Question: Is there a way to modify BAM record content (e.g., QNAME) in noodles-bam?

[Wan-Yifei]

Hi @zaeleus ,

Does noodles-bam provide any public API to modify other record fields (QNAME, sequence, flags, etc.)? I’m exploring noodles-bam and noticed that the Record struct encapsulates its internal fields, and fields_mut() is pub(crate). I would like to programmatically modify the content of a BAM record.

Thanks!

[zaeleus]

Yes, you can convert read-only format buffers to the mutable buffer type sam::alignment::RecordBuf using RecordBuf::try_from_alignment_record.

[Wan-Yifei]

One more question: How to convert the updated RecordBuf back to Record?

[zaeleus]

When reading from multiple record types, you would typically interact with the fields via the sam::alignment::Record trait, e.g.,

fn main() {
    let bam_record = bam::Record::default();
    get_name(&bam_record);

    let sam_record = sam::Record::default();
    get_name(&sam_record);

    let record_buf = sam::alignment::RecordBuf::default();
    get_name(&record_buf);
}

fn get_name<R>(record: &R) -> Option<&BStr>
where
    R: sam::alignment::Record,
{
    record.name()
}

If you need to serialize any record to a particular format record, I would recommend going through the format's I/O, e.g.,

fn main() -> io::Result<()> {
    let header = sam::Header::default();

    let bam_record = bam::Record::default();
    try_into_bam_record(&header, &bam_record)?;

    let sam_record = sam::Record::default();
    try_into_bam_record(&header, &sam_record)?;

    let record_buf = sam::alignment::RecordBuf::default();
    try_into_bam_record(&header, &record_buf)?;

    Ok(())
}

fn try_into_bam_record<R>(header: &sam::Header, record: &R) -> io::Result<bam::Record>
where
    R: sam::alignment::Record,
{
    let mut writer = bam::io::Writer::from(Vec::new());
    writer.write_alignment_record(header, record)?;

    let src = writer.into_inner();
    let mut reader = bam::io::Reader::from(&src[..]);
    let mut dst = bam::Record::default();
    reader.read_record(&mut dst)?;

    Ok(dst)
}

[Wan-Yifei]

Thanks for your timely reply! I tried it and it works as expected. While looking into related discussions, I noticed others also asked about converting RecordBuf back to Record. Since updating record contents is quite common in BAM processing workflows, it might be helpful to add a short note in the documentation for RecordBuf::try_from_alignment_record to clarify this use case. Thanks again for your help!