public static List<String> getIncludeSamplesList(Query query, Set<VariantField> fields) { List<String> samples; if (!fields.contains(VariantField.STUDIES_SAMPLES_DATA)) { samples = Collections.emptyList(); } else { //Remove the studyName, if any samples = getIncludeSamplesList(query); } return samples; }
public static List<String> getIncludeSamplesList(Query query, QueryOptions options) { return getIncludeSamplesList(query, VariantField.getIncludeFields(options)); }
public static boolean isIncludeSamplesDefined(Query query, Set<VariantField> fields) { if (getIncludeSamplesList(query, fields) != null) { return true; } return isValidParam(query, FILE, true) || isValidParam(query, INCLUDE_FILE, true); }
List<String> includeSamplesList = getIncludeSamplesList(query, options); LinkedHashSet<String> includeSamplesSet = includeSamplesList != null ? new LinkedHashSet<>(includeSamplesList) : null; boolean includeAllSamples = query.getString(VariantQueryParam.INCLUDE_SAMPLE.key()).equals(ALL);
Query query, Collection<Integer> studyIds, Set<VariantField> fields, Function<Integer, StudyConfiguration> studyProvider) { List<String> includeSamplesList = getIncludeSamplesList(query); List<String> includeFilesList = getIncludeFilesList(query, fields); boolean returnAllFiles = ALL.equals(query.getString(INCLUDE_FILE.key()));
List<String> incSamples = VariantQueryUtils.getIncludeSamplesList(query, queryOptions); if (incSamples != null && incSamples.size() == 0) {