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; }
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); } }
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); } }
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; } }