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feat: Add support for updating existing aux tags inplace. #481

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Merged
merged 1 commit into from
Oct 14, 2025
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feat: Add support for updating existing aux tags inplace. #481

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154 changes: 154 additions & 0 deletions src/bam/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1068,6 +1068,160 @@ impl Record {
}
}

/// Update or add auxiliary data.
pub fn update_aux(&mut self, tag: &[u8], value: Aux<'_>) -> Result<()> {
// Update existing aux data for the given tag if already present in the record
// without changing the ordering of tags in the record or append aux data at
// the end of the existing aux records if it is a new tag.

let ctag = tag.as_ptr() as *mut c_char;
let ret = unsafe {
match value {
Aux::Char(_v) => return Err(Error::BamAuxTagUpdatingNotSupported),
Aux::I8(v) => htslib::bam_aux_update_int(self.inner_ptr_mut(), ctag, v as i64),
Aux::U8(v) => htslib::bam_aux_update_int(self.inner_ptr_mut(), ctag, v as i64),
Aux::I16(v) => htslib::bam_aux_update_int(self.inner_ptr_mut(), ctag, v as i64),
Aux::U16(v) => htslib::bam_aux_update_int(self.inner_ptr_mut(), ctag, v as i64),
Aux::I32(v) => htslib::bam_aux_update_int(self.inner_ptr_mut(), ctag, v as i64),
Aux::U32(v) => htslib::bam_aux_update_int(self.inner_ptr_mut(), ctag, v as i64),
Aux::Float(v) => htslib::bam_aux_update_float(self.inner_ptr_mut(), ctag, v),
// Not part of specs but implemented in `htslib`:
Aux::Double(v) => {
htslib::bam_aux_update_float(self.inner_ptr_mut(), ctag, v as f32)
}
Aux::String(v) => {
let c_str = ffi::CString::new(v).map_err(|_| Error::BamAuxStringError)?;
htslib::bam_aux_update_str(
self.inner_ptr_mut(),
ctag,
(v.len() + 1) as i32,
c_str.as_ptr() as *const c_char,
)
}
Aux::HexByteArray(_v) => return Err(Error::BamAuxTagUpdatingNotSupported),
// Not sure it's safe to cast an immutable slice to a mutable pointer in the following branches
Aux::ArrayI8(aux_array) => match aux_array {
AuxArray::TargetType(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'c',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
AuxArray::RawLeBytes(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'c',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
},
Aux::ArrayU8(aux_array) => match aux_array {
AuxArray::TargetType(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'C',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
AuxArray::RawLeBytes(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'C',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
},
Aux::ArrayI16(aux_array) => match aux_array {
AuxArray::TargetType(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b's',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
AuxArray::RawLeBytes(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b's',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
},
Aux::ArrayU16(aux_array) => match aux_array {
AuxArray::TargetType(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'S',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
AuxArray::RawLeBytes(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'S',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
},
Aux::ArrayI32(aux_array) => match aux_array {
AuxArray::TargetType(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'i',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
AuxArray::RawLeBytes(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'i',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
},
Aux::ArrayU32(aux_array) => match aux_array {
AuxArray::TargetType(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'I',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
AuxArray::RawLeBytes(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'I',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
},
Aux::ArrayFloat(aux_array) => match aux_array {
AuxArray::TargetType(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'f',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
AuxArray::RawLeBytes(inner) => htslib::bam_aux_update_array(
self.inner_ptr_mut(),
ctag,
b'f',
inner.len() as u32,
inner.slice.as_ptr() as *mut ::libc::c_void,
),
},
}
};

if ret < 0 {
Err(Error::BamAux)
} else {
Ok(())
}
}

// Delete auxiliary tag.
pub fn remove_aux(&mut self, tag: &[u8]) -> Result<()> {
let c_str = ffi::CString::new(tag).map_err(|_| Error::BamAuxStringError)?;
Expand Down
2 changes: 2 additions & 0 deletions src/errors.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,8 @@ pub enum Error {
BamAuxUnknownType,
#[error("failed to add aux field, tag is already present")]
BamAuxTagAlreadyPresent,
#[error("updating the aux field for this datatype is not supported")]
BamAuxTagUpdatingNotSupported,

// Errors for base modification fields
#[error("no base modification tag found for record")]
Expand Down
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