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README.md

BGZFStreams

Build Status codecov.io

BGZF is a compression format that supports random access using virtual file offsets.

See the SAM/BAM file format specs for the details of BGZF: https://samtools.github.io/hts-specs/SAMv1.pdf.

Synopsis

using BGZFStreams

# The first argument is a filename or an IO object (e.g. IOStream).
stream = BGZFStream("data.bgz")

# BGZFStream is a subtype of IO and works like a usual IO object.
while !eof(stream)
    byte = read(stream, UInt8)
    # do something...
end

# BGZFStream is also seekable with a VirtualOffset.
seek(stream, VirtualOffset(0, 2))

# The current virtual file offset is available.
virtualoffset(stream)

close(stream)

Usage

The BGZFStreams.jl package exports three types and a function to the package user:

  • Types:
    • BGZFStream: an IO stream of the BGZF file format
    • VirtualOffset: data offset in a BGZF file
    • BGZFDataError: an error type thrown when reading a malformed byte stream
  • Function:
    • virtualoffset(stream): returns the current virtual file offset of stream

The BGZFStream type wraps an underlying IO object and transparently inflate (for reading) or deflate (for writing) data. Since it is a subtype of IO, an instance of it behaves like other IO objects, but the seek method takes a virtual offset instead of a normal file offset as its second argument.

The VirtualOffset type represents a 64-bit virtual file offset as described in the specification of the SAM file format. That is, the most significant 48-bit integer of a virtual offset is a byte offset to the BGZF file to the beginning position of a BGZF block and the least significant 16-bit integer is a byte offset to the uncompressed byte(s).

The BGZFDataError type is a subtype of Exception and used to throw an exception when invalid data are read.

The virtualoffset(stream::BGZFStream) returns the current virtual file offset. More specifically, it returns the virtual offset of the next reading byte while reading and the next writing byte while writing.

Parallel Processing

A major bottleneck of processing a BGZF file is the inflation and deflation process. The throughput of reading data is ~100 MiB/s, which is quite slower than that of raw reading from a file. In order to alleviate this problem, this package supports parallelized inflation when reading compressed data. This requires the support of multi-threading introduced in Julia 0.5. The JULIA_NUM_THREADS environmental variable sets the number of threads used for processing.

bash-3.2$ JULIA_NUM_THREADS=2 julia -q
julia> using Base.Threads

julia> nthreads()
2