BGZFCodec{T, IO} <: Codec

Codec used to compress or decompress data from the input IO source of type IO. T must be LibDeflate.Compressor or LibDeflate.Decompressor.

BGZFCompressorStream(io::IO; threads=nthreads(), compresslevel=6)

Create a TranscodingStream which block-gzip compresses data from the underlying io with the given compresslevel. The stream will compress up to threads block concurrently.

BGZFDecompressorStream(io::IO; threads=nthreads())

Create a TranscodingStream which decompresses block-gzipped data from the underlying io. The stream will compress up to threads block concurrently.

BGZFError(message::String)

BGZF de/compressor errored with message when processing data."

VirtualOffset(block_offset::Integer, inblock_offset::Integer)

Create a virtual file offset from block_offset and inblock_offset. Get the two offsets with offsets(v).

block_offset is an offset pointing to the beginning position of a BGZF block in a BGZF file and inblock_offset is an offset pointing to the begining position of a binary data within a uncompressed BGZF block. These values are zero-based and their valid ranges are [0, 1 << 48) and [0, 1 << 16), respectively.

VirtualOffset(stream::BGZFDecompressorStream)

Obtain the VirtualOffset of the curret position of stream. If stream's input stream is seekable, seeking to this offset will leave the stream in an equivalent state to its current state. A BGZFDecompressorStream only tracks the offset of the 16 previous blocks. If more than 16 blocks are stored in stream's output buffer, this operation will fail.

seek(stream::BGZFDecompressorStream, v::VirtualOffset)

Seek stream to the given VirtualOffsetv. v must be a valid virtual offset for the given stream, i.e. its coffset must be the offset of a valid BGZF block, and its uoffset must be an integer in [0, block_len]. Furthermore, stream's underlying stream must be seekable.

seekstart(stream::BGZFDecompressorStream)

Seek the stream's input stream to its beginning, and resets the stream.

Return data already prepared in the current block

Get the offset for the soon-to-be indexed block based on the previous block

Get the offset for the soon-to-be indexed block based on the previous block

gzi(io::IO)

Construct a Vector{UInt8} with the GZI of a BGZF file of an IO representing a BGZF file. GZI files contain offsets for each block and its decompressed payload in a BGZF file. A GZI file is approximately 1/4000th the size of the decompressed data in a BGZF file.

Examples

julia open(gzi, "/my/bgzip/file.bgz")
102744-element Array{UInt8,1}:
 0x15
 0x19
 0x00
 0x00
 0x00
[ ... ]

Switches the code to the next block to process, given whether the input stream is eof. Returns block index, or nothing if there are no more blocks to process

Get relevant positions of the compressed block in data

Prepare the block to be de/compressed. Unlike the queue operation, the loading function may mutate the codec, and is therefore not threadsafe.

Add the current block's offsets and lengths to the codex offset vector

Process the block in another thread

Get number of remaning bytes in the codec's buffer before a new block can be indexed