diff --git a/PairHMM_JNI/LoadTimeInitializer.cc b/PairHMM_JNI/LoadTimeInitializer.cc
index 946451952..534043371 100644
--- a/PairHMM_JNI/LoadTimeInitializer.cc
+++ b/PairHMM_JNI/LoadTimeInitializer.cc
@@ -27,8 +27,8 @@ LoadTimeInitializer::LoadTimeInitializer()		//will be called when library is loa
 void LoadTimeInitializer::print_profiling()
 {
   double mean_val;
-  cout << "Compute time "<<m_compute_time<<"\n";
-  cout << "Data initialization time "<<m_data_transfer_time<<"\n";
+  cout << "Compute time "<<m_compute_time*1e-9<<"\n";
+  cout << "Data initialization time "<<m_data_transfer_time*1e-9<<"\n";
   cout <<"Invocations : "<<m_num_invocations<<"\n";
   cout << "term\tsum\tsumSq\tmean\tvar\tmax\n";
   mean_val = m_sumNumReads/m_num_invocations;
diff --git a/PairHMM_JNI/LoadTimeInitializer.h b/PairHMM_JNI/LoadTimeInitializer.h
index 8a03ea0f4..cbda057a8 100644
--- a/PairHMM_JNI/LoadTimeInitializer.h
+++ b/PairHMM_JNI/LoadTimeInitializer.h
@@ -26,8 +26,8 @@ class LoadTimeInitializer
     unsigned m_maxNumTestcases;
     unsigned m_num_invocations;
     //timing
-    double m_compute_time;
-    double m_data_transfer_time;
+    uint64_t m_compute_time;
+    uint64_t m_data_transfer_time;
   private:
     std::map<std::string, std::ofstream*> m_filename_to_fptr;
 };
diff --git a/PairHMM_JNI/Makefile b/PairHMM_JNI/Makefile
index 7506279ef..9b461a833 100644
--- a/PairHMM_JNI/Makefile
+++ b/PairHMM_JNI/Makefile
@@ -1,5 +1,5 @@
-OMPCFLAGS=-fopenmp
-OMPLFLAGS=-fopenmp #-openmp-link static
+#OMPCFLAGS=-fopenmp
+#OMPLFLAGS=-fopenmp #-openmp-link static
 
 #CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q            -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
 #CFLAGS=-O2             -W -Wall -march=corei7 -mfpmath=sse -msse4.2 -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
@@ -11,7 +11,7 @@ COMMON_COMPILATION_FLAGS=$(JNI_COMPILATION_FLAGS) -O3 -W -Wall -pedantic $(OMPCF
 CC=icc
 CXX=icc
 
-LDFLAGS=-lm $(OMPLDFLAGS)
+LDFLAGS=-lm -lrt $(OMPLDFLAGS)
 
 BIN=libJNILoglessPairHMM.so pairhmm-template-main checker
 #BIN=checker
@@ -54,7 +54,7 @@ pairhmm-template-main:	pairhmm-template-main.o $(COMMON_OBJECTS)
 	$(CXX) $(OMPLFLAGS) -o $@ $^ $(LDFLAGS)
 
 libJNILoglessPairHMM.so: $(LIBOBJECTS) 
-	$(CXX) $(OMPLFLAGS) -shared -o $@ $(LIBOBJECTS) 
+	$(CXX) $(OMPLFLAGS) -shared -o $@ $(LIBOBJECTS) ${LDFLAGS}
 
