if (variant.getAnnotation().getConservation() != null) { List<Double> phastCons = variant.getAnnotation().getConservation().stream() .filter(t -> t.getSource().equalsIgnoreCase("phastCons")) .map(Score::getScore) if (variant.getAnnotation().getConservation() != null) { List<Double> phylop = variant.getAnnotation().getConservation().stream() .filter(t -> t.getSource().equalsIgnoreCase("phylop")) .map(Score::getScore)
if (variant.getAnnotation().getConservation() != null) { List<Double> phastCons = variant.getAnnotation().getConservation().stream() .filter(t -> t.getSource().equalsIgnoreCase("phastCons")) .map(Score::getScore) if (variant.getAnnotation().getConservation() != null) { List<Double> phylop = variant.getAnnotation().getConservation().stream() .filter(t -> t.getSource().equalsIgnoreCase("phylop")) .map(Score::getScore)
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()); } }
map.put(CLINICAL_SIGNIFICANCE, clinicalSignificanceSet.stream().map(ClinicalSignificance::toString).collect(Collectors.toList())); if (variantAnnotation.getConservation() != null) { for (Score score : variantAnnotation.getConservation()) { PhoenixHelper.Column column = VariantPhoenixHelper.getConservationScoreColumn(score.getSource()); map.put(column, score.getScore());
if (variantAnnotation.getConservation() != null) { for (Score score : variantAnnotation.getConservation()) { switch (score.getSource()) { case "phastCons":
&& ListUtils.isNotEmpty(consequenceType.getProteinVariantAnnotation().getSubstitutionScores()) && ListUtils.isNotEmpty(variant.getAnnotation().getFunctionalScore()) && ListUtils.isNotEmpty(variant.getAnnotation().getConservation())) { double sift = Double.MIN_VALUE; double polyphen = Double.MIN_VALUE; for (Score score: variant.getAnnotation().getConservation()) { if ("gerp".equals(score.getSource())) { gerp = score.getScore();
if (variantAnnotation.getConservation() != null) { List<Document> conservedRegionScores = new LinkedList<>(); for (Score score : variantAnnotation.getConservation()) { if (score != null) { if (score.getSource().equals(PHYLOP)) {
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { if (origin != null) { destination.setId(origin.getId()); destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); destination.setConservation(origin.getConservation()); destination.setGeneExpression(origin.getGeneExpression()); destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); destination.setFunctionalScore(origin.getFunctionalScore()); } }
List<Score> conservation = annotation.getConservation(); if (conservation != null) { for (Score score: conservation) {