text: /**
   * @file
   *
   * @author jeffrey.daily@gmail.com
   *
   * Copyright (c) 2015 Battelle Memorial Institute.
   */
  #include "config.h"
  
  #include <stdint.h>
  #include <stdlib.h>
  
  #if defined(_MSC_VER)
  #include <intrin.h>
  #else
  #include <emmintrin.h>
  #endif
  
  #include "parasail.h"
  #include "parasail/memory.h"
  #include "parasail/internal_sse.h"
  
  #define SG_TRACE
  #define SG_SUFFIX _scan_sse2_128_64
  #define SG_SUFFIX_PROF _scan_profile_sse2_128_64
  #include "sg_helper.h"
  
  
  static inline __m128i _mm_cmpeq_epi64_rpl(__m128i a, __m128i b) {
      __m128i_64_t A;
      __m128i_64_t B;
      A.m = a;
      B.m = b;
      A.v[0] = (A.v[0]==B.v[0]) ? 0xFFFFFFFFFFFFFFFF : 0;
      A.v[1] = (A.v[1]==B.v[1]) ? 0xFFFFFFFFFFFFFFFF : 0;
      return A.m;
  }
  
  static inline __m128i _mm_blendv_epi8_rpl(__m128i a, __m128i b, __m128i mask) {
      a = _mm_andnot_si128(mask, a);
      a = _mm_or_si128(a, _mm_and_si128(mask, b));
      return a;
  }
  
  static inline __m128i _mm_cmpgt_epi64_rpl(__m128i a, __m128i b) {
      __m128i_64_t A;
      __m128i_64_t B;
      A.m = a;
      B.m = b;
      A.v[0] = (A.v[0]>B.v[0]) ? 0xFFFFFFFFFFFFFFFF : 0;
      A.v[1] = (A.v[1]>B.v[1]) ? 0xFFFFFFFFFFFFFFFF : 0;
      return A.m;
  }
  
  static inline __m128i _mm_insert_epi64_rpl(__m128i a, int64_t i, const int imm) {
      __m128i_64_t A;
      A.m = a;
      A.v[imm] = i;
      return A.m;
  }
  
  static inline __m128i _mm_max_epi64_rpl(__m128i a, __m128i b) {
      __m128i_64_t A;
      __m128i_64_t B;
      A.m = a;
      B.m = b;
      A.v[0] = (A.v[0]>B.v[0]) ? A.v[0] : B.v[0];
      A.v[1] = (A.v[1]>B.v[1]) ? A.v[1] : B.v[1];
      return A.m;
  }
  
  #if HAVE_SSE2_MM_SET_EPI64X
  #define _mm_set_epi64x_rpl _mm_set_epi64x
  #else
  static inline __m128i _mm_set_epi64x_rpl(int64_t e1, int64_t e0) {
      __m128i_64_t A;
      A.v[0] = e0;
      A.v[1] = e1;
      return A.m;
  }
  #endif
  
  static inline int64_t _mm_extract_epi64_rpl(__m128i a, const int imm) {
      __m128i_64_t A;
      A.m = a;
      return A.v[imm];
  }
  
  static inline __m128i _mm_min_epi64_rpl(__m128i a, __m128i b) {
      __m128i_64_t A;
      __m128i_64_t B;
      A.m = a;
      B.m = b;
      A.v[0] = (A.v[0]<B.v[0]) ? A.v[0] : B.v[0];
      A.v[1] = (A.v[1]<B.v[1]) ? A.v[1] : B.v[1];
      return A.m;
  }
  
  static inline __m128i _mm_cmplt_epi64_rpl(__m128i a, __m128i b) {
      __m128i_64_t A;
      __m128i_64_t B;
      A.m = a;
      B.m = b;
      A.v[0] = (A.v[0]<B.v[0]) ? 0xFFFFFFFFFFFFFFFF : 0;
      A.v[1] = (A.v[1]<B.v[1]) ? 0xFFFFFFFFFFFFFFFF : 0;
      return A.m;
  }
  
