private void fixReference(List<VariantAnnotation> variantAnnotationList) throws RocksDBException { for (VariantAnnotation variantAnnotation : variantAnnotationList) { if (!variantAnnotation.getReference().isEmpty() && !variantAnnotation.getReference().equals("-")) { variantAnnotation.setReference(fastaIndexManager.query(variantAnnotation.getChromosome(), variantAnnotation.getStart(), variantAnnotation.getStart() + variantAnnotation.getReference().length() - 1)); } } }
protected void logUpdate(List<VariantAnnotation> list) { if (progressLogger != null) { progressLogger.increment(list.size(), () -> { VariantAnnotation annotation = list.get(list.size() - 1); return ", up to position " + annotation.getChromosome() + ":" + annotation.getStart() + ":" + annotation.getReference() + ":" + annotation.getAlternate(); }); } }
private List<Variant> createEmptyVariantList(List<VariantAnnotation> variantAnnotationList) { List<Variant> newVariantList = new ArrayList<>(variantAnnotationList.size()); for (VariantAnnotation variantAnnotation : variantAnnotationList) { Variant variant = new Variant(variantAnnotation.getChromosome(), variantAnnotation.getStart(), variantAnnotation.getEnd(), variantAnnotation.getReference(), variantAnnotation.getAlternate()); variant.resetType(); variant.resetLength(); newVariantList.add(variant); } return newVariantList; }
StringBuilder stringBuilder = new StringBuilder(variantAnnotationDiff.getVariantAnnotation().getChromosome()); stringBuilder.append("\t"); stringBuilder.append(variantAnnotationDiff.getVariantAnnotation().getStart()); stringBuilder.append("\t"); stringBuilder.append(variantAnnotationDiff.getVariantAnnotation().getReference());
Put buildPut(VariantAnnotation variantAnnotation) { Map<PhoenixHelper.Column, ?> map = convert(variantAnnotation); byte[] bytesRowKey = null; if (variantAnnotation.getAdditionalAttributes() != null) { AdditionalAttribute additionalAttribute = variantAnnotation.getAdditionalAttributes().get(GROUP_NAME.key()); if (additionalAttribute != null) { String variantString = additionalAttribute .getAttribute() .get(VARIANT_ID.key()); if (StringUtils.isNotEmpty(variantString)) { bytesRowKey = generateVariantRowKey(new Variant(variantString)); } } } if (bytesRowKey == null) { bytesRowKey = VariantPhoenixKeyFactory.generateSimpleVariantRowKey( variantAnnotation.getChromosome(), variantAnnotation.getStart(), variantAnnotation.getReference(), variantAnnotation.getAlternate()); } Put put = new Put(bytesRowKey); for (PhoenixHelper.Column column : VariantPhoenixHelper.PRIMARY_KEY) { map.remove(column); } map.forEach((column, value) -> add(put, column, value)); return put; }
Variant variant = iterator.next(); if (!variant.getChromosome().equals(variantAnnotation.getChromosome()) || !variant.getStart().equals(variantAnnotation.getStart()) || !variant.getReference().equals(variantAnnotation.getReference()) || !variant.getAlternate().equals(variantAnnotation.getAlternate())) { throw unexpectedVariantOrderException(variant, variantAnnotation.getChromosome() + ':' + variantAnnotation.getStart() + ':' + variantAnnotation.getReference() + ':' + variantAnnotation.getAlternate());
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()); } }
id = variantConverter.buildStorageId(new Variant(variantString)); } else { id = variantConverter.buildStorageId(variantAnnotation.getChromosome(), variantAnnotation.getStart(), variantAnnotation.getReference(), variantAnnotation.getAlternate());
map.put(POSITION, variantAnnotation.getStart()); map.put(REFERENCE, variantAnnotation.getReference()); map.put(ALTERNATE, variantAnnotation.getAlternate());
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()); } }
public static VariantAnnotationProto.VariantAnnotation createVariantAnnotation(VariantAnnotation annotation) { VariantAnnotationProto.VariantAnnotation.Builder builder = VariantAnnotationProto.VariantAnnotation.newBuilder() .setChromosome(annotation.getChromosome()) .setStart(annotation.getStart()) .setReference(annotation.getReference()) .setAlternate(annotation.getAlternate())