private boolean transcriptAnnotationUpdated(Variant variant, String ensemblTranscriptId) { if (variant.getAnnotation().getAdditionalAttributes() != null && variant.getAnnotation().getAdditionalAttributes().get("phasedTranscripts") != null && variant.getAnnotation().getAdditionalAttributes().get("phasedTranscripts") .getAttribute().containsKey(ensemblTranscriptId)) { return true; } return false; }
private boolean transcriptAnnotationUpdated(Variant variant, String ensemblTranscriptId) { if (variant.getAnnotation().getAdditionalAttributes() != null && variant.getAnnotation().getAdditionalAttributes().get("phasedTranscripts") != null && variant.getAnnotation().getAdditionalAttributes().get("phasedTranscripts") .getAttribute().containsKey(ensemblTranscriptId)) { return true; } return false; }
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); } }
/** * Updates VariantAnnotation objects in variantAnnotationList. * * @param variantList List of Variant objects. variantList and variantAnnotationList must contain variants in the * SAME order: variantAnnotation at position i must correspond to variant i */ public void run(List<Variant> variantList) { for (int i = 0; i < variantList.size(); i++) { Map<String, AdditionalAttribute> customAnnotation = getCustomAnnotation(variantList.get(i)); // Update only if there are annotations for this variant. customAnnotation may be empty if the variant // exists in the vcf but the info field does not contain any of the required attributes if (customAnnotation != null && customAnnotation.get(fileId).getAttribute().size() > 0) { VariantAnnotation variantAnnotation = variantList.get(i).getAnnotation(); if (variantAnnotation != null) { Map<String, AdditionalAttribute> additionalAttributes = variantAnnotation.getAdditionalAttributes(); if (additionalAttributes == null) { // variantList and variantAnnotationList must contain variants in the SAME order: variantAnnotation // at position i must correspond to variant i variantAnnotation.setAdditionalAttributes(customAnnotation); } else { additionalAttributes.putAll(customAnnotation); // variantList and variantAnnotationList must contain variants in the SAME order: variantAnnotation // at position i must correspond to variant i // variantAnnotation.setAdditionalAttributes(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); } }
Variant variant = iterator.next(); if (variant.getAnnotation() != null && variant.getAnnotation().getAdditionalAttributes() != null && variant.getAnnotation().getAdditionalAttributes().get(GROUP_NAME.key()) != null) { AdditionalAttribute additionalAttribute = variant.getAnnotation().getAdditionalAttributes().get(GROUP_NAME.key()); String sync = additionalAttribute.getAttribute().get(AdditionalAttributes.INDEX_SYNCHRONIZATION.key()); if (VariantStorageEngine.SyncStatus.SYNCHRONIZED.key().equals(sync)) {
for (Variant variant : entry.getValue()) { if (variant.getAnnotation() != null && variant.getAnnotation().getAdditionalAttributes() != null && variant.getAnnotation().getAdditionalAttributes().get(GROUP_NAME.key()) != null) { AdditionalAttribute additionalAttribute = variant.getAnnotation().getAdditionalAttributes().get(GROUP_NAME.key()); String indexedStudies = additionalAttribute.getAttribute().get(INDEX_STUDIES.key());
Put buildPut(VariantAnnotation variantAnnotation) { Map<PhoenixHelper.Column, ?> map = convert(variantAnnotation); byte[] bytesRowKey = null; if (variantAnnotation.getAdditionalAttributes() != null) { AdditionalAttribute additionalAttribute = variantAnnotation.getAdditionalAttributes().get(GROUP_NAME.key()); if (additionalAttribute != null) { String variantString = additionalAttribute .getAttribute() .get(VARIANT_ID.key()); if (StringUtils.isNotEmpty(variantString)) { bytesRowKey = generateVariantRowKey(new Variant(variantString)); } } } if (bytesRowKey == null) { bytesRowKey = VariantPhoenixKeyFactory.generateSimpleVariantRowKey( variantAnnotation.getChromosome(), variantAnnotation.getStart(), variantAnnotation.getReference(), variantAnnotation.getAlternate()); } Put put = new Put(bytesRowKey); for (PhoenixHelper.Column column : VariantPhoenixHelper.PRIMARY_KEY) { map.remove(column); } map.forEach((column, value) -> add(put, column, value)); return put; }
