@Override public Variant convert(Result result) { Variant variant = extractVariantFromVariantRowKey(result.getRow()); try { VariantAnnotation annotation = annotationConverter.convert(result); Map<Integer, StudyEntry> studies; if (selectVariantElements != null && selectVariantElements.getStudies().isEmpty()) { studies = Collections.emptyMap(); } else { studies = studyEntryConverter.convert(result); } return convert(variant, studies, annotation); } catch (RuntimeException e) { throw new IllegalStateException("Fail to parse variant: " + variant, e); } } }
Set<VariantField> returnedFields = selectVariantElements.getFields(); Map<Integer, List<Integer>> returnedSamples = selectVariantElements.getSamples(); Collection<Integer> studyIds = selectVariantElements.getStudies();
List<Integer> studiesIds = selectVariantElements.getStudies();
if (!isValidParam(query, INCLUDE_STUDY)) { List<String> includeStudy = new ArrayList<>(); for (Integer studyId : selectVariantElements.getStudies()) { includeStudy.add(selectVariantElements.getStudyConfigurations().get(studyId).getStudyName());
for (Integer studyId : selectElements.getStudies()) { scan.addColumn(family, VariantPhoenixHelper.getStudyColumn(studyId).bytes()); scan.addColumn(family, VariantPhoenixHelper.getFillMissingColumn(studyId).bytes());
VariantQueryUtils.parseSelectElements(query, options, studyConfigurationManager); if (selectVariantElements.getStudies().size() != 1) { return null; Integer studyId = selectVariantElements.getStudies().get(0); StudyConfiguration studyConfiguration = selectVariantElements.getStudyConfigurations().get(studyId); Set<String> samples = new HashSet<>();
private DocumentToVariantConverter getDocumentToVariantConverter(Query query, SelectVariantElements selectVariantElements) { List<Integer> returnedStudies = selectVariantElements.getStudies(); DocumentToSamplesConverter samplesConverter; samplesConverter = new DocumentToSamplesConverter(studyConfigurationManager);
public VariantMetadata makeVariantMetadata(Query query, QueryOptions queryOptions) throws StorageEngineException { VariantQueryUtils.SelectVariantElements selectElements = VariantQueryUtils.parseSelectElements(query, queryOptions, scm); Map<Integer, List<Integer>> returnedSamples = selectElements.getSamples(); Map<Integer, List<Integer>> returnedFiles = selectElements.getFiles(); ProjectMetadata projectMetadata = scm.getProjectMetadata().first(); List<StudyConfiguration> studyConfigurations = new ArrayList<>(selectElements.getStudies().size()); for (Integer studyId : selectElements.getStudies()) { studyConfigurations.add(scm.getStudyConfiguration(studyId, QueryOptions.empty()).first()); } return makeVariantMetadata(studyConfigurations, projectMetadata, returnedSamples, returnedFiles, queryOptions); }