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
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168

//! SAM writer.

mod builder;
mod header;
mod num;
pub mod record;

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

pub use self::builder::Builder;
use self::header::write_header;
pub(crate) use self::record::write_record;
use crate::{Header, Record};

/// A SAM writer.
///
/// The SAM format is comprised of two parts: 1) a header and 2) a list of records.
///
/// Each header line is prefixed with an `@` (at sign). The header is optional and may be empty.
///
/// SAM records are line-based and follow directly after the header or the start of the file until
/// EOF.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_sam as sam;
///
/// let mut writer = sam::io::Writer::new(Vec::new());
///
/// let header = sam::Header::builder().add_comment("noodles-sam").build();
/// writer.write_header(&header)?;
///
/// let record = sam::Record::default();
/// writer.write_record(&header, &record)?;
///
/// let expected = b"@CO\tnoodles-sam
/// *\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*
/// ";
///
/// assert_eq!(&writer.get_ref()[..], &expected[..]);
/// # Ok::<(), io::Error>(())
/// ```
pub struct Writer<W>
where
    W: Write,
{
    inner: W,
}

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

    /// Returns a reference to the underlying writer.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_sam as sam;
    /// let writer = sam::io::Writer::new(Vec::new());
    /// assert!(writer.get_ref().is_empty());
    /// ```
    pub fn get_ref(&self) -> &W {
        &self.inner
    }

    /// Returns a mutable reference to the underlying writer.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_sam as sam;
    /// let mut writer = sam::io::Writer::new(Vec::new());
    /// assert!(writer.get_mut().is_empty());
    /// ```
    pub fn get_mut(&mut self) -> &mut W {
        &mut self.inner
    }

    /// Returns the underlying writer.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_sam as sam;
    /// let writer = sam::io::Writer::new(Vec::new());
    /// assert!(writer.into_inner().is_empty());
    /// ```
    pub fn into_inner(self) -> W {
        self.inner
    }

    /// Writes a SAM header.
    ///
    /// The SAM header is optional, though recommended to include. A call to this method can be
    /// omitted if it is empty.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_sam as sam;
    /// let mut writer = sam::io::Writer::new(Vec::new());
    /// let header = sam::Header::builder().add_comment("noodles-sam").build();
    /// writer.write_header(&header)?;
    /// assert_eq!(writer.get_ref(), b"@CO\tnoodles-sam\n");
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn write_header(&mut self, header: &Header) -> io::Result<()> {
        write_header(&mut self.inner, header)
    }

    /// Writes a SAM record.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_sam as sam;
    ///
    /// let mut writer = sam::io::Writer::new(Vec::new());
    ///
    /// let header = sam::Header::default();
    /// let record = sam::Record::default();
    /// writer.write_record(&header, &record)?;
    ///
    /// assert_eq!(writer.get_ref(), b"*\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*\n");
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn write_record(&mut self, header: &Header, record: &Record) -> io::Result<()> {
        write_record(&mut self.inner, header, record)
    }
}

impl<W> crate::alignment::io::Write for Writer<W>
where
    W: Write,
{
    fn write_alignment_header(&mut self, header: &Header) -> io::Result<()> {
        self.write_header(header)
    }

    fn write_alignment_record(
        &mut self,
        header: &Header,
        record: &dyn crate::alignment::Record,
    ) -> io::Result<()> {
        write_record(&mut self.inner, header, record)
    }

    fn finish(&mut self, _: &Header) -> io::Result<()> {
        Ok(())
    }
}