BGZFStreams issue #22

BGZFStreams_issue22.jl

import Pkg
Pkg.activate(".")
Pkg.add(url="https://github.com/CiaranOMara/BGZFStreams.jl#develop")
using BGZFStreams

# Overwrite
@inline function BGZFStreams.ensure_buffered_data(stream)
    #@assert stream.mode == READ_MODE
    @label doit
    while stream.block_index ≤ lastindex(stream.blocks)
        @inbounds block = stream.blocks[stream.block_index]
        if BGZFStreams.is_eof_block(block.compressed_block) # Note: `read_blocks!` does not necessarily fill/overwrite blocks till `lastindex(stream.blocks)`, we need to stop incrementing `stream.block_index` when an eof block is encountered.
            break
        end
        if block.position ≤ block.size
            return stream.block_index
        end
        stream.block_index += 1
    end
    if !BGZFStreams.eof(stream.io)
        BGZFStreams.read_blocks!(stream)
        @goto doit
    end
    return 0
end

n = 6

i = mod(n, 1:Threads.nthreads())

data = rand(0x00:0xf0, (n-1)*(BGZFStreams.BGZF_MAX_BLOCK_SIZE - 256) + 2)

# Setup buffer
buffer = IOBuffer()
stream = BGZFStream(buffer, "w")
stream.onclose = io -> nothing # HACK: do not close the buffer after the stream is closed
write(stream, data)
close(stream)
seekstart(buffer)

stream = BGZFStream(buffer)

@info "Environment" Threads.nthreads() length(stream.blocks)

offsets = BGZFStreams.VirtualOffset[]

while !eof(stream)
    push!(offsets, virtualoffset(stream))
    read(stream, UInt8)
end

println("Last offsets: ", offsets[end-n-1:end])
println("block_offset: ", map(b->b.block_offset, stream.blocks))
println("position: ", map(b->b.position, stream.blocks))
println("size: ", map(b->b.size, stream.blocks))
println("is_eof_block: ", map(b->BGZFStreams.is_eof_block(b.compressed_block), stream.blocks))

println("virtualoffset(stream): ", virtualoffset(stream))