John Marshall

> If anything is missing here, and this is minor, its a call that says yes I'm an htsget server and this is what I'm serving The intention would be...

It is true that discussion has stalled, partly because until yesterday we had not had an htsget meeting in quite a while. This issue took up most of the time...

> The basic problem is there is no way to discover what referenceNames are present in a dataset As noted in https://github.com/samtools/hts-specs/pull/311#issue-187673445 which motivated their addition, [`class=header` requests](http://samtools.github.io/hts-specs/htsget.html#query-parameters) provide this...

The relevant VCF header is `##contig` (§1.4.7 in the v4.3 spec), which “is recommended for VCF, and required for BCF”. In my experience, it's pretty commonly supplied in the wild...

> BTW servers must already be "divining" the reference names in a dataset since they are supposed to return an error if a request is made for a reference name...

> There's a way for BAM files, but not for VCF Please be explicit. What do you consider is lacking for VCF? (Other than the minor “my VCF file does...

Header requests work whether or not the files contain `@SQ`/`##contig` headers; they just may not supply the information the client is looking for, but that can be considered to be...

It would be possible to invent another form of request (e.g. `class=referenceNames`?) that would return the names as divined by some other method such as from tabix indexes. But htsget...

This repository contains numerous specification texts with (historically semi-intentionally) no clear copyright status, currently no software (other than infrastructure scripts), and example files in the various formats either embedded and...

(Appropriate licensing conditions for the specification texts themselves is something that is already under consideration within GA4GH. So let's keep this issue about only the examples and example files.)