noodles_fastq/io/
writer.rs

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
//! FASTQ writer.

mod builder;
mod record;

use std::io::{self, Write};

pub use self::builder::Builder;
use self::record::write_record;
use crate::Record;

pub(crate) const DEFAULT_DEFINITION_SEPARATOR: u8 = b' ';

/// A FASTQ writer.
pub struct Writer<W> {
    inner: W,
    definition_separator: u8,
}

impl<W> Writer<W> {
    /// Returns a reference to the underlying writer.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq as fastq;
    /// let writer = fastq::io::Writer::new(io::sink());
    /// let _inner = writer.get_ref();
    /// ```
    pub fn get_ref(&self) -> &W {
        &self.inner
    }

    /// Returns a mutable reference to the underlying writer.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq as fastq;
    /// let mut writer = fastq::io::Writer::new(io::sink());
    /// let _inner = writer.get_mut();
    /// ```
    pub fn get_mut(&mut self) -> &mut W {
        &mut self.inner
    }

    /// Unwraps and returns the underlying writer.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq as fastq;
    /// let writer = fastq::io::Writer::new(io::sink());
    /// let _inner = writer.into_inner();
    /// ```
    pub fn into_inner(self) -> W {
        self.inner
    }
}

impl<W> Writer<W>
where
    W: Write,
{
    /// Creates a FASTQ writer.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_fastq as fastq;
    /// let writer = fastq::io::Writer::new(Vec::new());
    /// ```
    pub fn new(inner: W) -> Self {
        Self {
            inner,
            definition_separator: DEFAULT_DEFINITION_SEPARATOR,
        }
    }

    /// Writes a FASTQ record.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq::{self as fastq, record::Definition};
    ///
    /// let mut writer = fastq::io::Writer::new(Vec::new());
    ///
    /// let record = fastq::Record::new(Definition::new("r0", ""), "ATCG", "NDLS");
    /// writer.write_record(&record)?;
    ///
    /// assert_eq!(writer.get_ref(), b"@r0\nATCG\n+\nNDLS\n");
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn write_record(&mut self, record: &Record) -> io::Result<()> {
        write_record(&mut self.inner, self.definition_separator, record)
    }
}