@lh3, when you say:
> It is in GAMappingPosition because the strand of the mate is important

That's the key question to me -- is it common for someone looking at a particular alignment to need to know its mate's strand, without also needing to know full info about that mate (e.g. flags, bases, qualities)? If so then I withdraw my suggestion (although I would like to understand more about that use case). But if not, then I think it's cleaner to strip down `GAMappingPosition` to only contain the information necessary to find the mate.

Re SAM file -- yes, I see that SAM flags contain
`0x20: SEQ of the next segment in the template being reversed`
And as I say above, if it's commonly used, no problem. But if not, then I think it's cleaner to drop it.
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