Bug: Running the tool with the variant `ENST00000302118:c.137G>A` results in an error: "Error: Cannot read properties of undefined (reading 'hgvsc')".

berntpopp commented 2 weeks ago

Steps to Reproduce

Run the tool with the variant ENST00000302118:c.137G>A.
```
variant-linker --variant 'ENST00000302118:c.137G>A'
```
Observe the error message.

Expected Behavior

The tool should correctly process the variant and return the expected annotations.

Actual Behavior

The tool fails with the error: "Error: Cannot read properties of undefined (reading 'hgvsc')".

Proposed Solution

Investigate the source of the error.
Ensure the variant data is correctly accessed and processed.

Acceptance Criteria

[x] The tool correctly processes the variant ENST00000302118:c.137G>A.
[x] The error "Cannot read properties of undefined (reading 'hgvsc')" is resolved.
[ ] Tests are added to verify the processing of similar variants.

berntpopp commented 2 weeks ago

This now relates to the change of hgvs to regions endpoint #14. The error (now "Error: Cannot read properties of undefined (reading 'vcf_string')") still persists as now apperetly two VCF notations are given:

[{"A":{"vcf_string":["1-55039974-G-A","LRG_275-5428-G-A"],"spdi":["NC_000001.11:55039973:G:A","LRG_275:5427:G:A"],"hgvsp":["ENSP00000303208.5:p.Arg46His","ENSP00000501004.1:p.Arg46His","ENSP00000501161.2:p.Arg46His","ENSP00000518176.1:p.Arg165His","ENSP00000519087.1:p.Arg46His","ENSP00000519088.1:p.Arg46His","ENSP00000519089.1:p.Arg46His","NP_001394169.1:p.Arg46His","NP_001394170.1:p.Arg46His","NP_001394171.1:p.Arg46His","NP_001394172.1:p.Arg46His","NP_001394173.1:p.Arg46His","NP_001394174.1:p.Arg46His","NP_001394176.1:p.Arg46His","NP_777596.2:p.Arg46His","LRG_275p1:p.Arg46His"],"input":"ENST00000302118:c.137G>A","hgvsg":["NC_000001.11:g.55039974G>A","LRG_275:g.5428G>A"],"id":["rs11591147","COSV56162404","CM061163"],"hgvsc":["ENST00000302118.5:c.137G>A","ENST00000673726.2:c.137G>A","ENST00000673913.2:c.137G>A","ENST00000710286.1:c.494G>A","ENST00000713785.1:c.137G>A","ENST00000713786.1:c.137G>A","ENST00000713787.1:c.137G>A","NM_001407240.1:c.137G>A","NM_001407241.1:c.137G>A","NM_001407242.1:c.137G>A","NM_001407243.1:c.137G>A","NM_001407244.1:c.137G>A","NM_001407245.1:c.137G>A","NM_001407246.1:c.-598G>A","NM_001407247.1:c.137G>A","NM_174936.4:c.137G>A","NR_110451.3:n.427G>A","NR_176318.1:n.427G>A","NR_176319.1:n.427G>A","NR_176320.1:n.427G>A","NR_176321.1:n.427G>A","NR_176322.1:n.427G>A","NR_176323.1:n.427G>A","NR_176324.1:n.427G>A","LRG_275t1:c.137G>A"]}}]

berntpopp commented 2 weeks ago

Testing will be resolved through #5

berntpopp / variant-linker