feature-improveclinical: still adapting ClinicalVariantParser to the new EvidenceEntry model
@@ -161,8 +161,19 @@ public class ClinVarIndexer extends ClinicalIndexer {
}
}
+ VariantClassification variantClassification = null;
+ if (!EtlCommons.isMissing(lineFields[VARIANT_SUMMARY_CLINSIG_COLUMN])) {
+ if (VariantAnnotationUtils.CLINVAR_CLINSIG_TO_ACMG.containsKey(lineFields[VARIANT_SUMMARY_CLINSIG_COLUMN])) {
+ variantClassification = new VariantClassification(VariantAnnotationUtils.CLINVAR_CLINSIG_TO_ACMG
+ .get(lineFields[VARIANT_SUMMARY_CLINSIG_COLUMN]), null, null, null, null);
+ } else {
+ logger.warn("No SO term found for allele origin {}. Skipping.", originString);
+ }
+ }
+
EvidenceEntry evidenceEntry = new EvidenceEntry(evidenceSource, null, null,
- "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + variationId, variationId, alleleOrigin, null,
+ "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + variationId, variationId,
+ !alleleOrigin.isEmpty() ? alleleOrigin : null, null, genomicFeatureList,
);
String clinicalSignificance = EtlCommons.isMissing(lineFields[VARIANT_SUMMARY_CLINSIG_COLUMN])
