John Marshall

> another related issue is, when comparing read names, maybe we can only compare the characters after >/@ and before the first white space. This was already considered in #521.

@bli25wisc Please see the previous reply on #521. It would be great if you would respond to the question there re which aligners you have observed exhibiting this bug.

The direct analogue to the VCF `?samples=S1,S2` proposal would be the same query parameter selecting a subset of `@RG` read groups from within a file, in which case the reference...

I think two commits would be appropriate: (1) fix existing `\log` instances, not really part of this PR; (2) add the new text, already with `\log` throughout. That way around,...

How `fields` is supposed to work is pretty underspecified in the spec. I assume it's supposed to be an interface to CRAM implementations' ability to avoid decoding specified column blocks...

Get rid of f2e0a75d54ad2e0fdf3e2682246fea483703cab8, as noted previously.

Please explain how this has been tested.

> biobambam2 (now archived) @keiranmraine: Moved, not archived. See https://twitter.com/jomarnz/status/1105509947083759617 and the not-very-prominent note at the top of the README in the GitHub repo.

Cf PR #620 which mentions `##source` as an example of an unstructured meta-information line that is not defined by the spec.

An alternative would be to distribute the excess as evenly as possible: 68 (= 3268 % 100) windows of length 33 and 32 of length 32 also comes out to...