text: /**
   * @file
   *
   * @author jeffrey.daily@gmail.com
   *
   * Copyright (c) 2015 Battelle Memorial Institute.
   */
  #include "config.h"
  
  #include <stdint.h>
  #include <stdlib.h>
  
  #define SG_STATS
  #define SG_SUFFIX _striped_altivec_128_8
  #define SG_SUFFIX_PROF _striped_profile_altivec_128_8
  #include "sg_helper.h"
  
  
  
  #include "parasail.h"
  #include "parasail/memory.h"
  #include "parasail/internal_altivec.h"
  
  #define SWAP(A,B) { vec128i* tmp = A; A = B; B = tmp; }
  
  
  
  #ifdef PARASAIL_TABLE
  static inline void arr_store_si128(
          int *array,
          vec128i vH,
          int32_t t,
          int32_t seglen,
          int32_t d,
          int32_t dlen)
  {
      array[1LL*( 0*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  0);
      array[1LL*( 1*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  1);
      array[1LL*( 2*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  2);
      array[1LL*( 3*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  3);
      array[1LL*( 4*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  4);
      array[1LL*( 5*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  5);
      array[1LL*( 6*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  6);
      array[1LL*( 7*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  7);
      array[1LL*( 8*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  8);
      array[1LL*( 9*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH,  9);
      array[1LL*(10*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH, 10);
      array[1LL*(11*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH, 11);
      array[1LL*(12*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH, 12);
      array[1LL*(13*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH, 13);
      array[1LL*(14*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH, 14);
      array[1LL*(15*seglen+t)*dlen + d] = (int8_t)_mm_extract_epi8(vH, 15);
  }
  #endif
  
  #ifdef PARASAIL_ROWCOL
  static inline void arr_store_col(
          int *col,
          vec128i vH,
          int32_t t,
          int32_t seglen)
  {
      col[ 0*seglen+t] = (int8_t)_mm_extract_epi8(vH,  0);
      col[ 1*seglen+t] = (int8_t)_mm_extract_epi8(vH,  1);
      col[ 2*seglen+t] = (int8_t)_mm_extract_epi8(vH,  2);
      col[ 3*seglen+t] = (int8_t)_mm_extract_epi8(vH,  3);
      col[ 4*seglen+t] = (int8_t)_mm_extract_epi8(vH,  4);
      col[ 5*seglen+t] = (int8_t)_mm_extract_epi8(vH,  5);
      col[ 6*seglen+t] = (int8_t)_mm_extract_epi8(vH,  6);
      col[ 7*seglen+t] = (int8_t)_mm_extract_epi8(vH,  7);
      col[ 8*seglen+t] = (int8_t)_mm_extract_epi8(vH,  8);
      col[ 9*seglen+t] = (int8_t)_mm_extract_epi8(vH,  9);
      col[10*seglen+t] = (int8_t)_mm_extract_epi8(vH, 10);
      col[11*seglen+t] = (int8_t)_mm_extract_epi8(vH, 11);
      col[12*seglen+t] = (int8_t)_mm_extract_epi8(vH, 12);
      col[13*seglen+t] = (int8_t)_mm_extract_epi8(vH, 13);
      col[14*seglen+t] = (int8_t)_mm_extract_epi8(vH, 14);
      col[15*seglen+t] = (int8_t)_mm_extract_epi8(vH, 15);
  }
  #endif
  
