pub mod field;
use std::{borrow::Borrow, io, iter};
use noodles_sam as sam;
use self::field::{decode_field, Tag, Value};
#[derive(Debug, Eq, PartialEq)]
pub struct Data<'a>(&'a [u8]);
impl<'a> Data<'a> {
pub(super) fn new(src: &'a [u8]) -> Self {
Self(src)
}
pub fn is_empty(&self) -> bool {
self.0.is_empty()
}
pub fn get<K>(&self, tag: &K) -> Option<io::Result<Value<'_>>>
where
K: Borrow<[u8; 2]>,
{
for result in self.iter() {
match result {
Ok((t, value)) => {
if &t == tag.borrow() {
return Some(Ok(value));
}
}
Err(e) => return Some(Err(e)),
};
}
None
}
pub fn iter(&self) -> impl Iterator<Item = io::Result<(Tag, Value<'_>)>> + '_ {
let mut src = self.0;
iter::from_fn(move || {
if src.is_empty() {
None
} else {
Some(decode_field(&mut src))
}
})
}
}
impl<'a> AsRef<[u8]> for Data<'a> {
fn as_ref(&self) -> &[u8] {
self.0
}
}
impl<'a> TryFrom<Data<'a>> for sam::record::Data {
type Error = io::Error;
fn try_from(bam_data: Data<'a>) -> Result<Self, Self::Error> {
use crate::record::codec::decoder::get_data;
let mut src = bam_data.0;
let mut sam_data = Self::default();
get_data(&mut src, &mut sam_data)
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;
Ok(sam_data)
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_get() -> io::Result<()> {
use sam::record::data::field::tag;
let data = Data::new(&[b'N', b'H', b'C', 0x01]);
assert!(data.get(&tag::ALIGNMENT_HIT_COUNT).is_some());
assert!(data.get(&[b'N', b'H']).is_some());
assert!(data.get(&tag::COMMENT).is_none());
Ok(())
}
#[test]
fn test_iter() -> io::Result<()> {
let data = Data::new(&[]);
assert!(data.iter().next().is_none());
let data = Data::new(&[b'N', b'H', b'C', 0x01]);
let actual: Vec<_> = data.iter().collect::<io::Result<_>>()?;
let expected = [([b'N', b'H'], Value::UInt8(1))];
assert_eq!(actual, expected);
Ok(())
}
}