String id = variant.toString(); List<String> variantIds = new ArrayList<>(variant.getIds());
variant.getStudies().get(0).setSamplesPosition(getSamplesPosition(fileId)); variantsPerFile.get(fileId).add(variant); ids.addAll(variant.getIds());
.setReference(variant.getReference()) .setAlternate(variant.getAlternate()) .addAllIdNonDefault(decodeIds(variant.getIds()));
v.setIds(var.getIds()); v.setStrand(var.getStrand()); v.setAnnotation(var.getAnnotation());
updateMongoDBOperations(mainVariant, variant.getIds(), fileDocuments, alternatesFromStage, alternateDocuments, gts, newStudy, newVariant, mongoDBOps);
.setReference(variant.getReference()) .setAlternate(variant.getAlternate()) .addAllIdNonDefault(encodeIds(variant.getIds()));
public void testGetAllVariants_rs(String key) { // This test queries a single ID with no more options Query query = new Query(key, "rs1137005"); queryResult = query(query, null); Variant variant = queryResult.first(); assertEquals(1, queryResult.getNumResults()); assertEquals(variant.getStart(), Integer.valueOf(1650807)); assertThat(variant.getIds(), hasItem("rs1137005")); query = new Query(key, "rs1137005,rs150535390"); queryResult = query(query, this.options); assertEquals(2, queryResult.getNumResults()); queryResult.getResult().forEach(v -> assertThat(v.getIds(), anyOf(hasItem("rs1137005"), hasItem("rs150535390")))); }
.append(DocumentToVariantConverter.ALTERNATE_FIELD, variant.getAlternate()) .append(DocumentToVariantConverter.TYPE_FIELD, variant.getType().name()) .append(DocumentToVariantConverter.IDS_FIELD, variant.getIds()) .append(DocumentToVariantConverter.ANNOTATION_FIELD, Collections.emptyList());
@Test public void testConvertToStorageTypeWithoutFiles() { DocumentToVariantConverter converter = new DocumentToVariantConverter(); Document converted = converter.convertToStorageType(variant); assertFalse(converted.containsKey(DocumentToVariantConverter.IDS_FIELD)); //IDs must be added manually. converted.put(DocumentToVariantConverter.IDS_FIELD, variant.getIds()); //Add IDs assertEquals(mongoVariant, converted); }
private Variant convert(org.opencb.biodata.models.variant.Variant var) { Variant build = Variant.newBuilder() .setChromosome(var.getChromosome()) .setStart(var.getStart()) .setEnd(var.getEnd()) .setLength(var.getLength()) .setReference(var.getReference()) .setAlternate(var.getAlternate()) .addAllIds(var.getIds()) .build(); return build; }
Document converted = converter.convertToStorageType(variant); converted.put(DocumentToVariantConverter.IDS_FIELD, variant.getIds()); //Add IDs mongoVariant.append(DocumentToVariantConverter.STATS_FIELD, Collections.emptyList()); assertEquals("\n" + mongoVariant.toJson() + "\n" + converted.toJson(), mongoVariant, converted);
assertEquals(message, originalVariant.getStart(), exportedVariant.getStart()); assertEquals(message, originalVariant.getEnd(), exportedVariant.getEnd()); assertWithConflicts(originalVariant, () -> assertEquals("At variant " + originalVariant, originalVariant.getIds(), exportedVariant.getIds())); assertEquals(message, originalVariant.getStudies().size(), exportedVariant.getStudies().size()); assertEquals(message, originalVariant.getSampleNames(STUDY_NAME), exportedVariant.getSampleNames(STUDY_NAME));