currentAnnotation.setConsequenceTypes(new ArrayList<ConsequenceType>());
List<ConsequenceType> consequenceTypeList = getConsequenceTypeList(normalizedVariantList.get(i), variantGeneList, true, QueryOptions.empty()); variantAnnotation.setConsequenceTypes(consequenceTypeList); if (phased) { checkAndAdjustPhasedConsequenceTypes(normalizedVariantList.get(i), variantBuffer); logger.error("Consequence type was not calculated for variant {}. Unrecognised variant format." + " Leaving an empty consequence type list.", normalizedVariantList.get(i).toString()); variantAnnotation.setConsequenceTypes(Collections.emptyList()); } catch (Exception e) { logger.error("Unhandled error when calculating consequence type for variant {}. Leaving an empty" + " consequence type list.", normalizedVariantList.get(i).toString()); e.printStackTrace(); variantAnnotation.setConsequenceTypes(Collections.emptyList());
List<ConsequenceType> consequenceTypeList = getConsequenceTypeList(normalizedVariantList.get(i), variantGeneList, true, QueryOptions.empty()); variantAnnotation.setConsequenceTypes(consequenceTypeList); if (phased) { checkAndAdjustPhasedConsequenceTypes(normalizedVariantList.get(i), variantBuffer); logger.error("Consequence type was not calculated for variant {}. Unrecognised variant format." + " Leaving an empty consequence type list.", normalizedVariantList.get(i).toString()); variantAnnotation.setConsequenceTypes(Collections.emptyList()); } catch (Exception e) { logger.error("Unhandled error when calculating consequence type for variant {}. Leaving an empty" + " consequence type list.", normalizedVariantList.get(i).toString()); e.printStackTrace(); variantAnnotation.setConsequenceTypes(Collections.emptyList());
variantAnnotation.setConsequenceTypes(Collections.emptyList());
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()); } }
@Test public void testExcludeAnnotation() { queryResult = query(new Query(), new QueryOptions(QueryOptions.EXCLUDE, "annotation")); assertEquals(allVariants.getResult().size(), queryResult.getResult().size()); VariantAnnotation defaultAnnotation = new VariantAnnotation(); defaultAnnotation.setConsequenceTypes(Collections.emptyList()); for (Variant variant : queryResult.getResult()) { assertThat(variant.getAnnotation(), anyOf(is((VariantAnnotation) null), is(defaultAnnotation))); } }
variantAnnotation.setConsequenceTypes(consequenceTypes);
@Override public List<VariantAnnotation> annotate(List<Variant> variants) throws VariantAnnotatorException { if (fail) { throw new VariantAnnotatorException("Fail because reasons"); } return variants.stream().map(v -> { VariantAnnotation a = new VariantAnnotation(); a.setChromosome(v.getChromosome()); a.setStart(v.getStart()); a.setEnd(v.getEnd()); a.setReference(v.getReference()); a.setAlternate(v.getAlternate()); a.setId("an id -- " + key); ConsequenceType ct = new ConsequenceType(); ct.setGeneName("a gene"); ct.setSequenceOntologyTerms(Collections.emptyList()); ct.setExonOverlap(Collections.emptyList()); ct.setTranscriptAnnotationFlags(Collections.emptyList()); a.setConsequenceTypes(Collections.singletonList(ct)); a.setAdditionalAttributes( Collections.singletonMap(GROUP_NAME.key(), new AdditionalAttribute(Collections.singletonMap(VARIANT_ID.key(), v.toString())))); return a; }).collect(Collectors.toList()); }
va.setConsequenceTypes(consequenceTypes); Integer displaySO = object.getInteger(DISPLAY_CONSEQUENCE_TYPE_FIELD); if (displaySO != null) {
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()); } }