List<String> popFreqList = new ArrayList<>(); for (PopulationFrequency pf: populationFrequencies) { popFreqList.add(pf.getStudy() + "_" + pf.getPopulation() + ":" + DECIMAL_FORMAT_7.format(pf.getAltAlleleFreq()));
@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 Math.min(populationFrequency.getAltAlleleFreq(), 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; } };
private Document convertPopulationFrequencyToStorage(PopulationFrequency populationFrequency) { Document dbObject = new Document(POPULATION_FREQUENCY_STUDY_FIELD, populationFrequency.getStudy()); putNotNull(dbObject, POPULATION_FREQUENCY_POP_FIELD, populationFrequency.getPopulation()); putNotNull(dbObject, POPULATION_FREQUENCY_REFERENCE_FREQUENCY_FIELD, populationFrequency.getRefAlleleFreq()); putNotNull(dbObject, POPULATION_FREQUENCY_ALTERNATE_FREQUENCY_FIELD, populationFrequency.getAltAlleleFreq()); putNotNull(dbObject, POPULATION_FREQUENCY_REF_HOM_GT_FIELD, populationFrequency.getRefHomGenotypeFreq()); putNotNull(dbObject, POPULATION_FREQUENCY_HET_GT_FIELD, populationFrequency.getHetGenotypeFreq()); putNotNull(dbObject, POPULATION_FREQUENCY_ALT_HOM_GT_FIELD, populationFrequency.getAltHomGenotypeFreq()); return dbObject; }
map = new HashMap<>(); for (PopulationFrequency p : variant.getAnnotation().getPopulationFrequencies()) { map.put(p.getStudy() + ":" + p.getPopulation(), p); map = new HashMap<>(); for (PopulationFrequency p : variant.getAnnotation().getPopulationFrequencies()) { map.put(p.getStudy() + ":" + p.getPopulation(), p);
Map<String, Float> populationFrequencies = new HashMap<>(); for (PopulationFrequency populationFrequency : variantAnnotation.getPopulationFrequencies()) { populationFrequencies.put("popFreq" + VariantSearchUtils.FIELD_SEPARATOR + populationFrequency.getStudy() + VariantSearchUtils.FIELD_SEPARATOR + populationFrequency.getPopulation(), populationFrequency.getAltAlleleFreq());
PhoenixHelper.Column column = VariantPhoenixHelper.getPopulationFrequencyColumn(pf.getStudy(), pf.getPopulation()); map.put(column, Arrays.asList(pf.getRefAlleleFreq(), pf.getAltAlleleFreq()));
VariantAnnotationProto.PopulationFrequency.Builder popFreqBuilder = VariantAnnotationProto.PopulationFrequency.newBuilder() .setStudy(pf.getStudy()) .setPopulation(pf.getPopulation()) .setRefAllele(pf.getRefAllele())