  #ifdef PARASAIL_TABLE
  #define FNAME parasail_sg_flags_stats_table_striped_altivec_128_8
  #define PNAME parasail_sg_flags_stats_table_striped_profile_altivec_128_8
  #else
  #ifdef PARASAIL_ROWCOL
  #define FNAME parasail_sg_flags_stats_rowcol_striped_altivec_128_8
  #define PNAME parasail_sg_flags_stats_rowcol_striped_profile_altivec_128_8
  #else
  #define FNAME parasail_sg_flags_stats_striped_altivec_128_8
  #define PNAME parasail_sg_flags_stats_striped_profile_altivec_128_8
  #endif
  #endif
  
  parasail_result_t* FNAME(
          const char * const restrict s1, const int s1Len,
          const char * const restrict s2, const int s2Len,
          const int open, const int gap, const parasail_matrix_t *matrix,
          int s1_beg, int s1_end, int s2_beg, int s2_end)
  {
      parasail_profile_t *profile = parasail_profile_create_stats_altivec_128_8(s1, s1Len, matrix);
      parasail_result_t *result = PNAME(profile, s2, s2Len, open, gap, s1_beg, s1_end, s2_beg, s2_end);
      parasail_profile_free(profile);
      return result;
  }
  
  parasail_result_t* PNAME(
          const parasail_profile_t * const restrict profile,
          const char * const restrict s2, const int s2Len,
          const int open, const int gap,
          int s1_beg, int s1_end, int s2_beg, int s2_end)
  {
      int32_t i = 0;
      int32_t j = 0;
      int32_t k = 0;
      const int s1Len = profile->s1Len;
      int32_t end_query = s1Len-1;
      int32_t end_ref = s2Len-1;
      const parasail_matrix_t *matrix = profile->matrix;
      const int32_t segWidth = 16; /* number of values in vector unit */
      const int32_t segLen = (s1Len + segWidth - 1) / segWidth;
      const int32_t offset = (s1Len - 1) % segLen;
      const int32_t position = (segWidth - 1) - (s1Len - 1) / segLen;
      vec128i* const restrict vProfile  = (vec128i*)profile->profile8.score;
      vec128i* const restrict vProfileM = (vec128i*)profile->profile8.matches;
      vec128i* const restrict vProfileS = (vec128i*)profile->profile8.similar;
      vec128i* restrict pvHStore        = parasail_memalign_vec128i(16, segLen);
      vec128i* restrict pvHLoad         = parasail_memalign_vec128i(16, segLen);
      vec128i* restrict pvHMStore       = parasail_memalign_vec128i(16, segLen);
      vec128i* restrict pvHMLoad        = parasail_memalign_vec128i(16, segLen);
      vec128i* restrict pvHSStore       = parasail_memalign_vec128i(16, segLen);
      vec128i* restrict pvHSLoad        = parasail_memalign_vec128i(16, segLen);
      vec128i* restrict pvHLStore       = parasail_memalign_vec128i(16, segLen);
      vec128i* restrict pvHLLoad        = parasail_memalign_vec128i(16, segLen);
      vec128i* const restrict pvE       = parasail_memalign_vec128i(16, segLen);
      vec128i* const restrict pvEM      = parasail_memalign_vec128i(16, segLen);
      vec128i* const restrict pvES      = parasail_memalign_vec128i(16, segLen);
      vec128i* const restrict pvEL      = parasail_memalign_vec128i(16, segLen);
      int8_t* const restrict boundary = parasail_memalign_int8_t(16, s2Len+1);
      const vec128i vGapO = _mm_set1_epi8(open);
      const vec128i vGapE = _mm_set1_epi8(gap);
      const int8_t NEG_LIMIT = (-open < matrix->min ?
          INT8_MIN + open : INT8_MIN - matrix->min) + 1;
      const int8_t POS_LIMIT = INT8_MAX - matrix->max - 1;
      const vec128i vZero = _mm_setzero_si128();
      const vec128i vOne = _mm_set1_epi8(1);
      int8_t score = NEG_LIMIT;
      int8_t matches = 0;
      int8_t similar = 0;
      int8_t length = 0;
      vec128i vNegLimit = _mm_set1_epi8(NEG_LIMIT);
      vec128i vPosLimit = _mm_set1_epi8(POS_LIMIT);
      vec128i vSaturationCheckMin = vPosLimit;
      vec128i vSaturationCheckMax = vNegLimit;
      vec128i vMaxH = vNegLimit;
      vec128i vMaxHM = vNegLimit;
      vec128i vMaxHS = vNegLimit;
      vec128i vMaxHL = vNegLimit;
      vec128i vPosMask = _mm_cmpeq_epi8(_mm_set1_epi8(position),
              _mm_set_epi8(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15));
  #ifdef PARASAIL_TABLE
      parasail_result_t *result = parasail_result_new_table3(segLen*segWidth, s2Len);
  #else
  #ifdef PARASAIL_ROWCOL
      parasail_result_t *result = parasail_result_new_rowcol3(segLen*segWidth, s2Len);
  #else
      parasail_result_t *result = parasail_result_new_stats();
  #endif
  #endif
  
