Michael Macias

Why not link to § 1.5 "[The alignment section: optional fields](https://samtools.github.io/hts-specs/SAMv1.pdf#subsection.1.5)", rather than duplicating the serialization format here? The introduction notes that this is a companion document, which associates the...

> SAM is _not_ specifically tied to 32-bit (signed or otherwise), and we've exploited this in the past when we've gone from 32-bit coordinates to 64-bit coordinates. SAM positions are...

I like this idea for its formality, but I'm not sure language-specific details or implementations belong with the specification. Libraries, in any particular language, probably should be providing such constants...

The current rule is clear that "for any other meaning [the following characters] must be represented with the capitalized percent encoding" ([§ 1.2](https://samtools.github.io/hts-specs/VCFv4.5.pdf#subsection.1.2) (2024-10-09)), supporting that percent-encoding the colon (`:`)...

> * The list in section 1.2 should be turned into a table indicating which fields reserve which characters Does this represent the expected explicit encoding rules for INFO and...

I added `.` (period) to the table above. It is used as a marker for missing values in both INFO and sample fields. (But also note that the former is...

Are you able to provide a complete example record or at least the INFO END value? I suspect the error is from an INFO END value

noodles is parsing the example record correctly. The variant caller is writing invalid data (END=0), and an error is subsequently thrown because it is a necessary, semantically relevant field in...