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Merged
eseiler merged 1 commit into from
Mar 11, 2026
+11 −10
Merged

fix(bgzf): datarace #3406

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21 changes: 11 additions & 10 deletions include/seqan3/contrib/stream/bgzf_istream.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ class basic_bgzf_istreambuf : public std::basic_streambuf<Elem, Tr>

std::mutex cs;
std::condition_variable readyEvent;
bool ready;
std::atomic<bool> ready;
bool bgzfEofMarker;

DecompressionJob() :
Expand All @@ -121,7 +121,7 @@ class basic_bgzf_istreambuf : public std::basic_streambuf<Elem, Tr>
size(other.size),
cs(),
readyEvent(),
ready(other.ready),
ready(other.ready.load()),
bgzfEofMarker(other.bgzfEofMarker)
{}
};
Expand Down Expand Up @@ -168,7 +168,7 @@ class basic_bgzf_istreambuf : public std::basic_streambuf<Elem, Tr>
job.readyEvent.wait(lock,
[&job]
{
return job.ready;
return job.ready.load();
});
assert(job.ready == true);
}
Expand Down Expand Up @@ -262,15 +262,16 @@ class basic_bgzf_istreambuf : public std::basic_streambuf<Elem, Tr>
if (!job.ready)
{
// decompress block
job.size = _decompressBlock(&job.buffer[0] + MAX_PUTBACK,
job.buffer.capacity(),
&job.inputBuffer[0],
job.compressedSize,
compressionCtx);
auto decompressed_size = _decompressBlock(&job.buffer[0] + MAX_PUTBACK,
job.buffer.capacity(),
&job.inputBuffer[0],
job.compressedSize,
compressionCtx);

// signal that job is ready
{
std::unique_lock<std::mutex> lock(job.cs);
job.size = decompressed_size;
job.ready = true;
}
job.readyEvent.notify_all();
Expand Down Expand Up @@ -366,7 +367,7 @@ class basic_bgzf_istreambuf : public std::basic_streambuf<Elem, Tr>
job.readyEvent.wait(lock,
[&job]
{
return job.ready;
return job.ready.load();
});
}

Expand Down Expand Up @@ -492,7 +493,7 @@ class basic_bgzf_istreambuf : public std::basic_streambuf<Elem, Tr>
job.readyEvent.wait(lock,
[&job]
{
return job.ready;
return job.ready.load();
});
}

Expand Down
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