      parasail_memset_vec128i(pvHMStore, vZero, segLen);
      parasail_memset_vec128i(pvHSStore, vZero, segLen);
      parasail_memset_vec128i(pvHLStore, vZero, segLen);
      parasail_memset_vec128i(pvEM, vZero, segLen);
      parasail_memset_vec128i(pvES, vZero, segLen);
      parasail_memset_vec128i(pvEL, vOne, segLen);
  
      /* initialize H and E */
      {
          int32_t index = 0;
          for (i=0; i<segLen; ++i) {
              int32_t segNum = 0;
              vec128i_8_t h;
              vec128i_8_t e;
              for (segNum=0; segNum<segWidth; ++segNum) {
                  int64_t tmp = s1_beg ? 0 : (-open-gap*(segNum*segLen+i));
                  h.v[segNum] = tmp < INT8_MIN ? INT8_MIN : tmp;
                  tmp = tmp - open;
                  e.v[segNum] = tmp < INT8_MIN ? INT8_MIN : tmp;
              }
              _mm_store_si128(&pvHStore[index], h.m);
              _mm_store_si128(&pvE[index], e.m);
              ++index;
          }
      }
  
      /* initialize uppder boundary */
      {
          boundary[0] = 0;
          for (i=1; i<=s2Len; ++i) {
              int64_t tmp = s2_beg ? 0 : (-open-gap*(i-1));
              boundary[i] = tmp < INT8_MIN ? INT8_MIN : tmp;
          }
      }
  
      /* outer loop over database sequence */
      for (j=0; j<s2Len; ++j) {
          vec128i vEF_opn;
          vec128i vE;
          vec128i vE_ext;
          vec128i vEM;
          vec128i vES;
          vec128i vEL;
          vec128i vF;
          vec128i vF_ext;
          vec128i vFM;
          vec128i vFS;
          vec128i vFL;
          vec128i vH;
          vec128i vH_dag;
          vec128i vHM;
          vec128i vHS;
          vec128i vHL;
          const vec128i* vP = NULL;
          const vec128i* vPM = NULL;
          const vec128i* vPS = NULL;
  
          /* Initialize F value to neg inf.  Any errors to vH values will
           * be corrected in the Lazy_F loop. */
          vF = vNegLimit;
          vFM = vZero;
          vFS = vZero;
          vFL = vOne;
  
          /* load final segment of pvHStore and shift left by 1 bytes */
          vH = _mm_load_si128(&pvHStore[segLen - 1]);
          vHM = _mm_load_si128(&pvHMStore[segLen - 1]);
          vHS = _mm_load_si128(&pvHSStore[segLen - 1]);
          vHL = _mm_load_si128(&pvHLStore[segLen - 1]);
          vH = _mm_slli_si128(vH, 1);
          vHM = _mm_slli_si128(vHM, 1);
          vHS = _mm_slli_si128(vHS, 1);
          vHL = _mm_slli_si128(vHL, 1);
  
          /* insert upper boundary condition */
          vH = _mm_insert_epi8(vH, boundary[j], 0);
  
          /* Correct part of the vProfile */
          vP = vProfile + matrix->mapper[(unsigned char)s2[j]] * segLen;
          vPM = vProfileM + matrix->mapper[(unsigned char)s2[j]] * segLen;
          vPS = vProfileS + matrix->mapper[(unsigned char)s2[j]] * segLen;
  
