Dan King

Just so I'm clear on what is acceptable: VCFv4.4 is backwards compatible if and only if, for any VCFv4.3 file, if I change the `fileformat` line to `VCFv4.4`, the interpretation...

### Numbers > > I'd prefer three new numbers (all of which are distinct from the ploidy): > > LOCAL-A. One element for each allele present in LA minus one...

> The reason for defining INFO END as I did was to avoid breaking VCF indexing. [...] > > If we're erring on the side of crashing instead of data...

Hi @pd3 ! I try to explain the decisions below but see also my final paragraph. I agree with all your comments on 1 and, in fact, this was our...

Minor nit: > This pull request proposes a new tag LA which includes the REF allele. This has already resulted in two competing implementations and their use in large datasets....

Regarding the desire to distinguish “missing LAA” from “only the reference is present”, I did not personally raise this concern so I’m trying to interpret others’ concerns. That said, I...

@pd3, I’d like to make a final nudge on LGT, but after this I’ll be quiet about it. I agree with your points one and two: LGT is not relevant...

> I don't find cognitive overhead a good argument. Few users look manually inside VCFs with hundreds of thousands of samples. Backward compatibility is a real concern, what matters is...

@d-cameron a bit delayed but: thank you for your tenacious commitment to this change. This is critical for the future of the community. I appreciate everyone's efforts at finding consensus!

Agreed, much better. Can we add some tests for some of this functionality?