libparasail-sys 0.2.1

/**
 * @file
 *
 * @author jeffrey.daily@gmail.com
 *
 * Copyright (c) 2015 Battelle Memorial Institute.
 */
#include "config.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"


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_insert_epi8_rpl(__m128i a, int8_t i, const int imm) {
    __m128i_8_t A;
    A.m = a;
    A.v[imm] = i;
    return A.m;
}

static inline __m128i _mm_max_epi8_rpl(__m128i a, __m128i b) {
    __m128i mask = _mm_cmpgt_epi8(a, b);
    a = _mm_and_si128(a, mask);
    b = _mm_andnot_si128(mask, b);
    return _mm_or_si128(a, b);
}

static inline int8_t _mm_extract_epi8_rpl(__m128i a, const int imm) {
    __m128i_8_t A;
    A.m = a;
    return A.v[imm];
}

static inline __m128i _mm_min_epi8_rpl(__m128i a, __m128i b) {
    __m128i mask = _mm_cmpgt_epi8(b, a);
    a = _mm_and_si128(a, mask);
    b = _mm_andnot_si128(mask, b);
    return _mm_or_si128(a, b);
}


#ifdef PARASAIL_TABLE
static inline void arr_store_si128(
        int *array,
        __m128i vWH,
        int32_t i,
        int32_t s1Len,
        int32_t j,
        int32_t s2Len)
{
    if (0 <= i+0 && i+0 < s1Len && 0 <= j-0 && j-0 < s2Len) {
        array[1LL*(i+0)*s2Len + (j-0)] = (int8_t)_mm_extract_epi8_rpl(vWH, 15);
    }
    if (0 <= i+1 && i+1 < s1Len && 0 <= j-1 && j-1 < s2Len) {
        array[1LL*(i+1)*s2Len + (j-1)] = (int8_t)_mm_extract_epi8_rpl(vWH, 14);
    }
    if (0 <= i+2 && i+2 < s1Len && 0 <= j-2 && j-2 < s2Len) {
        array[1LL*(i+2)*s2Len + (j-2)] = (int8_t)_mm_extract_epi8_rpl(vWH, 13);
    }
    if (0 <= i+3 && i+3 < s1Len && 0 <= j-3 && j-3 < s2Len) {
        array[1LL*(i+3)*s2Len + (j-3)] = (int8_t)_mm_extract_epi8_rpl(vWH, 12);
    }
    if (0 <= i+4 && i+4 < s1Len && 0 <= j-4 && j-4 < s2Len) {
        array[1LL*(i+4)*s2Len + (j-4)] = (int8_t)_mm_extract_epi8_rpl(vWH, 11);
    }
    if (0 <= i+5 && i+5 < s1Len && 0 <= j-5 && j-5 < s2Len) {
        array[1LL*(i+5)*s2Len + (j-5)] = (int8_t)_mm_extract_epi8_rpl(vWH, 10);
    }
    if (0 <= i+6 && i+6 < s1Len && 0 <= j-6 && j-6 < s2Len) {
        array[1LL*(i+6)*s2Len + (j-6)] = (int8_t)_mm_extract_epi8_rpl(vWH, 9);
    }
    if (0 <= i+7 && i+7 < s1Len && 0 <= j-7 && j-7 < s2Len) {
        array[1LL*(i+7)*s2Len + (j-7)] = (int8_t)_mm_extract_epi8_rpl(vWH, 8);
    }
    if (0 <= i+8 && i+8 < s1Len && 0 <= j-8 && j-8 < s2Len) {
        array[1LL*(i+8)*s2Len + (j-8)] = (int8_t)_mm_extract_epi8_rpl(vWH, 7);
    }
    if (0 <= i+9 && i+9 < s1Len && 0 <= j-9 && j-9 < s2Len) {
        array[1LL*(i+9)*s2Len + (j-9)] = (int8_t)_mm_extract_epi8_rpl(vWH, 6);
    }
    if (0 <= i+10 && i+10 < s1Len && 0 <= j-10 && j-10 < s2Len) {
        array[1LL*(i+10)*s2Len + (j-10)] = (int8_t)_mm_extract_epi8_rpl(vWH, 5);
    }
    if (0 <= i+11 && i+11 < s1Len && 0 <= j-11 && j-11 < s2Len) {
        array[1LL*(i+11)*s2Len + (j-11)] = (int8_t)_mm_extract_epi8_rpl(vWH, 4);
    }
    if (0 <= i+12 && i+12 < s1Len && 0 <= j-12 && j-12 < s2Len) {
        array[1LL*(i+12)*s2Len + (j-12)] = (int8_t)_mm_extract_epi8_rpl(vWH, 3);
    }
    if (0 <= i+13 && i+13 < s1Len && 0 <= j-13 && j-13 < s2Len) {
        array[1LL*(i+13)*s2Len + (j-13)] = (int8_t)_mm_extract_epi8_rpl(vWH, 2);
    }
    if (0 <= i+14 && i+14 < s1Len && 0 <= j-14 && j-14 < s2Len) {
        array[1LL*(i+14)*s2Len + (j-14)] = (int8_t)_mm_extract_epi8_rpl(vWH, 1);
    }
    if (0 <= i+15 && i+15 < s1Len && 0 <= j-15 && j-15 < s2Len) {
        array[1LL*(i+15)*s2Len + (j-15)] = (int8_t)_mm_extract_epi8_rpl(vWH, 0);
    }
}
#endif

