Bug: Variants with resolved ClinVar calls are reporting Intervar call in final output

[rjcorb]

Provide the command used or report the bug here

There are variant with conflicting ClinVar interpretations that are resolved by analyzing submissions, but in final output the Intervar call is taken despite ClinVar being listed as reasoning. For example:

chr	start	ref	alt	rs_id	gene_symbol_vep	variant_classification_vep	HGVSg	HGVSc	HGVSp	autogvp_call	autogvp_call_reason	clinvar_stars	clinvar_clinsig	intervar_evidence	gnomad_3_1_1_AF_non_cancer
chr17	7675189	G	C	rs1057519977	TP53	missense_variant	chr17:g.7675189G>C	c.423C>G	p.Cys141Trp	Uncertain_significance	ClinVar	1NR	Likely pathogenic	InterVar: Uncertain significance PVS1=0 PS=[0, 0, 0, 0, 0] PM=[1, 1, 0, 0, 0, 0, 0] PP=[0, 0, 1, 0, 0, 0] BA1=0 BS=[0, 0, 0, 0, 0] BP=[0, 0, 0, 0, 0, 0, 0, 0]	0

What version are you using?

Latest release

Add error message here (if applicable)

Add Session info

Run sessionInfo() and post the output below

[naqvia]

Good catch. 1NRs shouldn't be going into the intervar re-calculation steps, so it could just be we not filtering it since they are labeled correctly. I think id like to merge the latest PRs, and see if this issue persists before tackling this bc there a lot of nuanced changes and the test data should pick this up as well.