noodles_sam/record/
quality_scores.rs

1//! Raw SAM record quality scores.
2
3use std::io;
4
5/// Raw SAM record quality scores.
6#[derive(Debug, Eq, PartialEq)]
7pub struct QualityScores<'a>(&'a [u8]);
8
9impl<'a> QualityScores<'a> {
10    /// Creates raw SAM record quality scores.
11    ///
12    /// # Examples
13    ///
14    /// ```
15    /// use noodles_sam::record::QualityScores;
16    /// let quality_scores = QualityScores::new(b"NDLS");
17    /// ```
18    pub fn new(buf: &'a [u8]) -> Self {
19        Self(buf)
20    }
21
22    /// Returns whether there are any scores.
23    ///
24    /// # Examples
25    ///
26    /// ```
27    /// use noodles_sam::record::QualityScores;
28    ///
29    /// let quality_scores = QualityScores::new(b"");
30    /// assert!(quality_scores.is_empty());
31    ///
32    /// let quality_scores = QualityScores::new(b"NDLS");
33    /// assert!(!quality_scores.is_empty());
34    /// ```
35    pub fn is_empty(&self) -> bool {
36        self.0.is_empty()
37    }
38
39    /// Returns the number of scores.
40    ///
41    /// # Examples
42    ///
43    /// ```
44    /// use noodles_sam::record::QualityScores;
45    /// let quality_scores = QualityScores::new(b"NDLS");
46    /// assert_eq!(quality_scores.len(), 4);
47    /// ```
48    pub fn len(&self) -> usize {
49        self.0.len()
50    }
51}
52
53impl crate::alignment::record::QualityScores for QualityScores<'_> {
54    fn is_empty(&self) -> bool {
55        self.is_empty()
56    }
57
58    fn len(&self) -> usize {
59        self.len()
60    }
61
62    fn iter(&self) -> Box<dyn Iterator<Item = io::Result<u8>> + '_> {
63        const OFFSET: u8 = b'!';
64
65        Box::new(self.as_ref().iter().map(|&b| {
66            b.checked_sub(OFFSET)
67                .ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "invalid score"))
68        }))
69    }
70}
71
72impl AsRef<[u8]> for QualityScores<'_> {
73    fn as_ref(&self) -> &[u8] {
74        self.0
75    }
76}
77
78#[cfg(test)]
79mod tests {
80    use crate::alignment::record::QualityScores as _;
81
82    use super::*;
83
84    #[test]
85    fn test_iter() -> io::Result<()> {
86        let quality_scores = QualityScores::new(b"NDLS");
87
88        assert_eq!(
89            quality_scores.iter().collect::<io::Result<Vec<_>>>()?,
90            [45, 35, 43, 50]
91        );
92
93        let quality_scores = QualityScores::new(&[0x00]);
94
95        assert!(matches!(
96            quality_scores.iter().collect::<io::Result<Vec<_>>>(),
97            Err(e) if e.kind() == io::ErrorKind::InvalidData
98        ));
99
100        Ok(())
101    }
102}
noodles_sam/record/quality_scores.rs

noodles_sam/record/
quality_scores.rs