          /* Swap the 2 H buffers. */
          SWAP(pvHLoad,  pvHStore)
          SWAP(pvHMLoad, pvHMStore)
          SWAP(pvHSLoad, pvHSStore)
          SWAP(pvHLLoad, pvHLStore)
  
          /* inner loop to process the query sequence */
          for (i=0; i<segLen; ++i) {
              vec128i case1;
              vec128i case2;
  
              vE = _mm_load_si128(pvE+ i);
              vEM = _mm_load_si128(pvEM+ i);
              vES = _mm_load_si128(pvES+ i);
              vEL = _mm_load_si128(pvEL+ i);
  
              /* Get max from vH, vE and vF. */
              vH_dag = _mm_adds_epi8(vH, _mm_load_si128(vP + i));
              vH = _mm_max_epi8(vH_dag, vE);
              vH = _mm_max_epi8(vH, vF);
              /* Save vH values. */
              _mm_store_si128(pvHStore + i, vH);
  
              case1 = _mm_cmpeq_epi8(vH, vH_dag);
              case2 = _mm_cmpeq_epi8(vH, vF);
  
              /* calculate vM */
              vHM = _mm_blendv_epi8(
                      _mm_blendv_epi8(vEM, vFM, case2),
                      _mm_adds_epi8(vHM, _mm_load_si128(vPM + i)),
                      case1);
              _mm_store_si128(pvHMStore + i, vHM);
  
              /* calculate vS */
              vHS = _mm_blendv_epi8(
                      _mm_blendv_epi8(vES, vFS, case2),
                      _mm_adds_epi8(vHS, _mm_load_si128(vPS + i)),
                      case1);
              _mm_store_si128(pvHSStore + i, vHS);
  
              /* calculate vL */
              vHL = _mm_blendv_epi8(
                      _mm_blendv_epi8(vEL, vFL, case2),
                      _mm_adds_epi8(vHL, vOne),
                      case1);
              _mm_store_si128(pvHLStore + i, vHL);
  
              vSaturationCheckMin = _mm_min_epi8(vSaturationCheckMin, vH);
              vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vH);
              vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vHM);
              vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vHS);
              vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vHL);
  #ifdef PARASAIL_TABLE
              arr_store_si128(result->stats->tables->matches_table, vHM, i, segLen, j, s2Len);
              arr_store_si128(result->stats->tables->similar_table, vHS, i, segLen, j, s2Len);
              arr_store_si128(result->stats->tables->length_table, vHL, i, segLen, j, s2Len);
              arr_store_si128(result->stats->tables->score_table, vH, i, segLen, j, s2Len);
  #endif
              vEF_opn = _mm_subs_epi8(vH, vGapO);
  
              /* Update vE value. */
              vE_ext = _mm_subs_epi8(vE, vGapE);
              vE = _mm_max_epi8(vEF_opn, vE_ext);
              case1 = _mm_cmpgt_epi8(vEF_opn, vE_ext);
              vEM = _mm_blendv_epi8(vEM, vHM, case1);
              vES = _mm_blendv_epi8(vES, vHS, case1);
              vEL = _mm_blendv_epi8(
                      _mm_adds_epi8(vEL, vOne),
                      _mm_adds_epi8(vHL, vOne),
                      case1);
              _mm_store_si128(pvE + i, vE);
              _mm_store_si128(pvEM + i, vEM);
              _mm_store_si128(pvES + i, vES);
              _mm_store_si128(pvEL + i, vEL);
  
              /* Update vF value. */
              vF_ext = _mm_subs_epi8(vF, vGapE);
              vF = _mm_max_epi8(vEF_opn, vF_ext);
              case1 = _mm_cmpgt_epi8(vEF_opn, vF_ext);
              vFM = _mm_blendv_epi8(vFM, vHM, case1);
              vFS = _mm_blendv_epi8(vFS, vHS, case1);
              vFL = _mm_blendv_epi8(
                      _mm_adds_epi8(vFL, vOne),
                      _mm_adds_epi8(vHL, vOne),
                      case1);
  