  #if HAVE_SSE2_MM_SET1_EPI64X
  #define _mm_set1_epi64x_rpl _mm_set1_epi64x
  #else
  static inline __m128i _mm_set1_epi64x_rpl(int64_t i) {
      __m128i_64_t A;
      A.v[0] = i;
      A.v[1] = i;
      return A.m;
  }
  #endif
  
  
  static inline void arr_store(
          __m128i *array,
          __m128i vH,
          int32_t t,
          int32_t seglen,
          int32_t d)
  {
      _mm_store_si128(array + (1LL*d*seglen+t), vH);
  }
  
  static inline __m128i arr_load(
          __m128i *array,
          int32_t t,
          int32_t seglen,
          int32_t d)
  {
      return _mm_load_si128(array + (1LL*d*seglen+t));
  }
  
  #define FNAME parasail_sg_flags_trace_scan_sse2_128_64
  #define PNAME parasail_sg_flags_trace_scan_profile_sse2_128_64
  
  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_sse_128_64(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 = 2; /* 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;
      __m128i* const restrict pvP  = (__m128i*)profile->profile64.score;
      __m128i* const restrict pvE  = parasail_memalign___m128i(16, segLen);
      int64_t* const restrict boundary = parasail_memalign_int64_t(16, s2Len+1);
      __m128i* const restrict pvHt = parasail_memalign___m128i(16, segLen);
      __m128i* const restrict pvH  = parasail_memalign___m128i(16, segLen);
      __m128i* const restrict pvGapper = parasail_memalign___m128i(16, segLen);
      __m128i vGapO = _mm_set1_epi64x_rpl(open);
      __m128i vGapE = _mm_set1_epi64x_rpl(gap);
      const int64_t NEG_LIMIT = (-open < matrix->min ?
          INT64_MIN + open : INT64_MIN - matrix->min) + 1;
      const int64_t POS_LIMIT = INT64_MAX - matrix->max - 1;
      __m128i vZero = _mm_setzero_si128();
      int64_t score = NEG_LIMIT;
      __m128i vNegLimit = _mm_set1_epi64x_rpl(NEG_LIMIT);
      __m128i vPosLimit = _mm_set1_epi64x_rpl(POS_LIMIT);
      __m128i vSaturationCheckMin = vPosLimit;
      __m128i vSaturationCheckMax = vNegLimit;
      __m128i vMaxH = vNegLimit;
      __m128i vPosMask = _mm_cmpeq_epi64_rpl(_mm_set1_epi64x_rpl(position),
              _mm_set_epi64x_rpl(0,1));
      __m128i vNegInfFront = vZero;
      __m128i vSegLenXgap;
      parasail_result_t *result = parasail_result_new_trace(segLen, s2Len, 16, sizeof(__m128i));
      __m128i vTIns  = _mm_set1_epi64x_rpl(PARASAIL_INS);
      __m128i vTDel  = _mm_set1_epi64x_rpl(PARASAIL_DEL);
      __m128i vTDiag = _mm_set1_epi64x_rpl(PARASAIL_DIAG);
      __m128i vTDiagE = _mm_set1_epi64x_rpl(PARASAIL_DIAG_E);
      __m128i vTInsE = _mm_set1_epi64x_rpl(PARASAIL_INS_E);
      __m128i vTDiagF = _mm_set1_epi64x_rpl(PARASAIL_DIAG_F);
      __m128i vTDelF = _mm_set1_epi64x_rpl(PARASAIL_DEL_F);
  
      vNegInfFront = _mm_insert_epi64_rpl(vNegInfFront, NEG_LIMIT, 0);
      vSegLenXgap = _mm_add_epi64(vNegInfFront,
              _mm_slli_si128(_mm_set1_epi64x_rpl(-segLen*gap), 8));
  
      /* initialize H and E */
      {
          int32_t index = 0;
          for (i=0; i<segLen; ++i) {
              int32_t segNum = 0;
              __m128i_64_t h;
              __m128i_64_t e;
              for (segNum=0; segNum<segWidth; ++segNum) {
                  int64_t tmp = s1_beg ? 0 : (-open-gap*(segNum*segLen+i));
                  h.v[segNum] = tmp < INT64_MIN ? INT64_MIN : tmp;
                  tmp = tmp - open;
                  e.v[segNum] = tmp < INT64_MIN ? INT64_MIN : tmp;
              }
              _mm_store_si128(&pvH[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 < INT64_MIN ? INT64_MIN : tmp;
          }
      }
  
