bio_types/
variant.rs

1use crate::genome;
2use crate::sequence::{Base, Sequence};
3
4#[cfg(feature = "serde")]
5use serde::{Deserialize, Serialize};
6
7/// A trait for providing variant information. This can e.g. be implemented by file readers.
8pub trait AbstractVariant: genome::AbstractLocus {
9    fn kind(&self) -> &Kind;
10}
11
12/// Possible genomic variants.
13#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
14#[derive(Debug, PartialEq, Eq, Clone, Hash)]
15pub enum Kind {
16    SNV(Base),
17    MNV(Sequence),
18    Insertion(Sequence),
19    Deletion(genome::Length),
20    Duplication(genome::Length),
21    Inversion(genome::Length),
22    None,
23}
24
25impl Kind {
26    /// Return variant length.
27    pub fn len(&self) -> genome::Length {
28        match *self {
29            Kind::SNV(_) => 1,
30            Kind::MNV(ref s) => s.len() as u64,
31            Kind::Insertion(ref s) => s.len() as u64,
32            Kind::Deletion(l) => l,
33            Kind::Duplication(l) => l,
34            Kind::Inversion(l) => l,
35            Kind::None => 1,
36        }
37    }
38    /// Check if length is zero
39    pub fn is_empty(&self) -> bool {
40        self.len() == 0
41    }
42}
bio_types/variant.rs

bio_types/
variant.rs