              /* Load the next vH. */
              vH = _mm_load_si128(pvHLoad + i);
              vHM = _mm_load_si128(pvHMLoad + i);
              vHS = _mm_load_si128(pvHSLoad + i);
              vHL = _mm_load_si128(pvHLLoad + i);
          }
  
          /* Lazy_F loop: has been revised to disallow adjecent insertion and
           * then deletion, so don't update E(i, i), learn from SWPS3 */
          for (k=0; k<segWidth; ++k) {
              vec128i vHp = _mm_load_si128(&pvHLoad[segLen - 1]);
              int64_t tmp = s2_beg ? -open : (boundary[j+1]-open);
              int8_t tmp2 = tmp < INT8_MIN ? INT8_MIN : tmp;
              vHp = _mm_slli_si128(vHp, 1);
              vF = _mm_slli_si128(vF, 1);
              vFM = _mm_slli_si128(vFM, 1);
              vFS = _mm_slli_si128(vFS, 1);
              vFL = _mm_slli_si128(vFL, 1);
              vHp = _mm_insert_epi8(vHp, boundary[j], 0);
              vF = _mm_insert_epi8(vF, tmp2, 0);
              vFL = _mm_insert_epi8(vFL, 1, 0);
              for (i=0; i<segLen; ++i) {
                  vec128i case1;
                  vec128i case2;
                  vec128i cond;
  
                  vHp = _mm_adds_epi8(vHp, _mm_load_si128(vP + i));
                  vH = _mm_load_si128(pvHStore + i);
                  vH = _mm_max_epi8(vH,vF);
                  _mm_store_si128(pvHStore + i, vH);
                  case1 = _mm_cmpeq_epi8(vH, vHp);
                  case2 = _mm_cmpeq_epi8(vH, vF);
                  cond = _mm_andnot_si128(case1, case2);
  
                  /* calculate vM */
                  vHM = _mm_load_si128(pvHMStore + i);
                  vHM = _mm_blendv_epi8(vHM, vFM, cond);
                  _mm_store_si128(pvHMStore + i, vHM);
  
                  /* calculate vS */
                  vHS = _mm_load_si128(pvHSStore + i);
                  vHS = _mm_blendv_epi8(vHS, vFS, cond);
                  _mm_store_si128(pvHSStore + i, vHS);
  
                  /* calculate vL */
                  vHL = _mm_load_si128(pvHLStore + i);
                  vHL = _mm_blendv_epi8(vHL, vFL, cond);
                  _mm_store_si128(pvHLStore + i, vHL);
  
                  vSaturationCheckMin = _mm_min_epi8(vSaturationCheckMin, vH);
                  vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vH);
                  vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vHM);
                  vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vHS);
                  vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vHL);
  #ifdef PARASAIL_TABLE
                  arr_store_si128(result->stats->tables->matches_table, vHM, i, segLen, j, s2Len);
                  arr_store_si128(result->stats->tables->similar_table, vHS, i, segLen, j, s2Len);
                  arr_store_si128(result->stats->tables->length_table, vHL, i, segLen, j, s2Len);
                  arr_store_si128(result->stats->tables->score_table, vH, i, segLen, j, s2Len);
  #endif
                  /* Update vF value. */
                  vEF_opn = _mm_subs_epi8(vH, vGapO);
                  vF_ext = _mm_subs_epi8(vF, vGapE);
                  if (! _mm_movemask_epi8(
                              _mm_or_si128(
                                  _mm_cmpgt_epi8(vF_ext, vEF_opn),
                                  _mm_cmpeq_epi8(vF_ext, vEF_opn))))
                      goto end;
                  /*vF = _mm_max_epi8(vEF_opn, vF_ext);*/
                  vF = vF_ext;
                  cond = _mm_cmpgt_epi8(vEF_opn, vF_ext);
                  vFM = _mm_blendv_epi8(vFM, vHM, cond);
                  vFS = _mm_blendv_epi8(vFS, vHS, cond);
                  vFL = _mm_blendv_epi8(
                          _mm_adds_epi8(vFL, vOne),
                          _mm_adds_epi8(vHL, vOne),
                          cond);
                  vHp = _mm_load_si128(pvHLoad + i);
              }
          }
  end:
          {
          }
  
