Create Record from scratch

[Poshi]

Hello! I'm trying to create Record objects for unit testing on some code I'm trying to develop, but I've been unable to do so.

I'm using Noodles to read BAM files and compute some simple statistics of them. In order to check that I'm counting what I need to count, the unit test would ideally get a particular Record and run it thru the stats collectors to check their behavior.
Right now, the only way I have to do that is to pre-generate as many BAM files as I need for the tests, bu it would be a lot better to be able to generate the Record objects on the fly.

So far, when trying to generate them on the fly, I hit some required private function in Noodles that stopped my efforts.
Is there any way to generate Record objects on the fly? If not, could that be implemented? Sorry if the question have an obvious solution, I'm quite new to rust and still learning.

[zaeleus]

You can build a sam::alignment::RecordBuf using its associated Builder. Alignment records implement sam::alignment::Record, which you would want to use between your implementation and tests.

Here's an example that counts the number of unmapped records in a BAM using a function that's generic over an alignment record.

// cargo add noodles@0.101.0 --features bam,sam

use std::{env, fs::File, io};

use noodles::{bam, sam};

fn main() -> io::Result<()> {
    let src = env::args().nth(1).expect("missing src");

    let mut reader = File::open(src).map(bam::io::Reader::new)?;
    let _header = reader.read_header()?;

    let mut record = bam::Record::default();
    let mut n = 0;

    while reader.read_record(&mut record)? != 0 {
        if record_is_unmapped(&record)? {
            n += 1;
        }
    }

    println!("{n}");

    Ok(())
}

fn record_is_unmapped<R>(record: &R) -> io::Result<bool>
where
    R: sam::alignment::Record,
{
    record.flags().map(|flags| flags.is_unmapped())
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_record_is_unmapped() -> io::Result<()> {
        use noodles::sam::alignment::record::Flags;

        let record = sam::alignment::RecordBuf::builder()
            .set_flags(Flags::UNMAPPED)
            .build();

        assert!(record_is_unmapped(&record)?);

        let record = sam::alignment::RecordBuf::builder()
            .set_flags(Flags::empty())
            .build();

        assert!(!record_is_unmapped(&record)?);

        Ok(())
    }
}

[Poshi]

Thanks a lot for your very quick answer!
I've been tinkering quite a lot after that until I realized that I was using noodles::bam::Record instead of noodles::sam::Record. After switching to the trait I've been able to make my code work with your suggestion. In fact, I already tried your suggestion, but I was stuck trying to convert the RecordBuf to the noodles::bam::Record object.
Now I think I got it working :-) Thanks a lot for your help and your crate!

[Wan-Yifei]

How do you convert the RecordBuf to bam::Record?