private Variant getPreferredVariant(QueryResult<Variant> variantQueryResult) { if (variantQueryResult.getNumResults() > 1 && variantQueryResult.first().getAnnotation().getPopulationFrequencies() == null) { for (int i = 1; i < variantQueryResult.getResult().size(); i++) { if (variantQueryResult.getResult().get(i).getAnnotation().getPopulationFrequencies() != null) { return variantQueryResult.getResult().get(i); } } } return variantQueryResult.first(); }
private Variant getPreferredVariant(QueryResult<Variant> variantQueryResult) { if (variantQueryResult.getNumResults() > 1 && variantQueryResult.first().getAnnotation().getPopulationFrequencies() == null) { for (int i = 1; i < variantQueryResult.getResult().size(); i++) { if (variantQueryResult.getResult().get(i).getAnnotation().getPopulationFrequencies() != null) { return variantQueryResult.getResult().get(i); } } } return variantQueryResult.first(); }
@Override protected Float featureValueOf(VariantAnnotation actual) { if (actual.getPopulationFrequencies() != null) { for (PopulationFrequency populationFrequency : actual.getPopulationFrequencies()) { if (populationFrequency.getStudy().equalsIgnoreCase(study) && populationFrequency.getPopulation().equalsIgnoreCase(population)) { return populationFrequency.getRefAlleleFreq(); } } } return 0F; } };
@Override protected Float featureValueOf(VariantAnnotation actual) { if (actual.getPopulationFrequencies() != null) { for (PopulationFrequency populationFrequency : actual.getPopulationFrequencies()) { if (populationFrequency.getStudy().equalsIgnoreCase(study) && populationFrequency.getPopulation().equalsIgnoreCase(population)) { return populationFrequency.getAltAlleleFreq(); } } } return 0F; } };
case "aa_maf": if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); currentAnnotation.getPopulationFrequencies().add(parsePopulationFrequency(keyValue[1], "ESP_6500", "African_American")); case "afr_maf": if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); currentAnnotation.getPopulationFrequencies().add(parsePopulationFrequency(keyValue[1], "1000GENOMES", "phase_1_AFR")); case "amr_maf": if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); currentAnnotation.getPopulationFrequencies().add(parsePopulationFrequency(keyValue[1], "1000GENOMES", "phase_1_AMR")); case "asn_maf": if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>());
@Override protected Float featureValueOf(VariantAnnotation actual) { if (actual.getPopulationFrequencies() != null) { for (PopulationFrequency populationFrequency : actual.getPopulationFrequencies()) { if (populationFrequency.getStudy().equalsIgnoreCase(study) && populationFrequency.getPopulation().equalsIgnoreCase(population)) { return Math.min(populationFrequency.getAltAlleleFreq(), populationFrequency.getRefAlleleFreq()); } } } return 0F; } };
.setPopulationFrequencies(cacheVariant.getAnnotation().getPopulationFrequencies()); mustRunAnnotationPositions.add(mustSearchVariationPositions.get(i)); mustRunAnnotation.add(mustSearchVariation.get(i));
.setPopulationFrequencies(cacheVariant.getAnnotation().getPopulationFrequencies()); mustRunAnnotationPositions.add(mustSearchVariationPositions.get(i)); mustRunAnnotation.add(mustSearchVariation.get(i));
private List<PopulationFrequency> getPopulationFrequencies(Variant variant) { try { byte[] variantKey = VariantAnnotationUtils.buildVariantId(variant.getChromosome(), variant.getStart(), variant.getReference(), variant.getAlternate()).getBytes(); byte[] dbContent = dbIndex.get(variantKey); if (dbContent == null) { return null; } else { // dbIndex.remove(variantKey); VariantAvro variantAvro = mapper.readValue(dbContent, VariantAvro.class); flagVisitedVariant(variantKey, variantAvro); return variantAvro.getAnnotation().getPopulationFrequencies(); } } catch (RocksDBException | IOException e) { e.printStackTrace(); return null; } }
List<PopulationFrequency> populationFrequencies = variant.getAnnotation().getPopulationFrequencies(); if (populationFrequencies != null) { List<String> popFreqList = new ArrayList<>();
List<PopulationFrequency> populationFrequencies = variant.getAnnotation().getPopulationFrequencies(); if (populationFrequencies != null) { stringBuilder.append(populationFrequencies.stream()
.setPopulationFrequencies(preferredVariant.getAnnotation().getPopulationFrequencies());
List<PopulationFrequency> populationFrequencies = variant.getAnnotation().getPopulationFrequencies(); if (populationFrequencies != null) { stringBuilder.append(populationFrequencies.stream()
.setPopulationFrequencies(preferredVariant.getAnnotation().getPopulationFrequencies());
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); if (annotatorSet.contains("variation")) { destination.setId(origin.getId()); } if (annotatorSet.contains("consequenceType")) { destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); } if (annotatorSet.contains("conservation")) { destination.setConservation(origin.getConservation()); } // destination.setGeneExpression(origin.getGeneExpression()); // destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); if (annotatorSet.contains("populationFrequencies")) { destination.setPopulationFrequencies(origin.getPopulationFrequencies()); } // destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); if (annotatorSet.contains("clinical")) { destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); } if (annotatorSet.contains("functionalScore")) { destination.setFunctionalScore(origin.getFunctionalScore()); } }
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); if (annotatorSet.contains("variation")) { destination.setId(origin.getId()); } if (annotatorSet.contains("consequenceType")) { destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); } if (annotatorSet.contains("conservation")) { destination.setConservation(origin.getConservation()); } // destination.setGeneExpression(origin.getGeneExpression()); // destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); if (annotatorSet.contains("populationFrequencies")) { destination.setPopulationFrequencies(origin.getPopulationFrequencies()); } // destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); if (annotatorSet.contains("clinical")) { destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); } if (annotatorSet.contains("functionalScore")) { destination.setFunctionalScore(origin.getFunctionalScore()); } }
.filter(variant -> { Map<String, PopulationFrequency> map; if (variant.getAnnotation().getPopulationFrequencies() == null) { map = Collections.emptyMap(); } else { map = new HashMap<>(); for (PopulationFrequency p : variant.getAnnotation().getPopulationFrequencies()) { map.put(p.getStudy() + ":" + p.getPopulation(), p); .map(variant -> { Map<String, PopulationFrequency> map; if (variant.getAnnotation().getPopulationFrequencies() == null) { map = Collections.emptyMap(); } else { map = new HashMap<>(); for (PopulationFrequency p : variant.getAnnotation().getPopulationFrequencies()) { map.put(p.getStudy() + ":" + p.getPopulation(), p);
if (variantAnnotation.getPopulationFrequencies() != null) { for (PopulationFrequency pf : variantAnnotation.getPopulationFrequencies()) { PhoenixHelper.Column column = VariantPhoenixHelper.getPopulationFrequencyColumn(pf.getStudy(), pf.getPopulation()); map.put(column, Arrays.asList(pf.getRefAlleleFreq(), pf.getAltAlleleFreq()));
if (ListUtils.isEmpty(variant.getAnnotation().getPopulationFrequencies())) { acmg.add("PM2"); } else { boolean above5 = false; boolean hasPopFreq = false; for (PopulationFrequency populationFrequency: variant.getAnnotation().getPopulationFrequencies()) {
List<PopulationFrequency> populationFrequencies = annotation.getPopulationFrequencies(); if (populationFrequencies != null) { for (PopulationFrequency pf: populationFrequencies) {