Daniel Cameron

Ok, there's quite a bit of discussion around `DUP` events. I think the real underlying issue is that we don't all agree on what a claim of a `DUP` is,...

Option 5. grandfather v4.2 or earlier, as ambiguous. Make an unambigous choice if the header is v4.3

> It seems to me that arbitrary symbolic alleles can still be allowed as long as they are not given an SVTYPE (which would trigger the more rigorous parsing that...

Alternative is to replace HOMLEN with HOMPOS.

The specifications are indeed unclear. >bcftools gladly accepts this and can also convert it back and forth through BCF preserving the ... Internally, the BCF format encodes a Character field...

I see three options: 1) Leave specs as-is, add test cases indicating that character fields should be separated by commas. Breaks htslib 2) Allow commas to be optional and leave...

As a general principle, as a specifications we should err on the side of data loss, rather than data corruption. In this particular instance, EOR will result in data corruption...

The answer is [321683, 321887] due to this sentences in S1.6.1: "If any of the ALT alleles is a symbolic allele (an angle-bracketed ID String “”) then the padding base...

I too agree that the ordering shouldn't matter but also agree that specs are unclear and lean towards an interpretation that does require a fixed header ordering. I'd like to...

> the ordering of the INFO subfields on a line conveys no meaning I think we should expand this to say the ordering of any subfields conveys no meaning. This...