80        Ok(Reader::new(inner))
81    }
82}
noodles_sam/io/reader/builder.rs

noodles_sam/io/reader/
builder.rs