#ifdef PARASAIL_ROWCOL
static inline void arr_store_rowcol(
        int *row,
        int *col,
        __m128i vWH,
        int32_t i,
        int32_t s1Len,
        int32_t j,
        int32_t s2Len)
{
    if (i+0 == s1Len-1 && 0 <= j-0 && j-0 < s2Len) {
        row[j-0] = (int8_t)_mm_extract_epi8_rpl(vWH, 15);
    }
    if (j-0 == s2Len-1 && 0 <= i+0 && i+0 < s1Len) {
        col[(i+0)] = (int8_t)_mm_extract_epi8_rpl(vWH, 15);
    }
    if (i+1 == s1Len-1 && 0 <= j-1 && j-1 < s2Len) {
        row[j-1] = (int8_t)_mm_extract_epi8_rpl(vWH, 14);
    }
    if (j-1 == s2Len-1 && 0 <= i+1 && i+1 < s1Len) {
        col[(i+1)] = (int8_t)_mm_extract_epi8_rpl(vWH, 14);
    }
    if (i+2 == s1Len-1 && 0 <= j-2 && j-2 < s2Len) {
        row[j-2] = (int8_t)_mm_extract_epi8_rpl(vWH, 13);
    }
    if (j-2 == s2Len-1 && 0 <= i+2 && i+2 < s1Len) {
        col[(i+2)] = (int8_t)_mm_extract_epi8_rpl(vWH, 13);
    }
    if (i+3 == s1Len-1 && 0 <= j-3 && j-3 < s2Len) {
        row[j-3] = (int8_t)_mm_extract_epi8_rpl(vWH, 12);
    }
    if (j-3 == s2Len-1 && 0 <= i+3 && i+3 < s1Len) {
        col[(i+3)] = (int8_t)_mm_extract_epi8_rpl(vWH, 12);
    }
    if (i+4 == s1Len-1 && 0 <= j-4 && j-4 < s2Len) {
        row[j-4] = (int8_t)_mm_extract_epi8_rpl(vWH, 11);
    }
    if (j-4 == s2Len-1 && 0 <= i+4 && i+4 < s1Len) {
        col[(i+4)] = (int8_t)_mm_extract_epi8_rpl(vWH, 11);
    }
    if (i+5 == s1Len-1 && 0 <= j-5 && j-5 < s2Len) {
        row[j-5] = (int8_t)_mm_extract_epi8_rpl(vWH, 10);
    }
    if (j-5 == s2Len-1 && 0 <= i+5 && i+5 < s1Len) {
        col[(i+5)] = (int8_t)_mm_extract_epi8_rpl(vWH, 10);
    }
    if (i+6 == s1Len-1 && 0 <= j-6 && j-6 < s2Len) {
        row[j-6] = (int8_t)_mm_extract_epi8_rpl(vWH, 9);
    }
    if (j-6 == s2Len-1 && 0 <= i+6 && i+6 < s1Len) {
        col[(i+6)] = (int8_t)_mm_extract_epi8_rpl(vWH, 9);
    }
    if (i+7 == s1Len-1 && 0 <= j-7 && j-7 < s2Len) {
        row[j-7] = (int8_t)_mm_extract_epi8_rpl(vWH, 8);
    }
    if (j-7 == s2Len-1 && 0 <= i+7 && i+7 < s1Len) {
        col[(i+7)] = (int8_t)_mm_extract_epi8_rpl(vWH, 8);
    }
    if (i+8 == s1Len-1 && 0 <= j-8 && j-8 < s2Len) {
        row[j-8] = (int8_t)_mm_extract_epi8_rpl(vWH, 7);
    }
    if (j-8 == s2Len-1 && 0 <= i+8 && i+8 < s1Len) {
        col[(i+8)] = (int8_t)_mm_extract_epi8_rpl(vWH, 7);
    }
    if (i+9 == s1Len-1 && 0 <= j-9 && j-9 < s2Len) {
        row[j-9] = (int8_t)_mm_extract_epi8_rpl(vWH, 6);
    }
    if (j-9 == s2Len-1 && 0 <= i+9 && i+9 < s1Len) {
        col[(i+9)] = (int8_t)_mm_extract_epi8_rpl(vWH, 6);
    }
    if (i+10 == s1Len-1 && 0 <= j-10 && j-10 < s2Len) {
        row[j-10] = (int8_t)_mm_extract_epi8_rpl(vWH, 5);
    }
    if (j-10 == s2Len-1 && 0 <= i+10 && i+10 < s1Len) {
        col[(i+10)] = (int8_t)_mm_extract_epi8_rpl(vWH, 5);
    }
    if (i+11 == s1Len-1 && 0 <= j-11 && j-11 < s2Len) {
        row[j-11] = (int8_t)_mm_extract_epi8_rpl(vWH, 4);
    }
    if (j-11 == s2Len-1 && 0 <= i+11 && i+11 < s1Len) {
        col[(i+11)] = (int8_t)_mm_extract_epi8_rpl(vWH, 4);
    }
    if (i+12 == s1Len-1 && 0 <= j-12 && j-12 < s2Len) {
        row[j-12] = (int8_t)_mm_extract_epi8_rpl(vWH, 3);
    }
    if (j-12 == s2Len-1 && 0 <= i+12 && i+12 < s1Len) {
        col[(i+12)] = (int8_t)_mm_extract_epi8_rpl(vWH, 3);
    }
    if (i+13 == s1Len-1 && 0 <= j-13 && j-13 < s2Len) {
        row[j-13] = (int8_t)_mm_extract_epi8_rpl(vWH, 2);
    }
    if (j-13 == s2Len-1 && 0 <= i+13 && i+13 < s1Len) {
        col[(i+13)] = (int8_t)_mm_extract_epi8_rpl(vWH, 2);
    }
    if (i+14 == s1Len-1 && 0 <= j-14 && j-14 < s2Len) {
        row[j-14] = (int8_t)_mm_extract_epi8_rpl(vWH, 1);
    }
    if (j-14 == s2Len-1 && 0 <= i+14 && i+14 < s1Len) {
        col[(i+14)] = (int8_t)_mm_extract_epi8_rpl(vWH, 1);
    }
    if (i+15 == s1Len-1 && 0 <= j-15 && j-15 < s2Len) {
        row[j-15] = (int8_t)_mm_extract_epi8_rpl(vWH, 0);
    }
    if (j-15 == s2Len-1 && 0 <= i+15 && i+15 < s1Len) {
        col[(i+15)] = (int8_t)_mm_extract_epi8_rpl(vWH, 0);
    }
}
#endif