      {
          __m128i vGapper = _mm_sub_epi64(vZero,vGapO);
          for (i=segLen-1; i>=0; --i) {
              _mm_store_si128(pvGapper+i, vGapper);
              vGapper = _mm_sub_epi64(vGapper, vGapE);
          }
      }
  
      /* outer loop over database sequence */
      for (j=0; j<s2Len; ++j) {
          __m128i vE;
          __m128i vE_ext;
          __m128i vE_opn;
          __m128i vHt;
          __m128i vF;
          __m128i vF_ext;
          __m128i vF_opn;
          __m128i vH;
          __m128i vHp;
          __m128i *pvW;
          __m128i vW;
          __m128i case1;
          __m128i case2;
          __m128i vGapper;
          __m128i vT;
          __m128i vET;
          __m128i vFT;
  
          /* calculate E */
          /* calculate Ht */
          /* calculate F and H first pass */
          vHp = _mm_load_si128(pvH+(segLen-1));
          vHp = _mm_slli_si128(vHp, 8);
          vHp = _mm_insert_epi64_rpl(vHp, boundary[j], 0);
          pvW = pvP + matrix->mapper[(unsigned char)s2[j]]*segLen;
          vHt = _mm_sub_epi64(vNegLimit, pvGapper[0]);
          vF = vNegLimit;
          for (i=0; i<segLen; ++i) {
              vH = _mm_load_si128(pvH+i);
              vE = _mm_load_si128(pvE+i);
              vW = _mm_load_si128(pvW+i);
              vGapper = _mm_load_si128(pvGapper+i);
              vE_opn = _mm_sub_epi64(vH, vGapO);
              vE_ext = _mm_sub_epi64(vE, vGapE);
              case1 = _mm_cmpgt_epi64_rpl(vE_opn, vE_ext);
              vET = _mm_blendv_epi8_rpl(vTInsE, vTDiagE, case1);
              arr_store(result->trace->trace_table, vET, i, segLen, j);
              vE = _mm_max_epi64_rpl(vE_opn, vE_ext);
              vSaturationCheckMin = _mm_min_epi64_rpl(vSaturationCheckMin, vE);
              vGapper = _mm_add_epi64(vHt, vGapper);
              vF = _mm_max_epi64_rpl(vF, vGapper);
              vHp = _mm_add_epi64(vHp, vW);
              vHt = _mm_max_epi64_rpl(vE, vHp);
              _mm_store_si128(pvE+i, vE);
              _mm_store_si128(pvHt+i, vHt);
              _mm_store_si128(pvH+i, vHp);
              vHp = vH;
          }
  
          /* pseudo prefix scan on F and H */
          vHt = _mm_slli_si128(vHt, 8);
          vHt = _mm_insert_epi64_rpl(vHt, boundary[j+1], 0);
          vGapper = _mm_load_si128(pvGapper);
          vGapper = _mm_add_epi64(vHt, vGapper);
          vF = _mm_max_epi64_rpl(vF, vGapper);
          for (i=0; i<segWidth-2; ++i) {
              __m128i vFt = _mm_slli_si128(vF, 8);
              vFt = _mm_add_epi64(vFt, vSegLenXgap);
              vF = _mm_max_epi64_rpl(vF, vFt);
          }
  
