noodles_sam/record/
sequence.rs

1/// A raw SAM record sequence.
2#[derive(Debug, Eq, PartialEq)]
3pub struct Sequence<'a>(&'a [u8]);
4
5impl<'a> Sequence<'a> {
6    pub(crate) fn new(buf: &'a [u8]) -> Self {
7        Self(buf)
8    }
9
10    /// Returns whether the sequence is empty.
11    pub fn is_empty(&self) -> bool {
12        self.0.is_empty()
13    }
14
15    /// Returns the base at the given index.
16    pub fn get(&self, i: usize) -> Option<u8> {
17        self.0.get(i).copied()
18    }
19
20    /// Returns the number of bases in the sequence.
21    pub fn len(&self) -> usize {
22        self.0.len()
23    }
24}
25
26impl AsRef<[u8]> for Sequence<'_> {
27    fn as_ref(&self) -> &[u8] {
28        self.0
29    }
30}
31
32impl crate::alignment::record::Sequence for Sequence<'_> {
33    fn is_empty(&self) -> bool {
34        self.is_empty()
35    }
36
37    fn len(&self) -> usize {
38        self.len()
39    }
40
41    fn get(&self, i: usize) -> Option<u8> {
42        self.get(i)
43    }
44
45    fn split_at_checked(
46        &self,
47        mid: usize,
48    ) -> Option<(
49        Box<dyn crate::alignment::record::Sequence + '_>,
50        Box<dyn crate::alignment::record::Sequence + '_>,
51    )> {
52        if mid <= self.len() {
53            let (left, right) = self.0.split_at(mid);
54            Some((
55                Box::new(Sequence::new(left)),
56                Box::new(Sequence::new(right)),
57            ))
58        } else {
59            None
60        }
61    }
62
63    fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_> {
64        Box::new(self.as_ref().iter().copied())
65    }
66}
67
68impl<'a> From<Sequence<'a>> for crate::alignment::record_buf::Sequence {
69    fn from(sequence: Sequence<'a>) -> Self {
70        Self::from(sequence.0.to_vec())
71    }
72}
73
74#[cfg(test)]
75mod tests {
76    use super::*;
77
78    #[test]
79    fn test_crate_alignment_record_sequence_iter() {
80        fn t(src: &[u8]) {
81            let sequence: &dyn crate::alignment::record::Sequence = &Sequence::new(src);
82            let actual: Vec<_> = sequence.iter().collect();
83            assert_eq!(actual, src);
84        }
85
86        t(&[]);
87        t(b"ACG");
88        t(b"ACGT");
89    }
90}
noodles_sam/record/sequence.rs

noodles_sam/record/
sequence.rs
