private Map<String, AdditionalAttribute> getAdditionalAttributes(String[] variationFields, String[] variationFeatureFields) { Map<String, AdditionalAttribute> additionalAttributes = new HashMap<>(); AdditionalAttribute additionalAttribute = new AdditionalAttribute(); additionalAttribute.setAttribute(new HashMap<String, String>()); if ((variationFeatureFields[11] != null && !variationFeatureFields[11].equals("\\N"))) { additionalAttribute.getAttribute().put("ensemblValidationStatus", variationFeatureFields[11]); } additionalAttributes.put("ensemblAnnotation", additionalAttribute); return additionalAttributes; }
public Map<String, AdditionalAttribute> convertAdditionalAttributesToDataModelType(Document customAnnotation) { Map<String, AdditionalAttribute> attributeMap = new HashMap<>(); for (String key : customAnnotation.keySet()) { Document document = customAnnotation.get(key, Document.class); HashMap<String, String> map = new HashMap<>(); document.forEach((k, value) -> map.put(k, value.toString())); AdditionalAttribute attribute = new AdditionalAttribute(map); attributeMap.put(key, attribute); } return attributeMap; }
private void flagTranscriptAnnotationUpdated(Variant variant, String ensemblTranscriptId) { Map<String, AdditionalAttribute> additionalAttributesMap = variant.getAnnotation().getAdditionalAttributes(); if (additionalAttributesMap == null) { additionalAttributesMap = new HashMap<>(); AdditionalAttribute additionalAttribute = new AdditionalAttribute(); Map<String, String> transcriptsSet = new HashMap<>(); transcriptsSet.put(ensemblTranscriptId, null); additionalAttribute.setAttribute(transcriptsSet); additionalAttributesMap.put("phasedTranscripts", additionalAttribute); variant.getAnnotation().setAdditionalAttributes(additionalAttributesMap); } else if (additionalAttributesMap.get("phasedTranscripts") == null) { AdditionalAttribute additionalAttribute = new AdditionalAttribute(); Map<String, String> transcriptsSet = new HashMap<>(); transcriptsSet.put(ensemblTranscriptId, null); additionalAttribute.setAttribute(transcriptsSet); additionalAttributesMap.put("phasedTranscripts", additionalAttribute); } else { additionalAttributesMap.get("phasedTranscripts").getAttribute().put(ensemblTranscriptId, null); } }
@Override public AdditionalAttribute build() { try { AdditionalAttribute record = new AdditionalAttribute(); record.attribute = fieldSetFlags()[0] ? this.attribute : (java.util.Map<java.lang.String,java.lang.String>) defaultValue(fields()[0]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
private void flagTranscriptAnnotationUpdated(Variant variant, String ensemblTranscriptId) { Map<String, AdditionalAttribute> additionalAttributesMap = variant.getAnnotation().getAdditionalAttributes(); if (additionalAttributesMap == null) { additionalAttributesMap = new HashMap<>(); AdditionalAttribute additionalAttribute = new AdditionalAttribute(); Map<String, String> transcriptsSet = new HashMap<>(); transcriptsSet.put(ensemblTranscriptId, null); additionalAttribute.setAttribute(transcriptsSet); additionalAttributesMap.put("phasedTranscripts", additionalAttribute); variant.getAnnotation().setAdditionalAttributes(additionalAttributesMap); } else if (additionalAttributesMap.get("phasedTranscripts") == null) { AdditionalAttribute additionalAttribute = new AdditionalAttribute(); Map<String, String> transcriptsSet = new HashMap<>(); transcriptsSet.put(ensemblTranscriptId, null); additionalAttribute.setAttribute(transcriptsSet); additionalAttributesMap.put("phasedTranscripts", additionalAttribute); } else { additionalAttributesMap.get("phasedTranscripts").getAttribute().put(ensemblTranscriptId, null); } }
map.put(OBSERVEDLOSS, fields[OBSERVEDLOSS_COLUMN]); AdditionalAttribute dgvSpecificAttributes = new AdditionalAttribute(map); additionalAttributes.put(DGV_SPECIFIC_ATTRIBUTES, dgvSpecificAttributes); VariantAnnotation annotation = new VariantAnnotation(variant.getChromosome(), variant.getStart(),
private Map<String, AdditionalAttribute> getCustomAnnotation(Variant variant) { try { byte[] dbContent = dbIndex.get((variant.getChromosome() + "_" + variant.getStart() + "_" + variant.getReference() + "_" + variant.getAlternate()).getBytes()); if (dbContent == null) { return null; } else { ObjectMapper mapper = new ObjectMapper(); AdditionalAttribute infoAttribute = new AdditionalAttribute(); infoAttribute.setAttribute(mapper.readValue(dbContent, Map.class)); Map<String, AdditionalAttribute> customAnnotation = new HashMap<>(1); customAnnotation.put(fileId, infoAttribute); return customAnnotation; } } catch (RocksDBException | IOException e) { return null; } }
additionalAttribute = variantAnnotation.getAdditionalAttributes().get(GROUP_NAME.key()); } else { additionalAttribute = new AdditionalAttribute(new HashMap<>()); variantAnnotation.getAdditionalAttributes().put(GROUP_NAME.key(), additionalAttribute);
new AdditionalAttribute(Collections.singletonMap(VARIANT_ID.key(), variant.toString())); if (variantAnnotation.getAdditionalAttributes() == null) { variantAnnotation
Query query = new Query(VariantQueryParam.REGION.key(), region); dbAdaptor.updateCustomAnnotations( query, key, new AdditionalAttribute(Collections.singletonMap("feature", gff.getFeature())), ts, QueryOptions.empty()); annotation.put(("score"), String.valueOf(bed.getScore())); annotation.put(("strand"), bed.getStrand()); AdditionalAttribute additionalAttribute = new AdditionalAttribute(annotation); dbAdaptor.updateCustomAnnotations(query, key, additionalAttribute, ts, QueryOptions.empty()); Query query = new Query(VariantQueryParam.REGION.key(), region); Map<String, String> info = variant.getStudies().get(0).getFiles().get(0).getAttributes(); AdditionalAttribute attribute = new AdditionalAttribute(info); dbAdaptor.updateCustomAnnotations(query, key, attribute, ts, new QueryOptions());
attribute.put(RELEASE.key(), String.valueOf(variantSearchModel.getRelease())); variantAnnotation.setAdditionalAttributes(new HashMap<>()); variantAnnotation.getAdditionalAttributes().put(GROUP_NAME.key(), new AdditionalAttribute(attribute));
additionalAttribute = annotation.getAdditionalAttributes().get(GROUP_NAME.key()); } else { additionalAttribute = new AdditionalAttribute(new HashMap<>()); annotation.getAdditionalAttributes().put(GROUP_NAME.key(), additionalAttribute);
@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()); }
if (value == null) { HashMap<String, String> map = new HashMap<>(1); value = new AdditionalAttribute(map);