          /* calculate final H */
          vF = _mm_slli_si128(vF, 8);
          vF = _mm_add_epi64(vF, vNegInfFront);
          vH = _mm_max_epi64_rpl(vF, vHt);
          for (i=0; i<segLen; ++i) {
              vET = arr_load(result->trace->trace_table, i, segLen, j);
              vHp = _mm_load_si128(pvH+i);
              vHt = _mm_load_si128(pvHt+i);
              vF_opn = _mm_sub_epi64(vH, vGapO);
              vF_ext = _mm_sub_epi64(vF, vGapE);
              vF = _mm_max_epi64_rpl(vF_opn, vF_ext);
              case1 = _mm_cmpgt_epi64_rpl(vF_opn, vF_ext);
              vFT = _mm_blendv_epi8_rpl(vTDelF, vTDiagF, case1);
              vH = _mm_max_epi64_rpl(vHt, vF);
              case1 = _mm_cmpeq_epi64_rpl(vH, vHp);
              case2 = _mm_cmpeq_epi64_rpl(vH, vF);
              vT = _mm_blendv_epi8_rpl(
                      _mm_blendv_epi8_rpl(vTIns, vTDel, case2),
                      vTDiag, case1);
              vT = _mm_or_si128(vT, vET);
              vT = _mm_or_si128(vT, vFT);
              arr_store(result->trace->trace_table, vT, i, segLen, j);
              _mm_store_si128(pvH+i, vH);
              vSaturationCheckMin = _mm_min_epi64_rpl(vSaturationCheckMin, vH);
              vSaturationCheckMin = _mm_min_epi64_rpl(vSaturationCheckMin, vF);
              vSaturationCheckMax = _mm_max_epi64_rpl(vSaturationCheckMax, vH);
          }
  
          /* extract vector containing last value from column */
          {
              __m128i vCompare;
              vH = _mm_load_si128(pvH + offset);
              vCompare = _mm_and_si128(vPosMask, _mm_cmpgt_epi64_rpl(vH, vMaxH));
              vMaxH = _mm_max_epi64_rpl(vH, vMaxH);
              if (_mm_movemask_epi8(vCompare)) {
                  end_ref = j;
              }
          }
      } 
  
      /* max last value from all columns */
      if (s2_end)
      {
          for (k=0; k<position; ++k) {
              vMaxH = _mm_slli_si128(vMaxH, 8);
          }
          score = (int64_t) _mm_extract_epi64_rpl(vMaxH, 1);
          end_query = s1Len-1;
      }
  
      /* max of last column */
      if (s1_end)
      {
          /* Trace the alignment ending position on read. */
          int64_t *t = (int64_t*)pvH;
          int32_t column_len = segLen * segWidth;
          for (i = 0; i<column_len; ++i, ++t) {
              int32_t temp = i / segWidth + i % segWidth * segLen;
              if (temp >= s1Len) continue;
              if (*t > score) {
                  score = *t;
                  end_query = temp;
                  end_ref = s2Len-1;
              }
              else if (*t == score && end_ref == s2Len-1 && temp < end_query) {
                  end_query = temp;
              }
          }
      }
  
      if (!s1_end && !s2_end) {
          /* extract last value from the last column */
          {
              __m128i vH = _mm_load_si128(pvH + offset);
              for (k=0; k<position; ++k) {
                  vH = _mm_slli_si128(vH, 8);
              }
              score = (int64_t) _mm_extract_epi64_rpl (vH, 1);
              end_ref = s2Len - 1;
              end_query = s1Len - 1;
          }
      }
  
      if (_mm_movemask_epi8(_mm_or_si128(
              _mm_cmplt_epi64_rpl(vSaturationCheckMin, vNegLimit),
              _mm_cmpgt_epi64_rpl(vSaturationCheckMax, vPosLimit)))) {
          result->flag |= PARASAIL_FLAG_SATURATED;
          score = 0;
          end_query = 0;
          end_ref = 0;
      }
  
      result->score = score;
      result->end_query = end_query;
      result->end_ref = end_ref;
      result->flag |= PARASAIL_FLAG_SG | PARASAIL_FLAG_SCAN
          | PARASAIL_FLAG_TRACE
          | PARASAIL_FLAG_BITS_64 | PARASAIL_FLAG_LANES_2;
      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;
  
      parasail_free(pvGapper);
      parasail_free(pvH);
      parasail_free(pvHt);
      parasail_free(boundary);
      parasail_free(pvE);
  
      return result;
  }
  
  SG_IMPL_ALL
  SG_IMPL_PROF_ALL
  
  
  