Correct ensure_buffered_data

The `read_blocks!` function does not necessarily fill/overwrite blocks till `lastindex(stream.blocks)`, we need to ensure `stream.block_index` does not increment past the index of the last loaded block.

src/bgzfstream.jl

@@ -84,6 +84,9 @@ 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
 
@@ -130,7 +133,7 @@ function BGZFStream(io::IO, mode::AbstractString="r")
         # Write mode is not (yet?) multi-threaded.
         blocks = [Block(mode′)]
     end
-    return BGZFStream(io, mode′, blocks, 1, true, io -> close(io))
+    return BGZFStream(io, mode′, blocks, 1, 0, true, io -> close(io))
 end
 
 function BGZFStream(filename::AbstractString, mode::AbstractString = "r")
@@ -315,16 +318,19 @@ 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 +370,7 @@ 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

@@ -174,7 +174,7 @@ end
     @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) )
+    data = rand(0x00:0xf0, ((n+1)*BGZFStreams.BGZF_SAFE_BLOCK_SIZE) )
 
     write_offsets = BGZFStreams.VirtualOffset[]