ClinSig changes for some halpotypes in join_data.R - become wrong! about clinvar HOT 2 OPEN

Looks like this is still an issue with the new python join script, except it outputs two lines now. Both are technically wrong.

variation_type = "Haplotype"
variation_id = "30359"
allele_id = "39315"

clinical_significance = "Benign/Likely benign"
clinical_significance_ordered = ["pathogenic"]

New Flags Look good.
"pathogenic":1,"likely_pathogenic":0,"uncertain_significance":"0","likely_benign":0,"benign":0

But....
allele_id = "39316"
clinical_significance = "Conflicting interpretations of pathogenicity"
clinical_significance_ordered = ["pathogenic"]

from clinvar.

This may be a clinvar data consistency issue:

join_variant_summary_with_clinvar_alleles.py
generates clinvar_alleles_combined.multi.tsv.gz by joining clinvar_alleles_grouped.multi.tsv.gz to variant_summary.txt.gz
using allele_id as the join key.
While doing this, it switches the clinical_significance column to the value from variant_summary.txt.gz (but doesn't update the clinical_significance_ordered column), so the values differ between the .xml release and variant_summary.txt.gz

I wonder if we should set these as 'conflicting interpretation' in both clinical_significance and clinical_significance_ordered columns?

from clinvar.