#ifdef PARASAIL_TABLE
#define FNAME parasail_sw_table_diag_sse2_128_8
#else
#ifdef PARASAIL_ROWCOL
#define FNAME parasail_sw_rowcol_diag_sse2_128_8
#else
#define FNAME parasail_sw_diag_sse2_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)
{
    /* declare local variables */
    int32_t N = 0;
    int32_t PAD = 0;
    int32_t PAD2 = 0;
    int32_t s1Len = 0;
    int32_t s1Len_PAD = 0;
    int32_t s2Len_PAD = 0;
    int8_t * restrict s1 = NULL;
    int8_t * restrict s2B = NULL;
    int8_t * restrict _H_pr = NULL;
    int8_t * restrict _F_pr = NULL;
    int8_t * restrict s2 = NULL;
    int8_t * restrict H_pr = NULL;
    int8_t * restrict F_pr = NULL;
    parasail_result_t *result = NULL;
    int32_t i = 0;
    int32_t j = 0;
    int32_t end_query = 0;
    int32_t end_ref = 0;
    int8_t NEG_LIMIT = 0;
    int8_t POS_LIMIT = 0;
    int8_t score = 0;
    __m128i vNegLimit;
    __m128i vPosLimit;
    __m128i vSaturationCheckMin;
    __m128i vSaturationCheckMax;
    __m128i vNegInf;
    __m128i vNegInf0;
    __m128i vOpen;
    __m128i vGap;
    __m128i vZero;
    __m128i vOne16;
    __m128i vNegOne16;
    __m128i vN16;
    __m128i vILo16;
    __m128i vIHi16;
    __m128i vJresetLo16;
    __m128i vJresetHi16;
    __m128i vMaxH;
    __m128i vEndILo;
    __m128i vEndIHi;
    __m128i vEndJLo;
    __m128i vEndJHi;
    __m128i vILimit16;
    __m128i vJLimit16;

