noodles-util 0.53.1

noodles support utilities
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110

//! Async alignment writer.

mod builder;

use noodles_bam as bam;
use noodles_cram as cram;
use noodles_sam as sam;
use tokio::io::{self, AsyncWrite, AsyncWriteExt};

pub use self::builder::Builder;

/// An async alignment writer.
pub enum Writer<W: AsyncWrite> {
    /// SAM.
    Sam(sam::r#async::io::Writer<W>),
    /// BAM.
    Bam(bam::r#async::io::Writer<W>),
    /// CRAM.
    Cram(cram::r#async::io::Writer<W>),
}

impl<W> Writer<W>
where
    W: AsyncWrite + Unpin,
{
    /// Writes a SAM header.
    ///
    /// # Examples
    ///
    /// ```
    /// # #[tokio::main]
    /// # async fn main() -> tokio::io::Result<()> {
    /// use noodles_sam as sam;
    /// use noodles_util::alignment::r#async::io::writer::Builder;
    /// use tokio::io::{self, AsyncWriteExt};
    ///
    /// let mut writer = Builder::default().build_from_writer(io::sink()).await?;
    ///
    /// let header = sam::Header::default();
    /// writer.write_header(&header).await?;
    /// # Ok(())
    /// # }
    /// ```
    pub async fn write_header(&mut self, header: &sam::Header) -> io::Result<()> {
        match self {
            Self::Sam(writer) => writer.write_header(header).await,
            Self::Bam(writer) => writer.write_header(header).await,
            Self::Cram(writer) => writer.write_header(header).await,
        }
    }

    /// Writes an alignment record.
    ///
    /// # Examples
    ///
    /// ```
    /// # #[tokio::main]
    /// # async fn main() -> tokio::io::Result<()> {
    /// use noodles_sam as sam;
    /// use noodles_util::alignment::r#async::io::writer::Builder;
    /// use tokio::io::{self, AsyncWriteExt};
    ///
    /// let mut writer = Builder::default().build_from_writer(io::sink()).await?;
    ///
    /// let header = sam::Header::default();
    /// let record = sam::Record::default();
    /// writer.write_record(&header, &record).await?;
    /// # Ok(())
    /// # }
    /// ```
    pub async fn write_record(
        &mut self,
        header: &sam::Header,
        record: &dyn sam::alignment::Record,
    ) -> io::Result<()> {
        match self {
            Self::Sam(writer) => writer.write_alignment_record(header, record).await,
            Self::Bam(writer) => writer.write_alignment_record(header, record).await,
            Self::Cram(writer) => writer.write_alignment_record(header, record).await,
        }
    }

    /// Shuts down the alignment format writer.
    ///
    /// # Examples
    ///
    /// ```
    /// # #[tokio::main]
    /// # async fn main() -> tokio::io::Result<()> {
    /// use noodles_sam as sam;
    /// use noodles_util::alignment::{self, io::Format};
    /// use tokio::io;
    ///
    /// let mut writer = alignment::r#async::io::writer::Builder::default()
    ///     .set_format(Format::Sam)
    ///     .build_from_writer(io::sink()).await?;
    ///
    /// let header = sam::Header::default();
    /// writer.shutdown(&header).await?;
    /// # Ok(())
    /// # }
    /// ```
    pub async fn shutdown(&mut self, header: &sam::Header) -> io::Result<()> {
        match self {
            Self::Sam(writer) => writer.get_mut().shutdown().await,
            Self::Bam(writer) => writer.shutdown().await,
            Self::Cram(writer) => writer.shutdown(header).await,
        }
    }
}