Clarify callCount and add sampleTotalCount (issue #237)

[sdelatorrep]

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[mbaudis]

@sdelatorrep Thanks for starting this - and driving a great topic for standardisation & documentation!

I have problems mostly with the variantCount definition - but this may be me, coming from a "queries match multiple variants" background.

Generally, I do not think that those numbers have to mimic anything VCF, but rather that they can be computed from VCF numbers.

So:

• variantCount should IMO be the number of distinct variants matched by a query. For most precise SNV queries, this would be just 1. However, for ranges/wildcards, this could be any number.
• callCount doesn't make sense as the basic no. of alleles; it should (logically) be the number the queried variant(s) has/have been observed in the dataset; the sum of 2n(1/1) + 1n(1/0) + 1*n(0/1) ... However: This isn't of great interest (IMO), biologically, since you cannot decompose it into individual contributions from homo- and heterozygous ... matches. Useful would be a de-composition of the different call combinations (1/0, 1/1 ...); but I wouldn't know how to do this w/o running into a "if we can do this, we can ..." scenario.

So maybe we need to get back to the drawing board for "meaningful quantitative Beacon responses"?

[jrambla]

Please, look at the presentation I've circulated based on the wiki page that Sabela has created but using an scaled down example.
For variantCount in wildcard/"multiple fuzzy variants", I would like to expand that in Beacon 2.0, but now, I guess that if we consider "any match" we should be returning them as if they were just "one", if someone is interested in specific variants, they can do that specific query. If someone wants to know about "which are the different variants" I believe we should refer to the "evidence" Beacon including the Variant SchemaBlock stuff.
I'm also believing that adding the karyotype details (1/1, 1/0...) could make sense, thus we can add counts for variantHomozygotesCount, variantHeterozygoteCount.