/** * Updates VariantAnnotation objects in variantAnnotationList. * * @param variantList List of Variant objects. variantList and variantAnnotationList must contain variants in the * SAME order: variantAnnotation at position i must correspond to variant i */ public void run(List<Variant> variantList) { for (int i = 0; i < variantList.size(); i++) { List<PopulationFrequency> populationFrequencies = getPopulationFrequencies(variantList.get(i)); // Update only if there are annotations for this variant. customAnnotation may be empty if the variant // exists in the vcf but the info field does not contain any of the required attributes if (populationFrequencies != null && populationFrequencies.size() > 0) { VariantAnnotation variantAnnotation = variantList.get(i).getAnnotation(); if (variantAnnotation != null) { // variantList and variantAnnotationList must contain variants in the SAME order: variantAnnotation // at position i must correspond to variant i variantAnnotation.setPopulationFrequencies(populationFrequencies); } } } }
.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));
@Override public boolean write(Variant variant) { ArrayList<PopulationFrequency> frequencies = new ArrayList<>(); for (StudyEntry studyEntry : variant.getStudies()) { for (Map.Entry<String, VariantStats> cohortEntry : studyEntry.getStats().entrySet()) { String studyId = studyEntry.getStudyId(); studyId = studyId.substring(studyId.lastIndexOf(":") + 1); PopulationFrequency populationFrequency = converter.convert(studyId, cohortEntry.getKey(), cohortEntry.getValue(), variant.getReference(), variant.getAlternate()); // Write only frequencies non zero if (populationFrequency.getAltAlleleFreq() > 0 && !populationFrequency.getAltAlleleFreq().isNaN()) { frequencies.add(populationFrequency); } } } Variant newVar = new Variant(variant.toString()); VariantAnnotation annotation = new VariantAnnotation(); annotation.setPopulationFrequencies(frequencies); newVar.setAnnotation(annotation); try { sequenceWriter.write(newVar); outputStream.write('\n'); } catch (IOException e) { throw new UncheckedIOException(e); } return true; } }
if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>()); if(parseFrequencies) { if(currentAnnotation.getPopulationFrequencies()==null) { currentAnnotation.setPopulationFrequencies(new ArrayList<PopulationFrequency>());
.setPopulationFrequencies(preferredVariant.getAnnotation().getPopulationFrequencies());
.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()); } }
variantAnnotation.setPopulationFrequencies(populationFrequencies);
va.setPopulationFrequencies(populationFrequencies);