Closed philipwfowler closed 1 year ago
Currently the mutations/effects are optional fields - only populating when there are values to go in them. If a sample has exclusively intergene variation, no gene-centric mutations exist, and no effects exist, so the fields aren't populated. I can change this to default to empty lists instead as it may may parsing it easier
This is a very edge case and only minor, but in testing on the 4,124 South African VCF files, one only has three rows, one of which is wildtype
0/0
and the other two fail a filter, hence it is identical to the H37Rv reference. This could happen more than we think in practice because labs may deliberately sequence H37Rv as a control. At presentgnomonicus
writes out no CSV files (which is ok) and the JSON contains the followingThink this is all ok, but should we have empty "mutations" and "effects" blocks within "data"? i.e.
site.10.subj.UH01321968.lab.UH01321968.iso.1.v0.12.4.per_sample.vcf.zip