block

Type Members

1. implicit final class BGZFBlocksToCheck extends AnyVal with IntWrapper

   

2. case class Block(bytes: Array[Byte], start: Long, compressedSize: Int) extends Iterator[Byte] with Product with Serializable

   

   Representation of an uncompressed BGZF block

   Representation of an uncompressed BGZF block

   bytes

   uncompressed bytes

   start

   (compressed) start-position in the file

   compressedSize

   size of compressed block

3. case class Header(size: Int, compressedSize: Int) extends Product with Serializable

   

   BGZF-block header

   BGZF-block header

   size

   size of header, in bytes

   compressedSize

   compressed size of block, parsed from header

4. case class HeaderParseException(idx: Int, actual: Byte, expected: Byte) extends Exception with Product with Serializable

   

   Exception indicating that a bgzf-header magic-byte was not as expected

5. case class HeaderSearchFailedException(path: Path, start: Long, positionsAttempted: Int) extends IOException with Product with Serializable

   

6. trait IntWrapper extends Any

   

7. case class Metadata(start: Long, compressedSize: Int, uncompressedSize: Int) extends Product with Serializable

   

   BGZF-block metadata

8. case class MetadataStream(ch: ByteChannel) extends SimpleIterator[Metadata] with Closeable with Product with Serializable

   

   Iterator over bgzf-block Metadata; useful when loading/decompressing Block payloads is unnecessary.

   Iterator over bgzf-block Metadata; useful when loading/decompressing Block payloads is unnecessary.

   ch

   input stream/channel containing compressed bgzf data

9. case class PosIterator(block: Long, uncompressedSize: Int) extends Iterator[Pos] with Product with Serializable

   

10. case class SeekableStream(compressedBytes: SeekableByteChannel) extends StreamI with Product with Serializable

    

11. case class SeekableUncompressedBytes(blockStream: SeekableStream) extends UncompressedBytesI[SeekableStream] with Product with Serializable

    

    Seekable UncompressedBytesI

12. case class Stream(compressedBytes: ByteChannel) extends StreamI with Product with Serializable

    

13. trait StreamI extends SimpleIterator[Block] with Closeable

    

    Iterator over BGZF Blocks pointed to by a BGZF-compressed InputStream

14. case class UncompressedBytes(blockStream: Stream) extends UncompressedBytesI[Stream] with Product with Serializable

    

    Non-seekable UncompressedBytesI

15. trait UncompressedBytesI[BlockStream <: StreamI] extends SimpleIterator[Byte] with Closeable

    

    Iterator of bgzf-decompressed bytes from a Stream of Blocks.

    Iterator of bgzf-decompressed bytes from a Stream of Blocks.

    BlockStream

    underlying Block-Stream type (basically: seekable or not?).