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Create test SAM data about noodles HOT 2 OPEN

mbhall88 avatar mbhall88 commented on July 21, 2024
Create test SAM data

from noodles.

Comments (2)

zaeleus avatar zaeleus commented on July 21, 2024

Note that &[u8] implements BufRead, so you can define a test helper that uses Reader::read_record (or Reader::read_record_buf) to build single records, e.g.,

fn build_record(src: &[u8]) -> io::Result<sam::Record> {
    let mut reader = sam::io::Reader::new(src);
    let mut record = sam::Record::default();
    reader.read_record(&mut record)?;
    Ok(record)
}

#[test]
fn test_some_function() -> io::Result<()> {
    let record = build_record(b"qry\t0\tchr\t1\t60\t5M\t*\t0\t0\tGCAGT\t!!!!!\tNM:i:1\t2T2")?;
    // ...
    Ok(())
}

We can consider adding a convenience conversion for sam::Record, given it's a format record specific to SAM; however, sam::alignment::RecordBuf is agnostic to serialized forms.

from noodles.

mbhall88 avatar mbhall88 commented on July 21, 2024

Wonderful! Boy would I love to do some paired programming with you. This library is so elegant it is beyond my comprehension.

A convenience conversion would be sensational, but not urgent given your function above allows me to write lots of test records now.

from noodles.

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