remove worker mutex

hisat_3n_table.cpp

@@ -289,7 +289,6 @@ int hisat_3n_table()
         // then load a new reference chromosome.
         auto old = positions->chromosome;
         if (samChromosome != (old ? *old : "")) {
-            positions->appendingFinished();
             positions->moveAllToOutput();
             positions->loadNewChromosome(std::move(samChromosome));
             reloadPos = loadingBlockSize;
@@ -297,7 +296,6 @@ int hisat_3n_table()
         }
         // if the samPos is larger than reloadPos, load 1 loadingBlockSize bp in from reference.
         while (samPos > reloadPos) {
-            positions->appendingFinished();
             positions->moveBlockToOutput();
             positions->loadMore();
             reloadPos += loadingBlockSize;
@@ -319,8 +317,6 @@ int hisat_3n_table()
         workers[i].join();
     }
 
-    // make sure all workers finished their appending work.
-    positions->appendingFinished();
     // move all position to outputPool
     positions->moveAllToOutput();
     // wait until outputPool is empty

position_3n_table.h

@@ -199,7 +199,6 @@ public:
     mutex mutex_;
     long long int refCoveredPosition; // this is the last position in reference chromosome we loaded in refPositions.
     ifstream refFile;
-    vector<mutex*> workerLock; // one lock for one worker thread.
     int nThreads = 1;
     ChromosomeFilePositions chromosomePos; // store the chromosome name and it's streamPos. To quickly find new chromosome in file.
     bool addedChrName = false;
@@ -209,23 +208,11 @@ public:
         nThreads = inputNThreads;
         addedChrName = inputAddedChrName;
         removedChrName = inputRemovedChrName;
-        for (int i = 0; i < nThreads; i++) {
-            workerLock.push_back(new mutex);
-        }
         refFile.open(inputRefFileName, ios_base::in);
         LoadChromosomeNamesPos();
     }
 
-    ~Positions() {
+    ~Positions() = default;
-        for (int i = 0; i < workerLock.size(); i++) {
-            delete workerLock[i];
-        }
-        Position* pos;
-        // freePositionPool.close();
-        // while(freePositionPool.recv(pos)) {
-        //     delete pos;
-        // }
-    }
 
     /**
      * given the target Position output the corresponding position index in refPositions.
@@ -309,16 +296,6 @@ public:
         location += line.size();
     }
 
-    /**
-     * if we can go through all the workerLock, that means no worker is appending new position.
-     */
-    void appendingFinished() {
-        for (int i = 0; i < nThreads; i++) {
-            workerLock[i]->lock();
-            workerLock[i]->unlock();
-        }
-    }
-
     /**
      * the output function for output thread.
      */
@@ -346,10 +323,22 @@ public:
         tableFile.close();
     }
 
+
+    /**
+     * if we can go through all the workerLock, that means no worker is appending new position.
+     */
+    void appendingFinished() {
+        while (!linePool.empty()) {
+            this_thread::sleep_for (std::chrono::microseconds(1));
+        }
+    }
+
+
     /**
      * move the position which position smaller than refCoveredPosition - loadingBlockSize, output it.
      */
     void moveBlockToOutput() {
+        appendingFinished();
         if (refPositions.empty()) {
             return;
         }
@@ -372,6 +361,7 @@ public:
      * move all the refPosition into output pool.
      */
     void moveAllToOutput() {
+        appendingFinished();
         if (refPositions.empty()) {
             return;
         }
@@ -496,9 +486,7 @@ public:
         Alignment newAlignment;
 
 
-        while (true) {
+        while (linePool.recv(line)) {
-            std::unique_lock<std::mutex> lk{*workerLock[threadID]};
-            if (!linePool.recv(line)) break;
             while (refPositions.empty()) {
                 this_thread::sleep_for (std::chrono::microseconds(1));
             }