@SuppressWarnings("SameParameterValue") private static Container readContainer(final int major, final InputStream inputStream, final int fromSlice, int howManySlices) throws IOException { final Container container = readContainerHeader(major, inputStream); if (container.isEOF()) { return container; } container.header = CompressionHeader.read(major, inputStream); howManySlices = Math.min(container.landmarks.length, howManySlices); if (fromSlice > 0) //noinspection ResultOfMethodCallIgnored inputStream.skip(container.landmarks[fromSlice]); final List<Slice> slices = new ArrayList<Slice>(); for (int sliceCount = fromSlice; sliceCount < howManySlices - fromSlice; sliceCount++) { final Slice slice = new Slice(); SliceIO.read(major, slice, inputStream); slice.index = sliceCount; slices.add(slice); } container.slices = slices.toArray(new Slice[slices.size()]); calculateSliceOffsetsAndSizes(container); log.debug("READ CONTAINER: " + container.toString()); return container; }
@SuppressWarnings("SameParameterValue") private static Container readContainer(final int major, final InputStream inputStream, final int fromSlice, int howManySlices) { final Container container = readContainerHeader(major, inputStream); if (container.isEOF()) { return container; } container.header = CompressionHeader.read(major, inputStream); howManySlices = Math.min(container.landmarks.length, howManySlices); try { if (fromSlice > 0) //noinspection ResultOfMethodCallIgnored inputStream.skip(container.landmarks[fromSlice]); } catch (final IOException e) { throw new RuntimeIOException(e); } final List<Slice> slices = new ArrayList<Slice>(); for (int sliceCount = fromSlice; sliceCount < howManySlices - fromSlice; sliceCount++) { final Slice slice = new Slice(); SliceIO.read(major, slice, inputStream); slice.index = sliceCount; slices.add(slice); } container.slices = slices.toArray(new Slice[slices.size()]); calculateSliceOffsetsAndSizes(container); log.debug("READ CONTAINER: " + container.toString()); return container; }
log.debug("CONTAINER WRITTEN: " + container.toString());
private boolean nextContainer() throws IOException { long offset = is.getCount(); Container c = ContainerIO.readContainer(cramHeader.getVersion(), is); if (c.isEOF()) return false; c.offset = offset; indexer.processContainer(c, ValidationStringency.DEFAULT_STRINGENCY); log.info("INDEXED: " + c.toString()); return true; }
private boolean nextContainer() throws IOException, IllegalArgumentException, IllegalAccessException { long offset = is.getCount(); Container c = ContainerIO.readContainer(cramHeader.getVersion(), is); if (c.isEOF()) return false; c.offset = offset; index.addContainer(c); log.info("INDEXED: " + c.toString()); return true; }
@Override public OrderedByteArray get() { OrderedByteArray cb = new OrderedByteArray(); Container containerHeader; try { containerHeader = ContainerIO.readContainerHeader(cramHeader.getVersion().major, is); log.debug("Read container: " + containerHeader.toString()); if (containerHeader.isEOF()) { log.info("EOF container"); return null; } ByteArrayOutputStream baos = new ByteArrayOutputStream(containerHeader.containerByteSize + 1024 * 10); ContainerIO.writeContainerHeader(cramHeader.getVersion().major, containerHeader, baos); byte[] blocks = InputStreamUtils.readFully(is, containerHeader.containerByteSize); baos.write(blocks); cb.bytes = baos.toByteArray(); cb.order = order++; return cb; } catch (IOException e) { throw new RuntimeIOException(e); } } }
length += byteArrayOutputStream.size(); log.debug("CONTAINER WRITTEN: " + container.toString());