protected Variant convert(Variant variant, Map<Integer, StudyEntry> studies, VariantAnnotation annotation) { for (StudyEntry studyEntry : studies.values()) { variant.addStudyEntry(studyEntry); } variant.setAnnotation(annotation); if (annotation != null && StringUtils.isNotEmpty(annotation.getId())) { variant.setId(annotation.getId()); } else { variant.setId(variant.toString()); } if (failOnEmptyVariants && variant.getStudies().isEmpty()) { throw new IllegalStateException("No Studies registered for variant!!! " + variant); } return variant; }
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()); } }
public void checkAnnotationSnapshot(VariantStorageEngine variantStorageEngine, String annotationName, String expectedAnnotationName, String expectedId, Query query) throws Exception { int count = 0; for (VariantAnnotation annotation: variantStorageEngine.getAnnotation(annotationName, query, null).getResult()) { assertEquals("an id -- " + expectedId, annotation.getId()); // assertEquals("1", annotation.getAdditionalAttributes().get("opencga").getAttribute().get("release")); assertEquals(expectedAnnotationName, annotation.getAdditionalAttributes().get(GROUP_NAME.key()) .getAttribute().get(VariantField.AdditionalAttributes.ANNOTATION_ID.key())); count++; } assertEquals(count, variantStorageEngine.count(query).first().intValue()); }
if((id=variantAnnotation.getId())==null) { id = "-";
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()); } }
.setReference(annotation.getReference()) .setAlternate(annotation.getAlternate()) .setId(annotation.getId()); List<Xref> xrefs = annotation.getXrefs(); if (xrefs != null) {