noodles-sam 0.85.0

use std::io::{self, Write};

use super::MISSING;
use crate::alignment::record::QualityScores;

const OFFSET: u8 = b'!';

pub(super) fn write_quality_scores<W, S>(
    writer: &mut W,
    base_count: usize,
    quality_scores: S,
) -> io::Result<()>
where
    W: Write,
    S: QualityScores,
{
    if quality_scores.is_empty() {
        writer.write_all(&[MISSING])?;
    } else if quality_scores.len() == base_count {
        for result in quality_scores.iter() {
            let n = result?;

            if is_valid_score(n) {
                // SAFETY: `n` <= 93.
                let m = n + OFFSET;
                writer.write_all(&[m])?;
            } else {
                return Err(io::Error::from(io::ErrorKind::InvalidInput));
            }
        }
    } else {
        return Err(io::Error::new(
            io::ErrorKind::InvalidInput,
            format!(
                "sequence-quality scores length mismatch: expected {}, got {}",
                base_count,
                quality_scores.len()
            ),
        ));
    }

    Ok(())
}

fn is_valid_score(score: u8) -> bool {
    const MAX_SCORE: u8 = b'~' - OFFSET;
    score <= MAX_SCORE
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::alignment::record_buf::QualityScores as QualityScoresBuf;

    #[test]
    fn test_write_quality_scores() -> Result<(), Box<dyn std::error::Error>> {
        fn t(
            buf: &mut Vec<u8>,
            base_count: usize,
            quality_scores: &QualityScoresBuf,
            expected: &[u8],
        ) -> io::Result<()> {
            buf.clear();
            write_quality_scores(buf, base_count, quality_scores)?;
            assert_eq!(buf, expected);
            Ok(())
        }

        let mut buf = Vec::new();

        t(&mut buf, 0, &QualityScoresBuf::default(), b"*")?;
        t(&mut buf, 4, &QualityScoresBuf::default(), b"*")?;

        let quality_scores = [45, 35, 43, 50].into_iter().collect();
        t(&mut buf, 4, &quality_scores, b"NDLS")?;

        let quality_scores = [45, 35, 43, 50].into_iter().collect();
        buf.clear();
        assert!(matches!(
            write_quality_scores(&mut buf, 3, &quality_scores),
            Err(e) if e.kind() == io::ErrorKind::InvalidInput
        ));

        let quality_scores = [255].into_iter().collect();
        buf.clear();
        assert!(matches!(
            write_quality_scores(&mut buf, 1, &quality_scores),
            Err(e) if e.kind() == io::ErrorKind::InvalidInput
        ));

        Ok(())
    }
}