noodles_vcf/record/samples/
series.rs

1//! VCF record samples series.
2
3pub mod value;
4
5use std::io;
6
7use super::Samples;
8use crate::{variant::record::samples::series::Value, Header};
9
10/// VCF record samples series.
11pub struct Series<'r> {
12    name: &'r str,
13    samples: &'r Samples<'r>,
14    i: usize,
15}
16
17impl<'r> Series<'r> {
18    pub(super) fn new(name: &'r str, samples: &'r Samples<'r>, i: usize) -> Self {
19        Self { name, samples, i }
20    }
21}
22
23impl crate::variant::record::samples::Series for Series<'_> {
24    fn name<'a, 'h: 'a>(&'a self, _: &'h Header) -> io::Result<&'a str> {
25        Ok(self.name)
26    }
27
28    fn get<'a, 'h: 'a>(
29        &'a self,
30        header: &'h Header,
31        i: usize,
32    ) -> Option<Option<io::Result<Value<'a>>>> {
33        let sample = self.samples.iter().nth(i)?;
34        sample.get_index(header, self.i)
35    }
36
37    fn iter<'a, 'h: 'a>(
38        &'a self,
39        header: &'h Header,
40    ) -> Box<dyn Iterator<Item = io::Result<Option<Value<'a>>>> + 'a> {
41        Box::new(
42            self.samples
43                .iter()
44                .map(|sample| match sample.get_index(header, self.i) {
45                    Some(value) => value.transpose(),
46                    None => Ok(None),
47                }),
48        )
49    }
50}
51
52#[cfg(test)]
53mod tests {
54    use super::*;
55    use crate::variant::record::{samples::keys::key, samples::Series as _};
56
57    #[test]
58    fn test_name() {
59        let header = Header::default();
60
61        let samples = Samples::new("GT:GQ\t0|0:13\t0/1:8");
62        let series = Series::new(key::CONDITIONAL_GENOTYPE_QUALITY, &samples, 1);
63
64        assert!(matches!(
65            series.name(&header),
66            Ok(name) if name == key::CONDITIONAL_GENOTYPE_QUALITY
67        ));
68    }
69
70    #[test]
71    fn test_get() {
72        let header = Header::default();
73
74        let samples = Samples::new("GT:GQ\t0|0:13\t0/1:8");
75        let series = Series::new(key::CONDITIONAL_GENOTYPE_QUALITY, &samples, 1);
76
77        assert!(matches!(
78            series.get(&header, 0),
79            Some(Some(Ok(Value::Integer(13))))
80        ));
81
82        assert!(matches!(
83            series.get(&header, 1),
84            Some(Some(Ok(Value::Integer(8))))
85        ));
86
87        assert!(series.get(&header, 2).is_none());
88    }
89}
noodles_vcf/record/samples/series.rs

noodles_vcf/record/samples/
series.rs
