Extending data/ API for VCF Genotype Search

[Don-Isdale]

Part of #383

Observable outcomes / Acceptance criteria :

Functions utilising API endpoint to :

• API endpoint to search for markers in a given VCF (parent reference dataset or block) P -> regions
• samples(block) P (returns Promise yielding) -> samples
• genotype(block, intervals, samples) P -> values

Measured with :

• JSON or screen-shot in web inspector of request and response,

---

services/

• data/
• • api / search / lookup :
• • • [1-2D] search for markers in a given VCF (parent reference dataset or block) P -> regions
• • • [3-6H] samples(block) P (returns Promise yielding) -> samples
• • • [4-8H] genotype(block, intervals, samples) P -> values

[Don-Isdale]

Status : Not yet required

This capability was included in the design of the MVP, but is not required for small VCF files.
Instead the include expression is used : -i ' ID="scaffold38755_1207866" || ID="... ..." ', which scans the VCF.
For larger files, some means of mapping SNP names to regions will be required, which will be accessed by the API defined in this issue.
The list of regions can then be passed in the vcfGenotypeLookup request.