How to use

htsjdk.tribble.TribbleException$CorruptedIndexFile

constructor

/**
 * Load in index from the specified stream. Note that the caller is responsible for decompressing the stream if necessary.
 *
 * @param source the stream source (typically the file name)
 * @param inputStream the raw byte stream of the index
 */
public static Index loadIndex(final String source, final InputStream inputStream) {
  // Must be buffered, because getIndexType uses mark and reset
  try (BufferedInputStream bufferedInputStream = new BufferedInputStream(inputStream, Defaults.NON_ZERO_BUFFER_SIZE)) {
    final Class<Index> indexClass = IndexType.getIndexType(bufferedInputStream).getIndexType();
    final Constructor<Index> ctor = indexClass.getConstructor(InputStream.class);
    return ctor.newInstance(bufferedInputStream);
  } catch (final TribbleException ex) {
    throw ex;
  } catch (final InvocationTargetException ex) {
    if (ex.getCause() instanceof EOFException) {
      throw new TribbleException.CorruptedIndexFile("Index file is corrupted", source, ex);
    }
    throw new RuntimeException(ex);
  } catch (final Exception ex) {
    throw new RuntimeException(ex);
  }
}

/**
 * Load in index from the specified stream. Note that the caller is responsible for decompressing the stream if necessary.
 *
 * @param source the stream source (typically the file name)
 * @param inputStream the raw byte stream of the index
 */
public static Index loadIndex(final String source, final InputStream inputStream) {
  // Must be buffered, because getIndexType uses mark and reset
  try (BufferedInputStream bufferedInputStream = new BufferedInputStream(inputStream, Defaults.NON_ZERO_BUFFER_SIZE)) {
    final Class<Index> indexClass = IndexType.getIndexType(bufferedInputStream).getIndexType();
    final Constructor<Index> ctor = indexClass.getConstructor(InputStream.class);
    return ctor.newInstance(bufferedInputStream);
  } catch (final TribbleException ex) {
    throw ex;
  } catch (final InvocationTargetException ex) {
    if (ex.getCause() instanceof EOFException) {
      throw new TribbleException.CorruptedIndexFile("Index file is corrupted", source, ex);
    }
    throw new RuntimeException(ex);
  } catch (final Exception ex) {
    throw new RuntimeException(ex);
  }
}