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use std::{convert::TryFrom, error, fmt, mem};
use byteorder::{ByteOrder, LittleEndian};
use noodles_sam::record::cigar::op::Kind;
const MAX_LENGTH: u32 = 268_435_455;
#[derive(Clone, Copy, Debug, Eq, PartialEq)]
pub struct Op {
kind: Kind,
len: u32,
}
#[derive(Clone, Debug, Eq, PartialEq)]
pub struct LengthError(u32);
impl error::Error for LengthError {}
impl fmt::Display for LengthError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(
f,
"expected operation length to be <= {}, got {}",
MAX_LENGTH, self.0
)
}
}
impl Op {
pub fn new(kind: Kind, len: u32) -> Result<Self, LengthError> {
if len <= MAX_LENGTH {
Ok(Self { kind, len })
} else {
Err(LengthError(len))
}
}
pub fn kind(self) -> Kind {
self.kind
}
pub fn len(self) -> u32 {
self.len
}
pub fn is_empty(self) -> bool {
self.len == 0
}
}
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum TryFromUIntError {
InvalidOp(u32),
InvalidLength(LengthError),
}
impl error::Error for TryFromUIntError {}
impl fmt::Display for TryFromUIntError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
match self {
Self::InvalidOp(n) => write!(f, "invalid op: expected 0..=8, got {}", n),
Self::InvalidLength(e) => write!(f, "invalid length: {}", e),
}
}
}
impl TryFrom<u32> for Op {
type Error = TryFromUIntError;
fn try_from(u: u32) -> Result<Self, Self::Error> {
let len = u >> 4;
let kind = match u & 0x0f {
0 => Kind::Match,
1 => Kind::Insertion,
2 => Kind::Deletion,
3 => Kind::Skip,
4 => Kind::SoftClip,
5 => Kind::HardClip,
6 => Kind::Pad,
7 => Kind::SeqMatch,
8 => Kind::SeqMismatch,
n => return Err(TryFromUIntError::InvalidOp(n)),
};
Self::new(kind, len).map_err(TryFromUIntError::InvalidLength)
}
}
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum TryFromByteSliceError {
Invalid(usize),
InvalidUInt(TryFromUIntError),
}
impl error::Error for TryFromByteSliceError {}
impl fmt::Display for TryFromByteSliceError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
match self {
Self::Invalid(len) => write!(f, "expected length to >= 4, got {}", len),
Self::InvalidUInt(e) => write!(f, "invalid u32: {}", e),
}
}
}
impl TryFrom<&[u8]> for Op {
type Error = TryFromByteSliceError;
fn try_from(buf: &[u8]) -> Result<Self, Self::Error> {
if buf.len() < mem::size_of::<u32>() {
return Err(TryFromByteSliceError::Invalid(buf.len()));
}
let u = LittleEndian::read_u32(buf);
Self::try_from(u).map_err(TryFromByteSliceError::InvalidUInt)
}
}
impl fmt::Display for Op {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(f, "{}{}", self.len(), self.kind())
}
}
impl From<Op> for u32 {
fn from(op: Op) -> Self {
let i = op.kind() as u32;
op.len() << 4 | i
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_try_from_u32() -> Result<(), LengthError> {
assert_eq!(Op::try_from(1 << 4), Ok(Op::new(Kind::Match, 1)?));
assert_eq!(Op::try_from(2 << 4 | 1), Ok(Op::new(Kind::Insertion, 2)?));
assert_eq!(Op::try_from(3 << 4 | 2), Ok(Op::new(Kind::Deletion, 3)?));
assert_eq!(Op::try_from(4 << 4 | 3), Ok(Op::new(Kind::Skip, 4)?));
assert_eq!(Op::try_from(5 << 4 | 4), Ok(Op::new(Kind::SoftClip, 5)?));
assert_eq!(Op::try_from(6 << 4 | 5), Ok(Op::new(Kind::HardClip, 6)?));
assert_eq!(Op::try_from(7 << 4 | 6), Ok(Op::new(Kind::Pad, 7)?));
assert_eq!(Op::try_from(8 << 4 | 7), Ok(Op::new(Kind::SeqMatch, 8)?));
assert_eq!(Op::try_from(9 << 4 | 8), Ok(Op::new(Kind::SeqMismatch, 9)?));
assert_eq!(
Op::try_from(10 << 4 | 9),
Err(TryFromUIntError::InvalidOp(9))
);
Ok(())
}
#[test]
fn test_try_from_u8_slice() -> Result<(), LengthError> {
let buf = [0x40, 0x02, 0x00, 0x00];
assert_eq!(Op::try_from(&buf[..]), Ok(Op::new(Kind::Match, 36)?));
let buf = [0x40, 0x02, 0x00, 0x00, 0x84, 0x00, 0x00, 0x00];
assert_eq!(Op::try_from(&buf[..]), Ok(Op::new(Kind::Match, 36)?));
let buf = [];
assert_eq!(
Op::try_from(&buf[..]),
Err(TryFromByteSliceError::Invalid(0))
);
let buf = [0x49, 0x02, 0x00, 0x00];
assert_eq!(
Op::try_from(&buf[..]),
Err(TryFromByteSliceError::InvalidUInt(
TryFromUIntError::InvalidOp(9)
))
);
Ok(())
}
#[test]
fn test_fmt() -> Result<(), LengthError> {
assert_eq!(Op::new(Kind::Match, 32)?.to_string(), "32M");
assert_eq!(Op::new(Kind::Deletion, 7)?.to_string(), "7D");
assert_eq!(Op::new(Kind::Skip, 11)?.to_string(), "11N");
assert_eq!(Op::new(Kind::Pad, 188)?.to_string(), "188P");
Ok(())
}
#[test]
fn test_from_op_for_u32() -> Result<(), LengthError> {
assert_eq!(u32::from(Op::new(Kind::Match, 1)?), 1 << 4);
assert_eq!(u32::from(Op::new(Kind::Insertion, 2)?), 2 << 4 | 1);
assert_eq!(u32::from(Op::new(Kind::Deletion, 3)?), 3 << 4 | 2);
assert_eq!(u32::from(Op::new(Kind::Skip, 4)?), 4 << 4 | 3);
assert_eq!(u32::from(Op::new(Kind::SoftClip, 5)?), 5 << 4 | 4);
assert_eq!(u32::from(Op::new(Kind::HardClip, 6)?), 6 << 4 | 5);
assert_eq!(u32::from(Op::new(Kind::Pad, 7)?), 7 << 4 | 6);
assert_eq!(u32::from(Op::new(Kind::SeqMatch, 8)?), 8 << 4 | 7);
assert_eq!(u32::from(Op::new(Kind::SeqMismatch, 9)?), 9 << 4 | 8);
Ok(())
}
}