 
 $(OBJECTS): %.o: %.cc
diff --git a/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc b/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
index 741957fc0..d575b8271 100644
--- a/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
+++ b/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
@@ -208,7 +208,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
   readBasesArrayVector.clear();
   readBasesArrayVector.resize(numReads);
 #ifdef DO_PROFILING
-  start_time = getCurrClk();
+  start_time = get_time();
 #endif
   for(unsigned i=0;i<numReads;++i)
   {
@@ -266,30 +266,26 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
       jbyte* haplotypeBasesArray = haplotypeBasesArrayVector[j].second;
       tc_array[tc_idx].rslen = (int)readLength;
       tc_array[tc_idx].haplen = (int)haplotypeLength;
-      tc_array[tc_idx].rs = (char*)readBasesArray;
       tc_array[tc_idx].hap = (char*)haplotypeBasesArray;
-      //Can be avoided 
-      for(unsigned k=0;k<readLength;++k)
-      {
-	tc_array[tc_idx].q[k] = (int)readQualsArray[k];
-	tc_array[tc_idx].i[k] = (int)insertionGOPArray[k];
-	tc_array[tc_idx].d[k] = (int)deletionGOPArray[k];
-	tc_array[tc_idx].c[k] = (int)overallGCPArray[k];
-      }
+      tc_array[tc_idx].rs = (char*)readBasesArray;
+      tc_array[tc_idx].q = (char*)readQualsArray;
+      tc_array[tc_idx].i = (char*)insertionGOPArray;
+      tc_array[tc_idx].d = (char*)deletionGOPArray;
+      tc_array[tc_idx].c = (char*)overallGCPArray;
       ++tc_idx;  
     }
-    RELEASE_BYTE_ARRAY_ELEMENTS(overallGCP, overallGCPArray, JNI_RO_RELEASE_MODE);	//order of GET-RELEASE is important
-    RELEASE_BYTE_ARRAY_ELEMENTS(deletionGOP, deletionGOPArray, JNI_RO_RELEASE_MODE);
-    RELEASE_BYTE_ARRAY_ELEMENTS(insertionGOP, insertionGOPArray, JNI_RO_RELEASE_MODE);
-    RELEASE_BYTE_ARRAY_ELEMENTS(readQuals, readQualsArray, JNI_RO_RELEASE_MODE);
-
-    //Release readBases at end because it is used by compute_full_prob
+    //Release read arrays at end because they are used by compute_full_prob
+    //Maintain order in which GET_BYTE_ARRAY_ELEMENTS called
     readBasesArrayVector[i].clear();
-    readBasesArrayVector[i].resize(1);
+    readBasesArrayVector[i].resize(5);
     readBasesArrayVector[i][0] = make_pair(readBases, readBasesArray);
+    readBasesArrayVector[i][1] = make_pair(readQuals, readQualsArray);
+    readBasesArrayVector[i][2] = make_pair(insertionGOP, insertionGOPArray);
+    readBasesArrayVector[i][3] = make_pair(deletionGOP, deletionGOPArray);
+    readBasesArrayVector[i][4] = make_pair(overallGCP, overallGCPArray);
   }
 #ifdef DO_PROFILING
-  g_load_time_initializer.m_data_transfer_time += (getCurrClk()-start_time);
+  g_load_time_initializer.m_data_transfer_time += get_time();
 #endif
 
   jdouble* likelihoodDoubleArray = (jdouble*)GET_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, &is_copy);
@@ -298,7 +294,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
   assert(env->GetArrayLength(likelihoodArray) == numTestCases);
 #endif
 #ifdef DO_PROFILING
-  start_time = getCurrClk();
+  start_time = get_time();
 #endif
 #pragma omp parallel for schedule (dynamic,10) private(tc_idx) num_threads(maxNumThreadsToUse) 
   for(tc_idx=0;tc_idx<numTestCases;++tc_idx)
@@ -315,7 +311,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
     likelihoodDoubleArray[tc_idx] = result;
   }
 #ifdef DO_PROFILING
-  g_load_time_initializer.m_compute_time += (getCurrClk()-start_time);
+  g_load_time_initializer.m_compute_time += get_time();
 #endif
 #ifdef DEBUG
   for(tc_idx=0;tc_idx<numTestCases;++tc_idx)
@@ -324,7 +320,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
   }
 #endif
 #ifdef DO_PROFILING
-  start_time = getCurrClk();
+  start_time = get_time();
 #endif
   RELEASE_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, likelihoodDoubleArray, 0); //release mode 0, copy back results to Java memory
   
