fix some possible memory leaks

#392

Author: sfchen

Diff for: src/peprocessor.cpp

@@ -58,6 +58,12 @@ PairEndProcessor::~PairEndProcessor() {
         delete mRightReadPool;
         mRightReadPool = NULL;
     }
+    for(int t=0; t<mOptions->thread; t++){
+        delete mLeftInputLists[t];
+        delete mRightInputLists[t];
+    }
+    delete[] mLeftInputLists;
+    delete[] mRightInputLists;
 }
 
 void PairEndProcessor::initOutput() {

Diff for: src/read.cpp

@@ -56,7 +56,6 @@ Read* Read::reverseComplement(){
 	string seq = Sequence::reverseComplement(mSeq);
 	string qual;
 	qual.assign(mQuality->rbegin(), mQuality->rend());
-	string* strand=new string("+");
 	return new Read(mName->c_str(), seq.c_str(), "+", qual.c_str());
 }
 

Diff for: src/readpool.cpp

@@ -31,8 +31,15 @@ bool ReadPool::input(int tid, Read* data) {
 }
 
 void ReadPool::cleanup() {
-    //TODO: delete unused pooled Reads.
-    //But since this is only called when the program exits, the one-by-one deletion can be skipped to save time
+    for(int t=0; t<mOptions->thread; t++) {
+        while(mBufferLists[t]->canBeConsumed()) {
+            Read* r = mBufferLists[t]->consume();
+            mConsumed++;
+            delete r;
+        }
+        delete mBufferLists[t];
+    }
+    delete[] mBufferLists;
 }
 
 void ReadPool::initBufferLists() {

Diff for: src/seprocessor.cpp

@@ -41,6 +41,10 @@ SingleEndProcessor::~SingleEndProcessor() {
         delete mReadPool;
         mReadPool = NULL;
     }
+    for(int t=0; t<mOptions->thread; t++){
+        delete mInputLists[t];
+    }
+    delete[] mInputLists;
 }
 
 void SingleEndProcessor::initOutput() {

Diff for: src/singleproducersingleconsumerlist.h

@@ -83,6 +83,8 @@ class SingleProducerSingleConsumerList {
             blocks[recycled & blocksRingBufferSizeMask] = NULL;
             recycled++;
         }
+        delete[] blocks;
+        blocks = NULL;
     }
     inline size_t size() {
         return produced -  consumed;

Diff for: src/threadconfig.cpp

@@ -41,6 +41,26 @@ void ThreadConfig::cleanup() {
         delete mRightInputList;
         mRightInputList = NULL;
     }
+    if(mPreStats1) {
+        delete mPreStats1;
+        mPreStats1 = NULL;
+    }
+    if(mPostStats1) {
+        delete mPostStats1;
+        mPostStats1 = NULL;
+    }
+    if(mPreStats2) {
+        delete mPreStats2;
+        mPreStats2 = NULL;
+    }
+    if(mPostStats2) {
+        delete mPostStats2;
+        mPostStats2 = NULL;
+    }
+    if(mFilterResult) {
+        delete mFilterResult;
+        mFilterResult = NULL;
+    }
 }
 
 

Diff for: src/writerthread.cpp

@@ -55,6 +55,11 @@ void WriterThread::input(int tid, string* data) {
 
 void WriterThread::cleanup() {
     deleteWriter();
+    for(int t=0; t<mOptions->thread; t++) {
+        delete mBufferLists[t];
+    }
+    delete[] mBufferLists;
+    mBufferLists = NULL;
 }
 
 void WriterThread::deleteWriter() {