          /* extract vector containing last value from the column */
          {
              vec128i cond_max;
              vH = _mm_load_si128(pvHStore + offset);
              vHM = _mm_load_si128(pvHMStore + offset);
              vHS = _mm_load_si128(pvHSStore + offset);
              vHL = _mm_load_si128(pvHLStore + offset);
              cond_max = _mm_cmpgt_epi8(vH, vMaxH);
              vMaxH = _mm_blendv_epi8(vMaxH, vH, cond_max);
              vMaxHM = _mm_blendv_epi8(vMaxHM, vHM, cond_max);
              vMaxHS = _mm_blendv_epi8(vMaxHS, vHS, cond_max);
              vMaxHL = _mm_blendv_epi8(vMaxHL, vHL, cond_max);
              if (_mm_movemask_epi8(_mm_and_si128(vPosMask, cond_max))) {
                  end_ref = j;
              }
          }
  #ifdef PARASAIL_ROWCOL
          for (k=0; k<position; ++k) {
              vH = _mm_slli_si128(vH, 1);
              vHM = _mm_slli_si128(vHM, 1);
              vHS = _mm_slli_si128(vHS, 1);
              vHL = _mm_slli_si128(vHL, 1);
          }
          result->stats->rowcols->score_row[j] = (int8_t) _mm_extract_epi8 (vH, 15);
          result->stats->rowcols->matches_row[j] = (int8_t) _mm_extract_epi8 (vHM, 15);
          result->stats->rowcols->similar_row[j] = (int8_t) _mm_extract_epi8 (vHS, 15);
          result->stats->rowcols->length_row[j] = (int8_t) _mm_extract_epi8 (vHL, 15);
  #endif
      }
  
  #ifdef PARASAIL_ROWCOL
      for (i=0; i<segLen; ++i) {
          vec128i vH = _mm_load_si128(pvHStore+i);
          vec128i vHM = _mm_load_si128(pvHMStore+i);
          vec128i vHS = _mm_load_si128(pvHSStore+i);
          vec128i vHL = _mm_load_si128(pvHLStore+i);
          arr_store_col(result->stats->rowcols->score_col, vH, i, segLen);
          arr_store_col(result->stats->rowcols->matches_col, vHM, i, segLen);
          arr_store_col(result->stats->rowcols->similar_col, vHS, i, segLen);
          arr_store_col(result->stats->rowcols->length_col, vHL, i, segLen);
      }
  #endif
  
      /* extract last value from the column maximums */
      if (s2_end)
      {
          for (k=0; k<position; ++k) {
              vMaxH = _mm_slli_si128(vMaxH, 1);
              vMaxHM = _mm_slli_si128(vMaxHM, 1);
              vMaxHS = _mm_slli_si128(vMaxHS, 1);
              vMaxHL = _mm_slli_si128(vMaxHL, 1);
          }
          end_query = s1Len-1;
          score = (int8_t) _mm_extract_epi8(vMaxH, 15);
          matches = (int8_t) _mm_extract_epi8(vMaxHM, 15);
          similar = (int8_t) _mm_extract_epi8(vMaxHS, 15);
          length = (int8_t) _mm_extract_epi8(vMaxHL, 15);
      }
  
