Adjust BGZFStreams.ensure_buffered_data

https://github.com/BioJulia/BGZFStreams.jl/issues/22

src/bam/bam.jl

@@ -15,6 +15,26 @@ import BioGenerics: isfilled, header
 
 import GenomicFeatures: eachoverlap
 
+# Overwrite `ensure_buffered_data` to address https://github.com/BioJulia/BGZFStreams.jl/issues/22.
+@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
 
 include("bai.jl")
 include("auxdata.jl")