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pub mod allele;
pub use self::allele::Allele;
use std::{error, fmt, str::FromStr};
#[derive(Clone, Debug, Eq, PartialEq)]
pub struct Genotype(Vec<Allele>);
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
Empty,
InvalidAllele(allele::ParseError),
}
impl error::Error for ParseError {}
impl fmt::Display for ParseError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
match self {
Self::Empty => f.write_str("empty input"),
Self::InvalidAllele(e) => write!(f, "invalid allele: {}", e),
}
}
}
impl FromStr for Genotype {
type Err = ParseError;
fn from_str(mut s: &str) -> Result<Self, Self::Err> {
if s.is_empty() {
return Err(ParseError::Empty);
}
let mut alleles = Vec::new();
while let Some(i) = s.chars().skip(1).position(|c| matches!(c, '/' | '|')) {
let allele = s[..i + 1].parse().map_err(ParseError::InvalidAllele)?;
alleles.push(allele);
s = &s[i + 1..];
}
let allele = s.parse().map_err(ParseError::InvalidAllele)?;
alleles.push(allele);
Ok(Self(alleles))
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_from_str() {
use allele::Phasing;
assert_eq!(
"0/1".parse(),
Ok(Genotype(vec![
Allele::new(Some(0), None),
Allele::new(Some(1), Some(Phasing::Unphased)),
]))
);
assert_eq!(
"0|1".parse(),
Ok(Genotype(vec![
Allele::new(Some(0), None),
Allele::new(Some(1), Some(Phasing::Phased)),
]))
);
assert_eq!(
"./.".parse(),
Ok(Genotype(vec![
Allele::new(None, None),
Allele::new(None, Some(Phasing::Unphased)),
]))
);
assert_eq!("0".parse(), Ok(Genotype(vec![Allele::new(Some(0), None)])));
assert_eq!(
"0/1/2".parse(),
Ok(Genotype(vec![
Allele::new(Some(0), None),
Allele::new(Some(1), Some(Phasing::Unphased)),
Allele::new(Some(2), Some(Phasing::Unphased)),
]))
);
assert_eq!(
"0/1|2".parse(),
Ok(Genotype(vec![
Allele::new(Some(0), None),
Allele::new(Some(1), Some(Phasing::Unphased)),
Allele::new(Some(2), Some(Phasing::Phased)),
]))
);
assert!(matches!(
"0:1".parse::<Genotype>(),
Err(ParseError::InvalidAllele(_))
));
}
}