if (variantAvro.getAnnotation().getAdditionalAttributes() == null) { dataWriter.write(new Variant(variantAvro));
&& preferredVariant.getAnnotation().getAdditionalAttributes() != null && preferredVariant.getAnnotation().getAdditionalAttributes().size() > 0) { variantAnnotationResultList.get(i).first() .setAdditionalAttributes(preferredVariant.getAnnotation().getAdditionalAttributes());
&& preferredVariant.getAnnotation().getAdditionalAttributes() != null && preferredVariant.getAnnotation().getAdditionalAttributes().size() > 0) { variantAnnotationResultList.get(i).first() .setAdditionalAttributes(preferredVariant.getAnnotation().getAdditionalAttributes());
if (variantAnnotation.getAdditionalAttributes() == null) { variantAnnotation.setAdditionalAttributes(new HashMap<>()); if (variantAnnotation.getAdditionalAttributes().containsKey(GROUP_NAME.key())) { additionalAttribute = variantAnnotation.getAdditionalAttributes().get(GROUP_NAME.key()); } else { additionalAttribute = new AdditionalAttribute(new HashMap<>()); variantAnnotation.getAdditionalAttributes().put(GROUP_NAME.key(), additionalAttribute);
if (variantAnnotation.getAdditionalAttributes() == null) { variantAnnotation .setAdditionalAttributes(Collections.singletonMap(GROUP_NAME.key(), additionalAttribute)); } else { variantAnnotation.getAdditionalAttributes().put(GROUP_NAME.key(), additionalAttribute);
@Test public void testRelease() throws Exception { List<Variant> variants = query(new Query(), new QueryOptions()).getResult(); for (Variant variant : variants) { Integer minFileId = variant.getStudies().stream() .flatMap(s -> s.getFiles().stream()) .map(FileEntry::getFileId) .map(s -> s.substring(30, 35)) .map(Integer::valueOf) .min(Integer::compareTo) .orElse(0); assertTrue(minFileId > 0); int expectedRelease = (minFileId - 12877/*first file loaded*/) / 2/*each release contains 2 files*/ + 1/*base-1*/; int release = Integer.valueOf(variant.getAnnotation().getAdditionalAttributes().get("opencga").getAttribute().get("release")); assertEquals(expectedRelease, release); } }
for (VariantAnnotation variantAnnotation : variantAnnotations) { String id; if (variantAnnotation.getAdditionalAttributes() != null && variantAnnotation.getAdditionalAttributes().containsKey(GROUP_NAME.key())) { String variantString = variantAnnotation.getAdditionalAttributes() .get(GROUP_NAME.key()) .getAttribute()
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 (annotation.getAdditionalAttributes() == null) { annotation.setAdditionalAttributes(new HashMap<>()); if (annotation.getAdditionalAttributes().containsKey(GROUP_NAME.key())) { additionalAttribute = annotation.getAdditionalAttributes().get(GROUP_NAME.key()); } else { additionalAttribute = new AdditionalAttribute(new HashMap<>()); annotation.getAdditionalAttributes().put(GROUP_NAME.key(), additionalAttribute);
Map<String, AdditionalAttribute> additionalAttributes; if (annotation != null) { additionalAttributes = annotation.getAdditionalAttributes(); } else { additionalAttributes = Collections.emptyMap();
Map<String, AdditionalAttribute> additionalAttributes; if (annotation != null) { additionalAttributes = annotation.getAdditionalAttributes(); } else { additionalAttributes = Collections.emptyMap();
Map<String, AdditionalAttribute> additionalAttributes; if (annotation != null) { additionalAttributes = annotation.getAdditionalAttributes(); } else { additionalAttributes = Collections.emptyMap();