diff --git a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h b/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h
index e7d9af626..8e45a4d94 100644
--- a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h
+++ b/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h
@@ -49,7 +49,7 @@ class LoadTimeInitializer
     LoadTimeInitializer();		//will be called when library is loaded
     ~LoadTimeInitializer()
     {
-      delete m_buffer;
+      delete[] m_buffer;
     }
     void print_profiling();
     void debug_dump(std::string filename, std::string s, bool to_append, bool add_newline=true);
diff --git a/public/VectorPairHMM/src/main/c++/jnidebug.h b/public/VectorPairHMM/src/main/c++/jnidebug.h
index 7fcab2a51..df2e207b6 100644
--- a/public/VectorPairHMM/src/main/c++/jnidebug.h
+++ b/public/VectorPairHMM/src/main/c++/jnidebug.h
@@ -40,8 +40,8 @@ class DataHolder
 
 #define FREE_MATRIX(X)								\
   for(int i=0;i<m_paddedMaxReadLength;++i)					\
-    delete X[i];								\
-  delete X;
+    delete[] X[i];								\
+  delete[] X;
 
   public:
     DataHolder() { m_is_initialized = false; }
@@ -53,7 +53,7 @@ class DataHolder
 	FREE_MATRIX(m_insertionMatrix); 
 	FREE_MATRIX(m_deletionMatrix); 
 	FREE_MATRIX(m_prior);
-	delete m_transition;
+	delete[] m_transition;
       }
       
       m_readMaxLength = readMaxLength;
diff --git a/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc b/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc
index 5d9a05830..00946d086 100644
--- a/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc
+++ b/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc
@@ -100,7 +100,7 @@ int main()
         aggregateTimeWrite += (getCurrClk() - lastClk) ;
     }
 
-    delete tc;
+    delete[] tc;
     printf("AVX Read Time: %.2f\n", aggregateTimeRead);
     printf("AVX Compute Time: %.2f\n", aggregateTimeCompute);
     printf("AVX Write Time: %.2f\n", aggregateTimeWrite);
diff --git a/public/VectorPairHMM/src/main/c++/utils.cc b/public/VectorPairHMM/src/main/c++/utils.cc
index b3de2c259..6c623e9e5 100644
--- a/public/VectorPairHMM/src/main/c++/utils.cc
+++ b/public/VectorPairHMM/src/main/c++/utils.cc
@@ -461,12 +461,12 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size,
       }
       for(unsigned i=0;i<tc_vector.size();++i)
       {
-	delete tc_vector[i].rs;
-	delete tc_vector[i].hap;
-	delete tc_vector[i].q;
-	delete tc_vector[i].i;
-	delete tc_vector[i].d;
-	delete tc_vector[i].c;
+	delete[] tc_vector[i].rs;
+	delete[] tc_vector[i].hap;
+	delete[] tc_vector[i].q;
+	delete[] tc_vector[i].i;
+	delete[] tc_vector[i].d;
+	delete[] tc_vector[i].c;
       }
       results_vec.clear();
       tc_vector.clear();