Remove 'Human reference sequence assembly version' component from variant observation
rhdolin opened this issue · 5 comments
'Human reference sequence assembly version' can be inferred from RefSeq, and doesn't always apply (e.g. for mitochondrial refSeq's).
@srgothi92 I would like to work on this issue. Please guide me.
@theanmolsharma Begin by reading the manual to understand high-level how translation works. Then focus on 'create variant observations' section. You'll see that each time the converter creates a FHIR Variant observation, that observation includes a component "LOINC 62374-4 'Human reference sequence assembly version' = GRCh37 or GRCh38, as determined from parameter value". You can see an example of this component by searching this example.
The idea here is to modify the code so that we are no longer creating this component with a variant observation.
@rhdolin I think I got what I need to do, I will start working on it right away.
Can you help me identify the function that is generating that component. I think it is here json_generator.py and I need to change the ref_seq. Correct me if I am wrong.
@theanmolsharma Take a look at lines 127-132 in fhir_helper.py to see where this component is getting added.
@rhdolin I removed the lines that generated that component.