John Marshall

Probably the best JSON representation for this would be a `"methods": ["GET", "POST"]` entry in an appropriate part of the service-info response. However IMHO it's not particularly necessary because: 1....

There is nothing related in the generic part of the service-info response at present. This isn't really htsget-specific so perhaps there should be, though it seems to me that the...

VCF files are often very wide, so I think there is some utility in showing complicated examples in the specification text. We could try [`\usepackage{pdflscape}` instead of `\usepackage{lscape}`](https://tex.stackexchange.com/questions/337/how-to-change-certain-pages-into-landscape-portrait-mode). With macOS...

I think there would be little appetite for adding a new different style of value for the ALT field, as that is something that would need to be implemented in...

Thanks everyone for the interesting discussion on the call just now — I for one think I have a better understanding of the issues than before! It might be useful...

For the non-expert such as myself, the Kutner document linked from ga4gh/vrs#363 (as mentioned in https://github.com/samtools/hts-specs/issues/619#issuecomment-1009244714) is a very informative primer. For current VCF, IMHO it would be appropriate to...

It's a known long-standing problem. I think it's never been a priority because most people map everything in a project to the same reference, so it usually doesn't arise. See...

Notice that in the OP's first case there are no `-r` options involved, so the BAM files are streamed sequentially and may not even be indexed. So now that there...

@tseemann: re `getrlimit()` etc, see also discussion in samtools/bcftools#376.

The only existing description of `cs` is the third table in the [minimap2 man page](https://lh3.github.io/minimap2/minimap2.html#10), which is very incomplete — in particular, as to what the intron string represents. So...