    /* validate inputs */
    PARASAIL_CHECK_NULL(_s2);
    PARASAIL_CHECK_GT0(s2Len);
    PARASAIL_CHECK_GE0(open);
    PARASAIL_CHECK_GE0(gap);
    PARASAIL_CHECK_NULL(matrix);
    if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
        PARASAIL_CHECK_NULL(_s1);
        PARASAIL_CHECK_GT0(_s1Len);
    }

    /* initialize stack variables */
    N = 16; /* number of values in vector */
    PAD = N-1;
    PAD2 = PAD*2;
    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    s1Len_PAD = s1Len+PAD;
    s2Len_PAD = s2Len+PAD;
    i = 0;
    j = 0;
    end_query = 0;
    end_ref = 0;
    NEG_LIMIT = (-open < matrix->min ? INT8_MIN + open : INT8_MIN - matrix->min) + 1;
    POS_LIMIT = INT8_MAX - matrix->max - 1;
    score = NEG_LIMIT;
    vNegLimit = _mm_set1_epi8(NEG_LIMIT);
    vPosLimit = _mm_set1_epi8(POS_LIMIT);
    vSaturationCheckMin = vPosLimit;
    vSaturationCheckMax = vNegLimit;
    vNegInf = _mm_set1_epi8(NEG_LIMIT);
    vNegInf0 = _mm_srli_si128(vNegInf, 1); /* shift in a 0 */
    vOpen = _mm_set1_epi8(open);
    vGap  = _mm_set1_epi8(gap);
    vZero = _mm_set1_epi8(0);
    vOne16 = _mm_set1_epi16(1);
    vNegOne16 = _mm_set1_epi16(-1);
    vN16 = _mm_set1_epi16(N);
    vILo16 = _mm_set_epi16(8,9,10,11,12,13,14,15);
    vIHi16 = _mm_set_epi16(0,1,2,3,4,5,6,7);
    vJresetLo16 = _mm_set_epi16(-8,-9,-10,-11,-12,-13,-14,-15);
    vJresetHi16 = _mm_set_epi16(0,-1,-2,-3,-4,-5,-6,-7);
    vMaxH = vNegInf;
    vEndILo = vNegInf;
    vEndIHi = vNegInf;
    vEndJLo = vNegInf;
    vEndJHi = vNegInf;
    vILimit16 = _mm_set1_epi16(s1Len);
    vJLimit16 = _mm_set1_epi16(s2Len);

    /* initialize result */
#ifdef PARASAIL_TABLE
    result = parasail_result_new_table1(s1Len, s2Len);
#else
#ifdef PARASAIL_ROWCOL
    result = parasail_result_new_rowcol1(s1Len, s2Len);
#else
    result = parasail_result_new();
#endif
#endif
    if (!result) return NULL;

    /* set known flags */
    result->flag |= PARASAIL_FLAG_SW | PARASAIL_FLAG_DIAG
        | PARASAIL_FLAG_BITS_8 | PARASAIL_FLAG_LANES_16;
#ifdef PARASAIL_TABLE
    result->flag |= PARASAIL_FLAG_TABLE;
#endif
#ifdef PARASAIL_ROWCOL
    result->flag |= PARASAIL_FLAG_ROWCOL;
#endif

    /* initialize heap variables */
    s2B= parasail_memalign_int8_t(16, s2Len+PAD2);
    _H_pr = parasail_memalign_int8_t(16, s2Len+PAD2);
    _F_pr = parasail_memalign_int8_t(16, s2Len+PAD2);
    s2 = s2B+PAD; /* will allow later for negative indices */
    H_pr = _H_pr+PAD;
    F_pr = _F_pr+PAD;

