/** * Convert a bunch of lines from VEP int a single Variant Annotation * @param lines All line must refer to the same variant * @return */ public static VariantAnnotation parse(List<String> lines) { VariantAnnotation variantAnnotation = new VariantAnnotation(); return null; }
/** * * @param csqFormatFields A String list with all the fields annotated, ie. * Allele|Consequence|SYMBOL|Feature_type|BIOTYPEcDNA_position|CDS_position|Protein_position * @param csqInfoField The CSQ field from the VCF INFO column * @return */ public static VariantAnnotation parseInfoCsq(List<String> csqFormatFields, String csqInfoField) { if (csqInfoField.startsWith("CSQ")) { csqInfoField = csqInfoField.replaceFirst("CSQ=", ""); } VariantAnnotation variantAnnotation = new VariantAnnotation(); return null; }
protected VariantAnnotation getVariantAnnotation(byte[] key) throws RocksDBException, IOException { byte[] dbContent = rdb.get(key); // List<EvidenceEntry> evidenceEntryList; VariantAnnotation variantAnnotation; if (dbContent == null) { variantAnnotation = new VariantAnnotation(); List<EvidenceEntry> evidenceEntryList = new ArrayList<>(); variantAnnotation.setTraitAssociation(evidenceEntryList); numberNewVariants++; } else { variantAnnotation = mapper.readValue(dbContent, VariantAnnotation.class); // List<EvidenceEntry> evidenceEntryList = mapper.readValue(dbContent, mapper.getTypeFactory() // .constructParametrizedType(List.class, List.class, EvidenceEntry.class)); numberVariantUpdates++; } return variantAnnotation; }
VariantAnnotation annotation = new VariantAnnotation(variant.getChromosome(), variant.getStart(), variant.getEnd(), variant.getReference(), variant.getAlternate(), null, null, null, null,
ExecutorService executor = Executors.newFixedThreadPool(numConsumers + numProducers); final BlockingQueue<VariantAnnotation> queue = new ArrayBlockingQueue<>(batchSize * numConsumers * 2); final VariantAnnotation lastElement = new VariantAnnotation();
VariantAnnotation variantAnnotation = new VariantAnnotation(); variantAnnotation.setDrugs(drugList); variantAnnotation.setTraitAssociation(evidenceEntryMap
variant.setType(type); variant.setSv(sv); VariantAnnotation ensemblVariantAnnotation = new VariantAnnotation(null, null, null, null, null, null, id, xrefs, hgvs, displayConsequenceType, conseqTypes, null, null, null, logger.warn("Variant {} annotation cannot be serialized to Json: {}", id, e.getMessage()); VariantAnnotation variantAnnotation = new VariantAnnotation(null, null, null, null, null, ancestralAllele, id, xrefs, hgvs, displayConsequenceType, conseqTypes, null, minorAllele, minorAlleleFreq,
mustSearchVariation.get(i).setAnnotation(new VariantAnnotation());
mustSearchVariation.get(i).setAnnotation(new VariantAnnotation());
@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; } }
currentAnnotation = new VariantAnnotation(); currentAnnotation.setChromosome(variantMap.get("chromosome")); currentAnnotation.setStart(Integer.valueOf(variantMap.get("start")));
return null; } else { variantAnnotation = new VariantAnnotation();
variantAnnotation = new VariantAnnotation(); normalizedVariantList.get(i).setAnnotation(variantAnnotation); } else {
variantAnnotation = new VariantAnnotation(); normalizedVariantList.get(i).setAnnotation(variantAnnotation); } else {
@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))); } }
protected static VariantAnnotation newVariantAnnotation(Variant variant) { VariantAnnotation va; va = new VariantAnnotation(); va.setChromosome(variant.getChromosome()); va.setReference(variant.getReference()); va.setAlternate(variant.getAlternate()); va.setStart(variant.getStart()); va.setEnd(variant.getEnd()); return va; }
VariantAnnotation variantAnnotation = new VariantAnnotation(); variantAnnotation.setChromosome(variant.getChromosome()); variantAnnotation.setStart(variant.getStart());
@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 = new VariantAnnotation();
@Override public VariantAnnotation build() { try { VariantAnnotation record = new VariantAnnotation(); record.chromosome = fieldSetFlags()[0] ? this.chromosome : (java.lang.String) defaultValue(fields()[0]); record.start = fieldSetFlags()[1] ? this.start : (java.lang.Integer) defaultValue(fields()[1]);