default VariantDBIterator iterator(Iterator<?> variants, Query query, QueryOptions options) { return iterator(variants, query, options, 100); }
default Stream<Variant> stream() { return StreamSupport.stream(spliterator(), false); }
@Override default void forEach(Consumer<? super Variant> action) { forEach(new Query(), action, new QueryOptions()); }
QueryOptions options = new QueryOptions(QueryOptions.SORT, true) .append(QueryOptions.EXCLUDE, Arrays.asList(VariantField.STUDIES, VariantField.ANNOTATION)); getVariantStorageManager().iterable(getSessionId()).forEach(query, variant -> { if (checkVariant(variant)) { if (region.overlaps(variant.getChromosome(), variant.getStart(), variant.getEnd())) {
default Spliterator<Variant> spliterator(Query query, QueryOptions options) { return Spliterators.spliteratorUnknownSize(iterator(query, options), 0); }
default Stream<Variant> stream(Query query, QueryOptions options) { return StreamSupport.stream(spliterator(query, options), false); }
default void forEach(Query query, Consumer<? super Variant> action, QueryOptions options) { Objects.requireNonNull(action); try (VariantDBIterator variantDBIterator = iterator(query, options)) { while (variantDBIterator.hasNext()) { action.accept(variantDBIterator.next()); } } catch (Exception e) { Throwables.propagate(e); } } }
@Override default VariantDBIterator iterator() { return iterator(new Query(), new QueryOptions()); }
@Override public boolean open() { if (iterator != null) { return true; } QueryOptions iteratorQueryOptions; if (options != null) { //Parse query options iteratorQueryOptions = new QueryOptions(options); } else { iteratorQueryOptions = new QueryOptions(); } iterator = iterable.iterator(query, iteratorQueryOptions); return iterator != null; }
.append(QueryOptions.INCLUDE, Collections.singletonList(VariantField.STUDIES_SAMPLES_DATA)) .append(QueryOptions.LIMIT, maxVariants + 1); try (VariantDBIterator iterator = iterable.iterator(query, options)) { if (!iterator.hasNext()) { return;