@@ -337,7 +333,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
   }
   readBasesArrayVector.clear();
 #ifdef DO_PROFILING
-  g_load_time_initializer.m_data_transfer_time += (getCurrClk()-start_time);
+  g_load_time_initializer.m_data_transfer_time += get_time();
 #endif
   tc_array.clear();
 #ifdef DO_PROFILING
diff --git a/PairHMM_JNI/pairhmm-1-base.cc b/PairHMM_JNI/pairhmm-1-base.cc
index 1a2dc9a7c..aaf45848b 100644
--- a/PairHMM_JNI/pairhmm-1-base.cc
+++ b/PairHMM_JNI/pairhmm-1-base.cc
@@ -44,7 +44,7 @@ int main(int argc, char** argv)
   vector<testcase> tc_vector;
   tc_vector.clear();
   testcase tc;
-  double total_time = 0;
+  uint64_t total_time = 0;
   while(1)
   {
     int break_value = use_old_read_testcase ? read_testcase(&tc, fptr) : read_mod_testcase(ifptr,&tc,true);
@@ -55,7 +55,7 @@ int main(int argc, char** argv)
       vector<double> results_vec;
       results_vec.clear();
       results_vec.resize(tc_vector.size());
-      double start_time = getCurrClk();
+      get_time();
 #pragma omp parallel for schedule(dynamic,chunk_size)  num_threads(12)
       for(unsigned i=0;i<tc_vector.size();++i)
       {
@@ -71,7 +71,8 @@ int main(int argc, char** argv)
 
 	results_vec[i] = result;
       }
-      total_time +=  (getCurrClk()-start_time);
+      total_time +=  get_time();
+#pragma omp parallel for schedule(dynamic,chunk_size)
       for(unsigned i=0;i<tc_vector.size();++i)
       {
 	testcase& tc = tc_vector[i];
@@ -83,6 +84,10 @@ int main(int argc, char** argv)
 	  cout << std::scientific << baseline_result << " "<<results_vec[i]<<"\n";
 	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();
@@ -90,7 +95,7 @@ int main(int argc, char** argv)
     if(break_value < 0)
       break;
   }
-  cout << "Total time "<< total_time << "\n";
+  cout << "Total time "<< ((double)total_time)/1e9 << "\n";
   if(use_old_read_testcase)
     fclose(fptr);
   else
diff --git a/PairHMM_JNI/run.sh b/PairHMM_JNI/run.sh
index eafb7ff79..1e82092e8 100755
--- a/PairHMM_JNI/run.sh
+++ b/PairHMM_JNI/run.sh
@@ -3,15 +3,15 @@ rm -f *.txt *.log
 GSA_ROOT_DIR=/home/karthikg/broad/gsa-unstable
 #-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed
 java  -Djava.library.path=${GSA_ROOT_DIR}/PairHMM_JNI -jar $GSA_ROOT_DIR/dist/GenomeAnalysisTK.jar   -T HaplotypeCaller \
--R /opt/Genomics/ohsu/dnapipeline/humanrefgenome/human_g1k_v37.fasta \
--I /data/simulated/sim1M_pairs_final.bam \
+-R /data/broad/samples/joint_variant_calling/broad_reference/human_g1k_v37_decoy.fasta \
+-I /data/broad/samples/joint_variant_calling/NA12878_low_coverage_alignment/NA12878.chrom11.ILLUMINA.bwa.CEU.low_coverage.20121211.bam \
 --dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \
 -stand_call_conf 50.0 \
 -stand_emit_conf 10.0 \
 --pair_hmm_implementation JNI_LOGLESS_CACHING \
--XL unmapped	\
 -o output.raw.snps.indels.vcf
 
+#-XL unmapped	\
 #--pair_hmm_implementation JNI_LOGLESS_CACHING \
 #-I /data/simulated/sim1M_pairs_final.bam \
 #-I /data/broad/samples/joint_variant_calling/NA12878_low_coverage_alignment/NA12878.chrom11.ILLUMINA.bwa.CEU.low_coverage.20121211.bam \
diff --git a/PairHMM_JNI/template.h b/PairHMM_JNI/template.h
index 0ba4f843d..ba6370de8 100644
--- a/PairHMM_JNI/template.h
+++ b/PairHMM_JNI/template.h
@@ -150,7 +150,8 @@ typedef struct
 {
         int rslen, haplen;
 	/*int *q, *i, *d, *c;*/
-	int q[MROWS], i[MROWS], d[MROWS], c[MROWS];
+	/*int q[MROWS], i[MROWS], d[MROWS], c[MROWS];*/
+	char *q, *i, *d, *c;
         char *hap, *rs;
 	int *ihap;
 	int *irs;
diff --git a/PairHMM_JNI/utils.cc b/PairHMM_JNI/utils.cc
index 5ed79e29d..da6509763 100644
--- a/PairHMM_JNI/utils.cc
+++ b/PairHMM_JNI/utils.cc
@@ -90,10 +90,10 @@ int read_testcase(testcase *tc, FILE* ifp)
 	tc->ihap = (int *) malloc(tc->haplen*sizeof(int));
 	tc->irs = (int *) malloc(tc->rslen*sizeof(int));
 
