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ga4gh-beacon / beacon-v2-Models

Models that leverage the Beacon Framework v2
Apache License 2.0
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[Q] variants start / end fuzzy range. #34

Closed redmitry closed 2 years ago

redmitry commented 3 years ago

Hello,

In the draft4 variants Position.start / end are defined as an array ("examples": ["[1000], [1000,1100]"]): https://github.com/ga4gh-beacon/beacon-v2-Models/blob/main/BEACON-V2-draft4-Model/genomicVariations/defaultSchema.json I understand the logic for the request parameters (to provide "fuzzy" search), but for the Beacon what is the meaning? Is this for structural variants? I see the current Beacon 2 draft implementation and do not see it is reflected in the database ("variant_table" start / end int4). https://github.com/EGA-archive/beacon-2.x/

Cheers,

Dmitry

mbaudis commented 3 years ago

Good point. You're basically correct (original intention in some drafts was to provide fuzzy positions). We've used previously the same method as for the search parameters to allow this (in contrast to the VCF way of adding optional CIPOS, CIEND values.

I'm neutral"ish" on this. In the end, this will be replaced by VRS or some VRS aligned standard over time...

jrambla commented 3 years ago

I'm confused. Aren't we using the brtacketed queries in the example queries document? Aren't we talking about that here?

redmitry commented 3 years ago

No. One thing is a fuzzy query (requestParameters ?) and another range position in the found beacon. I do not object, but the meaning may be different - for the query, we search for beacons those start position is within a range. For the concrete beacon "fuzzy" position should mean different thing. Is this related to the:

##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">

? I took a look at the CRG implementation and found that it is still a number in the postgres database.

Cheers,

Dmitry