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perf(bam): Remove unnecessary heap allocation in Record::aux #498

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perf(bam): Remove unnecessary heap allocation in Record::aux #498

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4 changes: 3 additions & 1 deletion src/bam/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1695,6 +1695,7 @@ CCCCCCCCCCCCCCCCCCC"[..],
// fix qual offset
let qual: Vec<u8> = quals[i].iter().map(|&q| q - 33).collect();
assert_eq!(rec.qual(), &qual[..]);
assert_eq!(rec.aux(b"X"), Err(Error::BamAuxStringError));
assert_eq!(rec.aux(b"NotAvailableAux"), Err(Error::BamAuxTagNotFound));
}

Expand Down Expand Up @@ -2009,7 +2010,8 @@ CCCCCCCCCCCCCCCCCCC"[..],
rec.remove_aux(b"YT").unwrap();
}

assert!(rec.remove_aux(b"ab").is_err());
assert_eq!(rec.remove_aux(b"X"), Err(Error::BamAuxStringError));
assert_eq!(rec.remove_aux(b"ab"), Err(Error::BamAuxTagNotFound));

assert_eq!(rec.aux(b"XS"), Err(Error::BamAuxTagNotFound));
assert_eq!(rec.aux(b"YT"), Err(Error::BamAuxTagNotFound));
Expand Down
12 changes: 8 additions & 4 deletions src/bam/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -644,11 +644,13 @@ impl Record {
/// Only the first two bytes of a given tag are used for the look-up of a field.
/// See [`Aux`] for more details.
pub fn aux(&self, tag: &[u8]) -> Result<Aux<'_>> {
let c_str = ffi::CString::new(tag).map_err(|_| Error::BamAuxStringError)?;
if tag.len() < 2 {
return Err(Error::BamAuxStringError);
}
let aux = unsafe {
htslib::bam_aux_get(
&self.inner as *const htslib::bam1_t,
c_str.as_ptr() as *mut c_char,
tag.as_ptr() as *const c_char,
)
};
unsafe { Self::read_aux_field(aux).map(|(aux_field, _length)| aux_field) }
Expand Down Expand Up @@ -1224,11 +1226,13 @@ impl Record {

// Delete auxiliary tag.
pub fn remove_aux(&mut self, tag: &[u8]) -> Result<()> {
let c_str = ffi::CString::new(tag).map_err(|_| Error::BamAuxStringError)?;
if tag.len() < 2 {
return Err(Error::BamAuxStringError);
}
let aux = unsafe {
htslib::bam_aux_get(
&self.inner as *const htslib::bam1_t,
c_str.as_ptr() as *mut c_char,
tag.as_ptr() as *const c_char,
)
};
unsafe {
Expand Down
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