      /* max of last column */
      if (s1_end)
      {
          /* Trace the alignment ending position on read. */
          int8_t *t = (int8_t*)pvHStore;
          int8_t *m = (int8_t*)pvHMStore;
          int8_t *s = (int8_t*)pvHSStore;
          int8_t *l = (int8_t*)pvHLStore;
          int32_t column_len = segLen * segWidth;
          for (i = 0; i<column_len; ++i, ++t, ++m, ++s, ++l) {
              int32_t temp = i / segWidth + i % segWidth * segLen;
              if (temp >= s1Len) continue;
              if (*t > score) {
                  score = *t;
                  end_query = temp;
                  end_ref = s2Len-1;
                  matches = *m;
                  similar = *s;
                  length = *l;
              }
              else if (*t == score && end_ref == s2Len-1 && temp < end_query) {
                  end_query = temp;
                  matches = *m;
                  similar = *s;
                  length = *l;
              }
          }
      }
  
      /* extract last value from the last column */
      if (!s1_end && !s2_end)
      {
          vec128i vH = _mm_load_si128(pvHStore + offset);
          vec128i vHM = _mm_load_si128(pvHMStore + offset);
          vec128i vHS = _mm_load_si128(pvHSStore + offset);
          vec128i vHL = _mm_load_si128(pvHLStore + offset);
          for (k=0; k<position; ++k) {
              vH = _mm_slli_si128(vH, 1);
              vHM = _mm_slli_si128(vHM, 1);
              vHS = _mm_slli_si128(vHS, 1);
              vHL = _mm_slli_si128(vHL, 1);
          }
          end_ref = s2Len - 1;
          end_query = s1Len - 1;
          score = (int8_t) _mm_extract_epi8 (vH, 15);
          matches = (int8_t) _mm_extract_epi8 (vHM, 15);
          similar = (int8_t) _mm_extract_epi8 (vHS, 15);
          length = (int8_t) _mm_extract_epi8 (vHL, 15);
      }
  
      if (_mm_movemask_epi8(_mm_or_si128(
              _mm_cmplt_epi8(vSaturationCheckMin, vNegLimit),
              _mm_cmpgt_epi8(vSaturationCheckMax, vPosLimit)))) {
          result->flag |= PARASAIL_FLAG_SATURATED;
          score = 0;
          matches = 0;
          similar = 0;
          length = 0;
          end_query = 0;
          end_ref = 0;
      }
  
      result->score = score;
      result->end_query = end_query;
      result->end_ref = end_ref;
      result->stats->matches = matches;
      result->stats->similar = similar;
      result->stats->length = length;
      result->flag |= PARASAIL_FLAG_SG | PARASAIL_FLAG_STRIPED
          | PARASAIL_FLAG_STATS
          | PARASAIL_FLAG_BITS_8 | PARASAIL_FLAG_LANES_16;
      result->flag |= s1_beg ? PARASAIL_FLAG_SG_S1_BEG : 0;
      result->flag |= s1_end ? PARASAIL_FLAG_SG_S1_END : 0;
      result->flag |= s2_beg ? PARASAIL_FLAG_SG_S2_BEG : 0;
      result->flag |= s2_end ? PARASAIL_FLAG_SG_S2_END : 0;
  #ifdef PARASAIL_TABLE
      result->flag |= PARASAIL_FLAG_TABLE;
  #endif
  #ifdef PARASAIL_ROWCOL
      result->flag |= PARASAIL_FLAG_ROWCOL;
  #endif
  
      parasail_free(boundary);
      parasail_free(pvEL);
      parasail_free(pvES);
      parasail_free(pvEM);
      parasail_free(pvE);
      parasail_free(pvHLLoad);
      parasail_free(pvHLStore);
      parasail_free(pvHSLoad);
      parasail_free(pvHSStore);
      parasail_free(pvHMLoad);
      parasail_free(pvHMStore);
      parasail_free(pvHLoad);
      parasail_free(pvHStore);
  
      return result;
  }
  
  SG_IMPL_ALL
  SG_IMPL_PROF_ALL
  
  
  