Merge pull request #29 from CiaranOMara/hotfix/ensure_buffered_data

Correct `ensure_buffered_data`

.github/workflows/UnitTests.yml

@@ -40,6 +40,8 @@ jobs:
         uses: julia-actions/julia-buildpkg@v1
       - name: Run Tests
         uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: "2"
       - name: Create CodeCov
         uses: julia-actions/julia-processcoverage@v1
       - name: Upload CodeCov

Project.toml

@@ -1,7 +1,7 @@
 name = "BGZFStreams"
 uuid = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
 authors = ["Sabrina Jaye Ward <sabrinajward@protonmail.com>", "Kenta Sato <bicycle1885@gmail.com>", "Daniel C. Jones <dcjones@cs.washington.edu>", "Tony Kelman <tony@kelman.net>", "Elliot Saba <staticfloat@gmail.com>", "Christian Theil Have"]
-version = "0.3.1"
+version = "0.3.2"
 
 [deps]
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"

src/bgzfstream.jl

@@ -84,13 +84,20 @@ mutable struct BGZFStream{T<:IO} <: IO
     # current block index
     block_index::Int
 
+    # index of the last block loaded
+    last_block_index::Int
+
     # whether stream is open
     isopen::Bool
 
     # callback function called when closing the stream
     onclose::Function
 end
 
+function BGZFStream(io, mode, blocks, block_index, isopen, onclose) # This method maintains compatibility after the inclusion of the `last_block_index` field to `BGZFStream`.
+    return BGZFStream(io, mode, blocks, block_index, 0, isopen, onclose)
+end
+
 # BGZF blocks are no larger than 64 KiB before and after compression.
 const BGZF_MAX_BLOCK_SIZE = UInt(64 * 1024)
 
@@ -315,16 +322,19 @@ end
 @inline function ensure_buffered_data(stream)
     #@assert stream.mode == READ_MODE
     @label doit
-    while stream.block_index ≤ lastindex(stream.blocks)
+    while stream.block_index < stream.last_block_index
         @inbounds block = stream.blocks[stream.block_index]
-        if 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 stream.block_index == stream.last_block_index
+        @inbounds block = stream.blocks[stream.block_index]
+        if block.position ≤ block.size
+            return stream.block_index
+        end
+    end
     if !eof(stream.io)
         read_blocks!(stream)
         @goto doit
@@ -364,6 +374,7 @@ function read_blocks!(stream)
     end
     while n_blocks < length(stream.blocks) && !eof(stream.io)
         block = stream.blocks[n_blocks += 1]
+        stream.last_block_index = n_blocks
         if has_position
             block.block_offset = position(stream.io)
         end

test/runtests.jl

@@ -1,6 +1,8 @@
 using BGZFStreams
 using Test
 
+@info "Environment" Threads.nthreads()
+
 @testset "VirtualOffset" begin
     voff = VirtualOffset(0, 0)
     @test voff == VirtualOffset(0, 0)
@@ -171,8 +173,8 @@ end
     @test stream.blocks |> length  == 1 # Note: only one block when writing,
     @test stream.blocks[1].size == BGZFStreams.BGZF_SAFE_BLOCK_SIZE
 
-    # Generate n blocks of data.
-    data = rand(0x00:0xf0, (n*BGZFStreams.BGZF_SAFE_BLOCK_SIZE) )
+    # Generate n+1 blocks of data.
+    data = rand(0x00:0xf0, ((n+1)*BGZFStreams.BGZF_SAFE_BLOCK_SIZE) )
 
     write_offsets = BGZFStreams.VirtualOffset[]