Merge pull request #3406 from eseiler/fix/datarace

fix(bgzf): datarace

Author: eseiler

include/seqan3/contrib/stream/bgzf_istream.hpp

@@ -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() :
@@ -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)
         {}
     };
@@ -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);
                 }
@@ -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();
@@ -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();
                                     });
             }
 
@@ -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();
                                             });
                     }