@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; } };
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; }
for (PopulationFrequency pf : variantAnnotation.getPopulationFrequencies()) { PhoenixHelper.Column column = VariantPhoenixHelper.getPopulationFrequencyColumn(pf.getStudy(), pf.getPopulation()); map.put(column, Arrays.asList(pf.getRefAlleleFreq(), pf.getAltAlleleFreq()));
.setRefAllele(pf.getRefAllele()) .setAltAllele(pf.getAltAllele()) .setRefAlleleFreq(pf.getRefAlleleFreq()) .setAltAlleleFreq(pf.getAltAlleleFreq()) .setRefHomGenotypeFreq(pf.getRefHomGenotypeFreq())