-	//tc->q = (int *) malloc(sizeof(int) * tc->rslen);
-	//tc->i = (int *) malloc(sizeof(int) * tc->rslen);
-	//tc->d = (int *) malloc(sizeof(int) * tc->rslen);
-	//tc->c = (int *) malloc(sizeof(int) * tc->rslen);
+	tc->q = (char *) malloc(sizeof(char) * tc->rslen);
+	tc->i = (char *) malloc(sizeof(char) * tc->rslen);
+	tc->d = (char *) malloc(sizeof(char) * tc->rslen);
+	tc->c = (char *) malloc(sizeof(char) * tc->rslen);
 
 	for (x = 0; x < tc->rslen; x++)
 	{
@@ -199,18 +199,22 @@ int read_mod_testcase(ifstream& fptr, testcase* tc, bool reformat)
   memcpy(tc->hap, tokens[0].c_str(), tokens[0].size());
   tc->rs = new char[tokens[1].size()+2];
   tc->rslen = tokens[1].size();
+  tc->q = new char[tc->rslen];
+  tc->i = new char[tc->rslen];
+  tc->d = new char[tc->rslen];
+  tc->c = new char[tc->rslen];
   //cout << "Lengths "<<tc->haplen <<" "<<tc->rslen<<"\n";
   memcpy(tc->rs, tokens[1].c_str(),tokens[1].size());
   assert(tokens.size() == 2 + 4*(tc->rslen));
   assert(tc->rslen < MROWS);
   for(unsigned j=0;j<tc->rslen;++j)
-    tc->q[j] = convToInt(tokens[2+0*tc->rslen+j]);
+    tc->q[j] = (char)convToInt(tokens[2+0*tc->rslen+j]);
   for(unsigned j=0;j<tc->rslen;++j)
-    tc->i[j] = convToInt(tokens[2+1*tc->rslen+j]);
+    tc->i[j] = (char)convToInt(tokens[2+1*tc->rslen+j]);
   for(unsigned j=0;j<tc->rslen;++j)
-    tc->d[j] = convToInt(tokens[2+2*tc->rslen+j]);
+    tc->d[j] = (char)convToInt(tokens[2+2*tc->rslen+j]);
   for(unsigned j=0;j<tc->rslen;++j)
-    tc->c[j] = convToInt(tokens[2+3*tc->rslen+j]);
+    tc->c[j] = (char)convToInt(tokens[2+3*tc->rslen+j]);
  
   if(reformat)
   {
@@ -245,3 +249,14 @@ double getCurrClk() {
   gettimeofday(&tv, NULL);
   return (double)tv.tv_sec + (double)tv.tv_usec / 1000000.0;
 }
+
+uint64_t get_time(struct timespec* store_struct)
+{
+  static struct timespec start_time;
+  struct timespec curr_time;
+  struct timespec* ptr = (store_struct == 0) ? &curr_time : store_struct;
+  clock_gettime(CLOCK_REALTIME, ptr);
+  uint64_t diff_time = (ptr->tv_sec-start_time.tv_sec)*1000000000+(ptr->tv_nsec-start_time.tv_nsec);
+  start_time = *ptr;
+  return diff_time;
+}
diff --git a/PairHMM_JNI/utils.h b/PairHMM_JNI/utils.h
index 3f7c2ff69..cc020ba40 100644
--- a/PairHMM_JNI/utils.h
+++ b/PairHMM_JNI/utils.h
@@ -27,4 +27,5 @@ template<class NUMBER>
 NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log=0);
 void initialize_function_pointers();
 double getCurrClk();
+uint64_t get_time(struct timespec* x=0);
 #endif
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java
index f926e4bd6..6cbd3510c 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java
@@ -68,8 +68,8 @@ import java.util.HashMap;
 public class JNILoglessPairHMM extends LoglessPairHMM {
 
     private static final boolean debug = false;	 //simulates ifdef
-    private static final boolean verify = debug || true;	 //simulates ifdef
-    private static final boolean debug0_1 = true;	 //simulates ifdef
+    private static final boolean verify = debug || false;	 //simulates ifdef
+    private static final boolean debug0_1 = false;	 //simulates ifdef
     private static final boolean debug1 = false; //simulates ifdef
     private static final boolean debug2 = false;
     private static final boolean debug3 = false;