clinvar.rs

use crate::seqvars::query::{
    annonars::Annotator,
    schema::{CaseQuery, SequenceVariant},
};

use annonars::clinvar_minimal::pbs::ClinicalSignificance::{self, *};

/// Determine whether the `SequenceVariant` passes the clinvar filter.
pub fn passes(
    query: &CaseQuery,
    annotator: &Annotator,
    seqvar: &SequenceVariant,
) -> Result<bool, anyhow::Error> {
    if !query.require_in_clinvar {
        return Ok(true);
    }

    if let Ok(record) = annotator.query_clinvar_minimal(seqvar) {
        let clinical_significance: ClinicalSignificance =
            record
                .clinical_significance
                .try_into()
                .map_err(|e| anyhow::anyhow!("could not convert clinical significance: {}", e))?;
        let result = match clinical_significance {
            Benign => query.clinvar_include_benign,
            LikelyBenign => query.clinvar_include_likely_benign,
            UncertainSignificance => query.clinvar_include_uncertain_significance,
            LikelyPathogenic => query.clinvar_include_likely_pathogenic,
            Pathogenic => query.clinvar_include_pathogenic,
        };
        if !result {
            tracing::trace!(
                "variant {:?} fails clinvar filter from query {:?}",
                seqvar,
                query
            );
        }
        Ok(result)
    } else {
        // Because of the annonars API, we currently need to swallow any error,
        // as "not found" currently maps to an error.
        //
        // TODO: fix annonars
        Ok(true)
    }
}