text: #include <vector>
  #include <math.h>
  #include <avx.h>
  #include "IntelSmithWaterman.h"
  #include "smithwaterman_common.h"
  
  #include <stdio.h>
  #include <stdlib.h>
  #include <stdint.h>
  #include <string.h>
  #include <immintrin.h>
  #include <assert.h>
  #include <debug.h>
  #include "avx2_impl.h"
  #ifndef __APPLE__
    #include "avx512_impl.h"
  #endif
  
  
  static jfieldID FID_reflength;
  static jfieldID FID_altlength;
  
  int32_t (*g_runSWOnePairBT)(int32_t match, int32_t mismatch, int32_t open, int32_t extend,uint8_t *seq1, uint8_t *seq2, int32_t len1, int32_t len2, int8_t overhangStrategy, char *cigarArray, int16_t *cigarCount);
  
  JNIEXPORT void JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_initNative
    (JNIEnv * env, jclass obj )
  {
  
  if(is_avx512_supported())
        {
      #ifndef __APPLE__
          DBG("Using CPU-supported AVX-512 instructions");
          g_runSWOnePairBT = runSWOnePairBT_fp_avx512;
  
      #else
          assert(false);
      #endif
        }
        else
        {
          g_runSWOnePairBT = runSWOnePairBT_fp_avx2;
        }
        return;
  }
  /*
   * Class:     com_intel_gkl_smithwaterman_IntelSmithWaterman
   * Method:    alignNative
   */
  JNIEXPORT jint JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_alignNative
    (JNIEnv * env, jclass obj, jbyteArray ref, jbyteArray alt, jbyteArray cigar, jint match, jint mismatch, jint open, jint extend, jint strategy)
  {
      jint refLength = env->GetArrayLength(ref);
      jint altLength = env->GetArrayLength(alt);
  
      jbyte* reference = (jbyte*)env->GetPrimitiveArrayCritical(ref, 0);
      jbyte* alternate = (jbyte*)env->GetPrimitiveArrayCritical(alt, 0);
      jbyte* cigarArray = (jbyte*)env->GetPrimitiveArrayCritical(cigar, 0);
  
      if (reference == NULL | alternate == NULL | cigarArray == NULL) {
           DBG("GetPrimitiveArrayCritical failed from JAVA unable to contiune"); 
           return -1;
      }
  
      jint count = 0;
      jint offset = 0;
  
      // call the low level routine
      offset = g_runSWOnePairBT(match, mismatch, open, extend,(uint8_t*) reference, (uint8_t*) alternate,refLength, altLength, strategy, (char *) cigarArray, (int16_t*) &count);
  
      // release buffers
      env->ReleasePrimitiveArrayCritical(ref, reference, 0);
      env->ReleasePrimitiveArrayCritical(alt, alternate, 0);
      env->ReleasePrimitiveArrayCritical(cigar, cigarArray, 0);
  
      return offset;
  }
  
  /*
   * Class:     com_intel_gkl_smithwaterman_IntelSmithWaterman
   * Method:    doneNative
   * Signature: ()V
   */
  JNIEXPORT void JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_doneNative
    (JNIEnv *, jclass)
  {
  
  }
  