Bam record should validate sequence and quality length before writing

[veldsla]

In the encoded bam there is one field that encodes the length for both the sequence and the base qualities. When writing a bam::Record this is not validated resulting in possibly corrupt BAM files.

According to the bam spec when base qualities are omitted 0xFF should be written instead.

This can be done in the writer code, but it's probably cleaner to do a validate function on the record? Should I do a PR?

[zaeleus]

Sure, if you'd like to do this, let'd do it in the BAM record writer. The SAM record writer can be used as reference:

noodles/noodles-bam/src/writer/sam_record.rs

Lines 101 to 124 in b4124cf

	// § 4.2.3 SEQ and QUAL encoding (2021-06-03)
	let sequence = record.sequence();
	let quality_scores = record.quality_scores();
	if !sequence.is_empty() {
	write_seq(writer, sequence)?;
	if sequence.len() == quality_scores.len() {
	write_qual(writer, quality_scores)?;
	} else if quality_scores.is_empty() {
	for _ in 0..sequence.len() {
	writer.write_u8(NULL_QUALITY_SCORE)?;
	}
	} else {
	return Err(io::Error::new(
	io::ErrorKind::InvalidInput,
	format!(
	"quality scores length mismatch: expected {}, got {}",
	sequence.len(),
	quality_scores.len()
	),
	));
	}
	}

.

[veldsla]

Looking at the specification there's another constraint that is enforced by the current version of samtools:

Sum of lengths of the M/I/S/=/X operations shall equal the length of SEQ.

It's probably best to also require this.