protected Variant convert(Variant variant, Map<Integer, StudyEntry> studies, VariantAnnotation annotation) { for (StudyEntry studyEntry : studies.values()) { variant.addStudyEntry(studyEntry); } variant.setAnnotation(annotation); if (annotation != null && StringUtils.isNotEmpty(annotation.getId())) { variant.setId(annotation.getId()); } else { variant.setId(variant.toString()); } if (failOnEmptyVariants && variant.getStudies().isEmpty()) { throw new IllegalStateException("No Studies registered for variant!!! " + variant); } return variant; }
VariantFileMetadata fileMetadata = new VariantFileMetadata(metadata.getFiles().get(0)); entry.setFileId(fileMetadata.getId()); variant.addStudyEntry(entry);
/** * Create an empty Variant (position, ref, alt) from a template with basic Study information without samples. * @param target Variant to take as a template * @return Variant filled with chromosome, start, end, ref, alt, study ID and format set to GT only, BUT no samples. */ public Variant createFromTemplate(Variant target) { Variant var = new Variant(target.getChromosome(), target.getStart(), target.getEnd(), target.getReference(), target.getAlternate()); var.setType(target.getType()); for(StudyEntry tse : target.getStudies()){ StudyEntry se = new StudyEntry(tse.getStudyId()); se.setFiles(Collections.singletonList(new FileEntry("", "", new HashMap<>()))); se.setFormat(Arrays.asList(getGtKey(), getFilterKey())); se.setSamplesPosition(new HashMap<>()); se.setSamplesData(new ArrayList<>()); var.addStudyEntry(se); } return var; }
StudyEntry se = new StudyEntry(studyId.toString(), new LinkedList<>(), format); se.setSamplesPosition(new HashMap<>()); var.addStudyEntry(se); StudyEntry se = new StudyEntry(studyIdStr, loadedSecondaryAlternates, format); se.setSamplesPosition(Collections.emptyMap()); mainVariantNew.addStudyEntry(se);
public void writeVariant(MongoDBVariantStageConverterTask converterTask, MongoDBVariantStageLoader loader, String variantStr) { Variant variant = new Variant(variantStr); variant.setNames(Collections.emptyList()); StudyEntry studyEntry = new StudyEntry("1", "1"); studyEntry.setFormat(Collections.emptyList()); variant.addStudyEntry(studyEntry); variantMap.put(variant.getChromosome(), variant); loader.write(converterTask.apply(Collections.singletonList(variant))); }
sampleVariant.addStudyEntry(se); variants.add(sampleVariant);
studyEntry.setSamplesData(new ArrayList<>()); mergedVariant.addStudyEntry(studyEntry); mergedVariant.setType(variant.getType());
StudyEntry studyEntry = new StudyEntry(studyIdStr, alternates, format); studyEntry.setSamplesPosition(Collections.emptyMap()); templateVariant.addStudyEntry(studyEntry);
variant.addStudyEntry(studyEntry); } else { variant.setStudies(null);
studyEntry.setSortedSamplesPosition(new LinkedHashMap<>()); studyEntry.setSamplesData(new ArrayList<>()); mergedVariant.addStudyEntry(studyEntry); mergedVariant.setType(variant.getType());
st.addSampleData(samplesMap.get(sampleId), Collections.singletonList("0/0")); variant.addStudyEntry(st); for (Integer cid : sc.getCalculatedStats()) { VariantStats stats = new VariantStats();
normalizedVariant.addStudyEntry(normalizedEntry); samplesData = newSamplesData(entry.getSamplesData().size(), entry.getFormat().size());
na002.put("DP", "5"); studyEntry.addSampleData("NA002", na002); variant.addStudyEntry(studyEntry);
Document dbo = (Document) o; if (returnStudies == null || returnStudies.contains(((Number) dbo.get(STUDYID_FIELD)).intValue())) { variant.addStudyEntry(variantStudyEntryConverter.convertToDataModelType(dbo));
@Test public void testConvertToStorageTypeWithFiles() { variant.addStudyEntry(studyEntry);
public Variant convert(VcfSliceProtos.VcfRecord vcfRecord, String chromosome, int slicePosition) { int start = getStart(vcfRecord, slicePosition); int end = getEnd(vcfRecord, slicePosition); Variant variant = new Variant(chromosome, start, end, vcfRecord.getReference(), vcfRecord.getAlternate()); variant.setType(getVariantType(vcfRecord.getType())); variant.setIds(vcfRecord.getIdNonDefaultList()); variant.resetLength(); FileEntry fileEntry = new FileEntry(); fileEntry.setFileId(fileId); Map<String, String> attributes = getFileAttributes(vcfRecord); fileEntry.setAttributes(attributes); fileEntry.setCall(vcfRecord.getCall().isEmpty() ? null : vcfRecord.getCall()); if (vcfRecord.getType().equals(VariantProto.VariantType.NO_VARIATION)) { attributes.put("END", Integer.toString(end)); } StudyEntry studyEntry = new StudyEntry(studyId); studyEntry.setFiles(Collections.singletonList(fileEntry)); studyEntry.setFormat(getFormat(vcfRecord)); studyEntry.setSamplesData(getSamplesData(vcfRecord, studyEntry.getFormatPositions())); studyEntry.setSamplesPosition(retrieveSamplePosition()); studyEntry.getFormatPositions(); // Initialize the map List<VariantProto.AlternateCoordinate> alts = vcfRecord.getSecondaryAlternatesList(); studyEntry.setSecondaryAlternates(getAlternateCoordinates(alts)); variant.addStudyEntry(studyEntry); studyEntry.getFormatPositions(); // Initialize the map return variant; }
.build(); expectedVariant.addStudyEntry(aux.getStudy("2"));