diff --git a/.gitignore b/.gitignore
index 16e86f25d..dcc44daa4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,5 @@
 tests
 .deps
 hmm_Mohammad
+pairhmm-template-main
+*.swp
diff --git a/Makefile b/Makefile
index df5dbc463..f858a7241 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-#OMPCFLAGS=-fopenmp
+OMPCFLAGS=-fopenmp
 #OMPLDFLAGS=-lgomp
 
 #CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q            -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
@@ -7,7 +7,7 @@
 JAVA_ROOT=/opt/jdk1.7.0_25/
 JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JAVA_ROOT}/include -I${JAVA_ROOT}/include/linux
 
-CFLAGS=-g -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas -xAVX
+CFLAGS=-O3 -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas -xAVX
 
 CXXFLAGS=$(CFLAGS)
 CC=icc
@@ -16,11 +16,12 @@ CXX=icc
 LDFLAGS=-lm $(OMPLDFLAGS)
 
 #BIN:=pairhmm-1-base #pairhmm-2-omp pairhmm-3-hybrid-float-double pairhmm-4-hybrid-diagonal pairhmm-5-hybrid-diagonal-homogeneus pairhmm-6-onlythreediags pairhmm-7-presse pairhmm-8-sse #pairhmm-dev
-BIN:=libJNILoglessPairHMM.so #pairhmm-2-omp pairhmm-3-hybrid-float-double pairhmm-4-hybrid-diagonal pairhmm-5-hybrid-diagonal-homogeneus pairhmm-6-onlythreediags pairhmm-7-presse pairhmm-8-sse #pairhmm-dev
+BIN:=libJNILoglessPairHMM.so pairhmm-template-main
 
 #SOURCES=pairhmm-1-base.cc input.cc 
-SOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc hmm_mask.cc
-OBJECTS=$(SOURCES:.cc=.o)
+LIBSOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc hmm_mask.cc
+SOURCES=$(LIBSOURCES) pairhmm-template-main.cc
+LIBOBJECTS=$(LIBSOURCES:.cc=.o)
 DEPDIR=.deps
 DF=$(DEPDIR)/$(*).d
 
@@ -28,11 +29,11 @@ all: $(BIN)
 
 -include $(addprefix $(DEPDIR)/,$(SOURCES:.cc=.d))
 
-pairhmm-1-base:	pairhmm-1-base.o input.o
-	$(CXX) -o $@ $^ $(LDFLAGS)
+pairhmm-template-main:	pairhmm-template-main.o hmm_mask.o
+	$(CXX) -fopenmp -o $@ $^ $(LDFLAGS)
 
-libJNILoglessPairHMM.so: $(OBJECTS) 
-	$(CXX) -shared -o libJNILoglessPairHMM.so $(OBJECTS) 
+libJNILoglessPairHMM.so: $(LIBOBJECTS) 
+	$(CXX) -shared -o $@ $(LIBOBJECTS) 
 
 %.o: %.cc
 	@mkdir -p $(DEPDIR)
diff --git a/define-double.h b/define-double.h
index b2de7520a..5d31741d6 100644
--- a/define-double.h
+++ b/define-double.h
@@ -23,6 +23,7 @@
         #undef VEC_ADD
 	#undef VEC_SUB
         #undef VEC_MUL
+        #undef VEC_DIV
         #undef VEC_BLEND
         #undef VEC_BLENDV
 	#undef VEC_CAST_256_128
@@ -82,6 +83,9 @@
 #define VEC_MUL(__v1, __v2)                     \
   _mm256_mul_pd(__v1, __v2)
 
