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

use std::{
    ffi::CString,
    io::{self, Write},
    num::NonZeroUsize,
};

use byteorder::{LittleEndian, WriteBytesExt};
use noodles_sam::{
    self as sam,
    header::{record::value::map, ReferenceSequences},
};

pub(super) fn write_header<W>(writer: &mut W, header: &sam::Header) -> io::Result<()>
where
    W: Write,
{
    write_raw_header(writer, header)?;
    write_reference_sequences(writer, header.reference_sequences())?;
    Ok(())
}

fn write_raw_header<W>(writer: &mut W, header: &sam::Header) -> io::Result<()>
where
    W: Write,
{
    use crate::MAGIC_NUMBER;

    writer.write_all(MAGIC_NUMBER)?;

    let text = header.to_string();
    let l_text =
        i32::try_from(text.len()).map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
    writer.write_i32::<LittleEndian>(l_text)?;

    writer.write_all(text.as_bytes())?;

    Ok(())
}

pub fn write_reference_sequences<W>(
    writer: &mut W,
    reference_sequences: &ReferenceSequences,
) -> io::Result<()>
where
    W: Write,
{
    let n_ref = i32::try_from(reference_sequences.len())
        .map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
    writer.write_i32::<LittleEndian>(n_ref)?;

    for (name, reference_sequence) in reference_sequences {
        write_reference_sequence(writer, name, reference_sequence.length())?;
    }

    Ok(())
}

fn write_reference_sequence<W>(
    writer: &mut W,
    reference_sequence_name: &map::reference_sequence::Name,
    length: NonZeroUsize,
) -> io::Result<()>
where
    W: Write,
{
    let c_name = CString::new(reference_sequence_name.as_bytes())
        .map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
    let name = c_name.as_bytes_with_nul();

    let l_name =
        u32::try_from(name.len()).map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
    writer.write_u32::<LittleEndian>(l_name)?;
    writer.write_all(name)?;

    let l_ref = i32::try_from(usize::from(length))
        .map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
    writer.write_i32::<LittleEndian>(l_ref)?;

    Ok(())
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_write_raw_header() -> Result<(), Box<dyn std::error::Error>> {
        use sam::header::record::value::{
            map::{self, header::Version},
            Map,
        };

        let header = sam::Header::builder()
            .set_header(Map::<map::Header>::new(Version::new(1, 6)))
            .build();

        let mut buf = Vec::new();
        write_raw_header(&mut buf, &header)?;

        let mut expected = vec![
            b'B', b'A', b'M', 0x01, // magic
            0x0b, 0x00, 0x00, 0x00, // l_text = 11
        ];
        expected.extend_from_slice(b"@HD\tVN:1.6\n"); // text

        assert_eq!(buf, expected);

        Ok(())
    }

    #[test]
    fn test_write_reference_sequences() -> Result<(), Box<dyn std::error::Error>> {
        use sam::header::record::value::{map::ReferenceSequence, Map};

        let reference_sequences = [(
            "sq0".parse()?,
            Map::<ReferenceSequence>::new(NonZeroUsize::try_from(8)?),
        )]
        .into_iter()
        .collect();

        let mut buf = Vec::new();
        write_reference_sequences(&mut buf, &reference_sequences)?;

        let expected = [
            0x01, 0x00, 0x00, 0x00, // n_ref = 1
            0x04, 0x00, 0x00, 0x00, // ref[0].l_name = 4
            b's', b'q', b'0', 0x00, // ref[0].name = b"sq0\x00"
            0x08, 0x00, 0x00, 0x00, // ref[0].l_ref = 8
        ];

        assert_eq!(buf, expected);

        Ok(())
    }

    #[test]
    fn test_write_reference_sequence() -> Result<(), Box<dyn std::error::Error>> {
        let mut buf = Vec::new();
        let reference_sequence_name = "sq0".parse()?;
        let length = NonZeroUsize::try_from(8)?;
        write_reference_sequence(&mut buf, &reference_sequence_name, length)?;

        let expected = [
            0x04, 0x00, 0x00, 0x00, // l_name = 4
            0x73, 0x71, 0x30, 0x00, // name = b"sq0\x00"
            0x08, 0x00, 0x00, 0x00, // l_ref = 8
        ];

        assert_eq!(buf, expected);

        Ok(())
    }
}