Closed redmitry closed 2 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...
I'm confused. Aren't we using the brtacketed queries in the example queries document? Aren't we talking about that here?
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
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