+#define VEC_DIV(__v1, __v2)                     \
+  _mm256_div_pd(__v1, __v2)
+
 #define VEC_BLEND(__v1, __v2, __mask)           \
   _mm256_blend_pd(__v1, __v2, __mask)
 
diff --git a/define-float.h b/define-float.h
index 4cba9a179..0e2822b2d 100644
--- a/define-float.h
+++ b/define-float.h
@@ -23,6 +23,7 @@
 	#undef VEC_ADD(__v1, __v2)
         #undef VEC_SUB(__v1, __v2)
 	#undef VEC_MUL(__v1, __v2)
+	#undef VEC_DIV(__v1, __v2)
 	#undef VEC_BLEND(__v1, __v2, __mask)
 	#undef VEC_BLENDV(__v1, __v2, __maskV)
         #undef VEC_CAST_256_128(__v1)
@@ -83,6 +84,9 @@
 #define VEC_MUL(__v1, __v2)                     \
   _mm256_mul_ps(__v1, __v2)
 
+#define VEC_DIV(__v1, __v2)                     \
+  _mm256_div_ps(__v1, __v2)
+
 #define VEC_BLEND(__v1, __v2, __mask)           \
   _mm256_blend_ps(__v1, __v2, __mask)
 
diff --git a/hmm_mask.cc b/hmm_mask.cc
index aace7acf2..f128a39d9 100644
--- a/hmm_mask.cc
+++ b/hmm_mask.cc
@@ -438,7 +438,7 @@ void test_mask_computations (testcase& tc, int tcID, bool printDebug=false) {
   //cout << "Finished validating entry " << endl ;
 }
 
-
+#ifdef HMM_MASK_MAIN
 int main () {
 
   #define BATCH_SIZE 10000
@@ -482,3 +482,4 @@ int main () {
 
   return 0 ;
 }
+#endif
diff --git a/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc b/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
index 80065b8c9..29668a306 100644
--- a/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
+++ b/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
@@ -15,6 +15,10 @@
 #include <immintrin.h>
 #include <emmintrin.h>
 #include <omp.h>
+using namespace std;
+//#define DEBUG3 1
+#define DEBUG 1
+
 
 #include "template.h"
 
@@ -22,7 +26,6 @@
 #include "shift_template.c"
 #include "pairhmm-template-kernel.cc"
 
-using namespace std;
 
 
 #define MM 0
@@ -32,22 +35,17 @@ using namespace std;
 #define MY 4
 #define YY 5
 
-//#define DEBUG3 1
-#define DEBUG 1
-
-template<class T>
-string to_string(T obj)
+class LoadTimeInitializer
 {
-  stringstream ss;
-  string ret_string;
-  ss.clear();
-  ss << std::scientific << obj;
-  ss >> ret_string;
-  ss.clear();
-  return ret_string;
-}
+  public:
+    LoadTimeInitializer()		//will be called when library is loaded
+    {
+      ConvertChar::init();
+    }
+};
+LoadTimeInitializer g_load_time_initializer;
 
-void debug_dump(string filename, string s, bool to_append, bool add_newline=true)
+void debug_dump(string filename, string s, bool to_append, bool add_newline)
 {
   ofstream fptr;
   fptr.open(filename.c_str(), to_append ? ofstream::app : ofstream::out);
diff --git a/pairhmm-template-kernel.cc b/pairhmm-template-kernel.cc
index dd71373b0..24bcf7d1a 100644
--- a/pairhmm-template-kernel.cc
+++ b/pairhmm-template-kernel.cc
@@ -157,8 +157,18 @@ template<class NUMBER> void GEN_INTRINSIC(initializeVectors, PRECISION)(int ROWS
                 *(ptr_p_GAPM+r-1) = ctx._(1.0) - ctx.ph2pr[_c];
                 *(ptr_p_MX+r-1) = ctx.ph2pr[_i];
                 *(ptr_p_XX+r-1) = ctx.ph2pr[_c];
-                *(ptr_p_MY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d];
-                *(ptr_p_YY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c];
+                *(ptr_p_MY+r-1) = ctx.ph2pr[_d];
+                *(ptr_p_YY+r-1) = ctx.ph2pr[_c];
+#ifdef DEBUG3
+		debug_dump("transitions_jni.txt",to_string(*(ptr_p_MM+r-1)  ),true);
+		debug_dump("transitions_jni.txt",to_string(*(ptr_p_GAPM+r-1)),true);
+		debug_dump("transitions_jni.txt",to_string(*(ptr_p_MX+r-1)  ),true);
+		debug_dump("transitions_jni.txt",to_string(*(ptr_p_XX+r-1)  ),true);
+		debug_dump("transitions_jni.txt",to_string(*(ptr_p_MY+r-1)  ),true);
+		debug_dump("transitions_jni.txt",to_string(*(ptr_p_YY+r-1)  ),true);
+#endif
+		//*(ptr_p_MY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d];
+		//*(ptr_p_YY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c];
         }
 
