Fix deadlocks in bgzf reading

src/bgzf.h

@@ -66,7 +66,18 @@ class BgzfMtReader {
     }
 
     ~BgzfMtReader() {
-        mStop = true;
+        // Publish mStop while holding every CV's mutex before notifying. mStop is a
+        // wait predicate for all three CVs; a thread that has evaluated its predicate
+        // as false but not yet parked still holds that mutex, so taking all three here
+        // serializes the stop+notify against that gap. Storing mStop outside the locks
+        // (as before) lets notify_all() slip into that window and be missed, leaving a
+        // worker parked forever and the join() below hung — an intermittent deadlock.
+        {
+            std::lock_guard<std::mutex> l1(mProduceMtx);
+            std::lock_guard<std::mutex> l2(mDecompMtx);
+            std::lock_guard<std::mutex> l3(mConsumeMtx);
+            mStop = true;
+        }
         mDecompCv.notify_all();
         mProduceCv.notify_all();
         mConsumeCv.notify_all();
@@ -95,7 +106,12 @@ class BgzfMtReader {
             mConsumeOffset += tocopy;
 
             if (mConsumeOffset >= s.decompLen) {
-                s.state.store(FREE, std::memory_order_release);
+                // Publish FREE under mProduceMtx so readerLoop, which waits on
+                // mProduceCv for this slot to free up, cannot miss the wakeup.
+                {
+                    std::lock_guard<std::mutex> lk(mProduceMtx);
+                    s.state.store(FREE, std::memory_order_release);
+                }
                 mConsumeOffset = 0;
                 mConsumeIdx++;
                 mProduceCv.notify_one();
@@ -134,8 +150,13 @@ class BgzfMtReader {
             }
 
             s.compLen = bsize;
-            s.state.store(COMPRESSED, std::memory_order_release);
-            mProduceIdx++;
+            // Publish the COMPRESSED slot (state + mProduceIdx, which claimSlot scans)
+            // under mDecompMtx so a decompWorker parked on mDecompCv cannot miss it.
+            {
+                std::lock_guard<std::mutex> lk(mDecompMtx);
+                s.state.store(COMPRESSED, std::memory_order_release);
+                mProduceIdx++;
+            }
             mDecompCv.notify_all();
         }
     }
@@ -162,7 +183,12 @@ class BgzfMtReader {
             int ret = isal_inflate_stateless(&ist);
             target->decompLen = (ret == ISAL_DECOMP_OK) ? (int)ist.total_out : 0;
 
-            target->state.store(READY, std::memory_order_release);
+            // Publish READY under mConsumeMtx so the consumer parked in read() on
+            // mConsumeCv cannot miss the wakeup for this slot.
+            {
+                std::lock_guard<std::mutex> lk(mConsumeMtx);
+                target->state.store(READY, std::memory_order_release);
+            }
             mConsumeCv.notify_one();
         }
     }
@@ -183,7 +209,14 @@ class BgzfMtReader {
     }
 
     void markDone(Slot& s) {
-        s.state.store(DONE, std::memory_order_release);
+        // Publish DONE under mConsumeMtx before notifying: the consumer in read()
+        // waits on mConsumeCv for READY/DONE, and at EOF this is the terminal
+        // notification (no further producer follows), so a lost wakeup here would
+        // strand the reader thread in read() forever.
+        {
+            std::lock_guard<std::mutex> lk(mConsumeMtx);
+            s.state.store(DONE, std::memory_order_release);
+        }
         mConsumeCv.notify_all();
         mDecompCv.notify_all();
     }