private VariantTraitAssociation convertToVariantTraitAssociation(List<EvidenceEntry> traitAssociation) { List<ClinVar> clinvarList = new ArrayList<>(); List<Cosmic> cosmicList = new ArrayList<>(traitAssociation.size()); for (EvidenceEntry evidenceEntry : traitAssociation) { switch (evidenceEntry.getSource().getName()) { case CLINVAR: clinvarList.add(parseClinvar(evidenceEntry)); break; case COSMIC: cosmicList.add(parseCosmic(evidenceEntry)); break; default: break; } } return new VariantTraitAssociation(clinvarList, null, cosmicList); }
private VariantTraitAssociation convertToVariantTraitAssociation(List<EvidenceEntry> traitAssociation) { List<ClinVar> clinvarList = new ArrayList<>(); List<Cosmic> cosmicList = new ArrayList<>(traitAssociation.size()); for (EvidenceEntry evidenceEntry : traitAssociation) { switch (evidenceEntry.getSource().getName()) { case CLINVAR: clinvarList.add(parseClinvar(evidenceEntry)); break; case COSMIC: cosmicList.add(parseCosmic(evidenceEntry)); break; default: break; } } return new VariantTraitAssociation(clinvarList, null, cosmicList); }
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)) { if ("clinvar".equals(evidenceEntry.getSource().getName()) && (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)) {