         NUMBER *ptr_distm1D = (NUMBER *)distm1D;
@@ -166,6 +176,9 @@ template<class NUMBER> void GEN_INTRINSIC(initializeVectors, PRECISION)(int ROWS
         {
                 int _q = tc->q[r-1] & 127;
                 ptr_distm1D[r-1] = ctx.ph2pr[_q];
+#ifdef DEBUG3
+		debug_dump("priors_jni.txt",to_string(ptr_distm1D[r-1]),true);
+#endif
         }
 }
 
@@ -187,13 +200,18 @@ template<class NUMBER> inline void GEN_INTRINSIC(stripINITIALIZATION, PRECISION)
 	NUMBER zero = ctx._(0.0);        
 	NUMBER init_Y = ctx.INITIAL_CONSTANT / (tc->haplen);
 	UNION_TYPE packed1;  packed1.d = VEC_SET1_VAL(1.0);
+#define TRISTATE_CORRECTION_FACTOR 3.0
+	UNION_TYPE packed3;  packed3.d = VEC_SET1_VAL(TRISTATE_CORRECTION_FACTOR);
 	
         /* compare rs and N */                                           
         //rs = VEC_LDPOPCVT_CHAR((tc->irs+i*AVX_LENGTH));        
         //rsN.d = VEC_CMP_EQ(N_packed256, rs);                             
                                                                          
         distm = distm1D[i];                                    
-        _1_distm = VEC_SUB(packed1.d, distm);                  
+        _1_distm = VEC_SUB(packed1.d, distm);
+#ifndef DO_NOT_USE_TRISTATE_CORRECTION
+	distm = VEC_DIV(distm, packed3.d); 
+#endif
                                                                          
         /* initialize M_t_2, M_t_1, X_t_2, X_t_1, Y_t_2, Y_t_1 */        
         M_t_2.d = VEC_SET1_VAL(zero);                                    
diff --git a/pairhmm-template-main.cc b/pairhmm-template-main.cc
index f20755b6b..87d50eb5b 100644
--- a/pairhmm-template-main.cc
+++ b/pairhmm-template-main.cc
@@ -16,7 +16,7 @@
 #define BATCH_SIZE  10000
 //#define RUN_HYBRID
 
-uint8_t ConvertChar::conversionTable[255] ;
+//uint8_t ConvertChar::conversionTable[255] ;
 int thread_level_parallelism_enabled = false ;
 
 double getCurrClk() {
diff --git a/template.h b/template.h
index ee8036a11..4c8a4b5e3 100644
--- a/template.h
+++ b/template.h
@@ -13,6 +13,7 @@
 #include <immintrin.h>
 
 #include <ctype.h>
+#include <string>
 
 #define MROWS  500
 #define MCOLS  1000
@@ -132,6 +133,20 @@ typedef struct
         int *irs;
 } testcase;
 
+
+template<class T>
+std::string to_string(T obj)
+{
+  stringstream ss;
+  string ret_string;
+  ss.clear();
+  ss << std::scientific << obj;
+  ss >> ret_string;
+  ss.clear();
+  return ret_string;
+}
+void debug_dump(std::string filename, std::string s, bool to_append, bool add_newline=true);
+
 int normalize(char c);