for (EvidenceEntry evidenceEntry : variant.getAnnotation().getTraitAssociation()) { if ("clinvar".equals(evidenceEntry.getSource().getName()) && (evidenceEntry.getVariantClassification().getClinicalSignificance() == org.opencb.biodata.models.variant.avro.ClinicalSignificance.pathogenic || evidenceEntry.getVariantClassification().getClinicalSignificance() == org.opencb.biodata.models.variant.avro.ClinicalSignificance.likely_pathogenic)) { acmg.add("PS1"); } else { && (evidenceEntry.getVariantClassification().getClinicalSignificance() == org.opencb.biodata.models.variant.avro.ClinicalSignificance.benign || evidenceEntry.getVariantClassification().getClinicalSignificance() == org.opencb.biodata.models.variant.avro.ClinicalSignificance.likely_benign)) { acmg.add("BP6"); } else if ("clinvar".equals(evidenceEntry.getSource().getName()) && (evidenceEntry.getVariantClassification().getClinicalSignificance() == org.opencb.biodata.models.variant.avro.ClinicalSignificance.pathogenic || evidenceEntry.getVariantClassification().getClinicalSignificance() == org.opencb.biodata.models.variant.avro.ClinicalSignificance.likely_pathogenic)) { acmg.add("PP5");
if (evidenceEntry.getVariantClassification() != null) { ClinicalSignificance clinicalSignificance = evidenceEntry.getVariantClassification().getClinicalSignificance(); if (clinicalSignificance != null) { clinicalSignificanceSet.add(clinicalSignificance);