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pub mod op;
use std::{error, fmt, ops::Deref, str::FromStr};
pub use self::op::Op;
use super::NULL_FIELD;
use self::op::Kind;
#[derive(Clone, Debug, Default, Eq, PartialEq)]
pub struct Cigar(Vec<Op>);
impl Cigar {
pub fn reference_len(&self) -> u32 {
self.iter()
.filter_map(|op| match op.kind() {
Kind::Match | Kind::Deletion | Kind::Skip | Kind::SeqMatch | Kind::SeqMismatch => {
Some(op.len())
}
_ => None,
})
.sum()
}
pub fn read_len(&self) -> u32 {
self.iter()
.filter_map(|op| match op.kind() {
Kind::Match
| Kind::Insertion
| Kind::SoftClip
| Kind::SeqMatch
| Kind::SeqMismatch => Some(op.len()),
_ => None,
})
.sum()
}
}
impl Deref for Cigar {
type Target = [Op];
fn deref(&self) -> &Self::Target {
&self.0
}
}
impl fmt::Display for Cigar {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
if self.is_empty() {
write!(f, "{}", NULL_FIELD)
} else {
for op in self.iter() {
write!(f, "{}", op)?;
}
Ok(())
}
}
}
impl From<Vec<Op>> for Cigar {
fn from(ops: Vec<Op>) -> Self {
Self(ops)
}
}
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
Empty,
Invalid,
InvalidOp(op::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::Invalid => f.write_str("invalid input"),
Self::InvalidOp(e) => write!(f, "invalid op: {}", e),
}
}
}
impl FromStr for Cigar {
type Err = ParseError;
fn from_str(s: &str) -> Result<Self, Self::Err> {
if s.is_empty() {
return Err(ParseError::Empty);
} else if s == NULL_FIELD {
return Ok(Self::default());
}
let mut ops = Vec::new();
let matches = s.match_indices(|c: char| !c.is_ascii_digit());
let mut start = 0;
for (end, raw_kind) in matches {
let op = s[start..=end].parse().map_err(ParseError::InvalidOp)?;
ops.push(op);
start = end + raw_kind.len();
}
if start == s.len() {
Ok(Self::from(ops))
} else {
Err(ParseError::Invalid)
}
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_is_empty() {
let cigar = Cigar::default();
assert!(cigar.is_empty());
let cigar = Cigar::from(vec![Op::new(Kind::Match, 1)]);
assert!(!cigar.is_empty());
}
#[test]
fn test_fmt() {
let cigar = Cigar::from(vec![
Op::new(Kind::Match, 1),
Op::new(Kind::Skip, 13),
Op::new(Kind::SoftClip, 144),
]);
assert_eq!(cigar.to_string(), "1M13N144S");
}
#[test]
fn test_fmt_when_cigar_has_no_ops() {
let cigar = Cigar::default();
assert_eq!(cigar.to_string(), "*");
}
#[test]
fn test_from_str() {
assert_eq!(
"1M13N144S".parse(),
Ok(Cigar::from(vec![
Op::new(Kind::Match, 1),
Op::new(Kind::Skip, 13),
Op::new(Kind::SoftClip, 144),
]))
);
assert_eq!("*".parse(), Ok(Cigar::default()));
assert_eq!("".parse::<Cigar>(), Err(ParseError::Empty));
assert_eq!("8M13".parse::<Cigar>(), Err(ParseError::Invalid));
}
}