    /* validate heap variables */
    if (!s2B) return NULL;
    if (!_H_pr) return NULL;
    if (!_F_pr) return NULL;

    /* convert _s1 from char to int in range 0-23 */
    if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
        s1 = parasail_memalign_int8_t(16, s1Len+PAD);
        if (!s1) return NULL;
        for (i=0; i<s1Len; ++i) {
            s1[i] = matrix->mapper[(unsigned char)_s1[i]];
        }
        /* pad back of s1 with dummy values */
        for (i=s1Len; i<s1Len_PAD; ++i) {
            s1[i] = 0; /* point to first matrix row because we don't care */
        }
    }

    /* convert _s2 from char to int in range 0-23 */
    for (j=0; j<s2Len; ++j) {
        s2[j] = matrix->mapper[(unsigned char)_s2[j]];
    }
    /* pad front of s2 with dummy values */
    for (j=-PAD; j<0; ++j) {
        s2[j] = 0; /* point to first matrix row because we don't care */
    }
    /* pad back of s2 with dummy values */
    for (j=s2Len; j<s2Len_PAD; ++j) {
        s2[j] = 0; /* point to first matrix row because we don't care */
    }

    /* set initial values for stored row */
    for (j=0; j<s2Len; ++j) {
        H_pr[j] = 0;
        F_pr[j] = NEG_LIMIT;
    }
    /* pad front of stored row values */
    for (j=-PAD; j<0; ++j) {
        H_pr[j] = NEG_LIMIT;
        F_pr[j] = NEG_LIMIT;
    }
    /* pad back of stored row values */
    for (j=s2Len; j<s2Len+PAD; ++j) {
        H_pr[j] = NEG_LIMIT;
        F_pr[j] = NEG_LIMIT;
    }

    /* iterate over query sequence */
    for (i=0; i<s1Len; i+=N) {
        __m128i vNH = vNegInf0;
        __m128i vWH = vNegInf0;
        __m128i vE = vNegInf;
        __m128i vF = vNegInf;
        __m128i vJLo16 = vJresetLo16;
        __m128i vJHi16 = vJresetHi16;
        const int * const restrict matrow0 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+0] : ((i+0 >= s1Len) ? s1Len-1 : i+0))];
        const int * const restrict matrow1 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+1] : ((i+1 >= s1Len) ? s1Len-1 : i+1))];
        const int * const restrict matrow2 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+2] : ((i+2 >= s1Len) ? s1Len-1 : i+2))];
        const int * const restrict matrow3 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+3] : ((i+3 >= s1Len) ? s1Len-1 : i+3))];
        const int * const restrict matrow4 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+4] : ((i+4 >= s1Len) ? s1Len-1 : i+4))];
        const int * const restrict matrow5 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+5] : ((i+5 >= s1Len) ? s1Len-1 : i+5))];
        const int * const restrict matrow6 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+6] : ((i+6 >= s1Len) ? s1Len-1 : i+6))];
        const int * const restrict matrow7 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+7] : ((i+7 >= s1Len) ? s1Len-1 : i+7))];
        const int * const restrict matrow8 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+8] : ((i+8 >= s1Len) ? s1Len-1 : i+8))];
        const int * const restrict matrow9 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+9] : ((i+9 >= s1Len) ? s1Len-1 : i+9))];
        const int * const restrict matrow10 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+10] : ((i+10 >= s1Len) ? s1Len-1 : i+10))];
        const int * const restrict matrow11 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+11] : ((i+11 >= s1Len) ? s1Len-1 : i+11))];
        const int * const restrict matrow12 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+12] : ((i+12 >= s1Len) ? s1Len-1 : i+12))];
        const int * const restrict matrow13 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+13] : ((i+13 >= s1Len) ? s1Len-1 : i+13))];
        const int * const restrict matrow14 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+14] : ((i+14 >= s1Len) ? s1Len-1 : i+14))];
        const int * const restrict matrow15 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+15] : ((i+15 >= s1Len) ? s1Len-1 : i+15))];
        __m128i vIltLimit = _mm_packs_epi16(
                    _mm_cmplt_epi16(vILo16, vILimit16),
                    _mm_cmplt_epi16(vIHi16, vILimit16));
        /* iterate over database sequence */
        for (j=0; j<s2Len+PAD; ++j) {
            __m128i vMat;
            __m128i vNWH = vNH;
            vNH = _mm_srli_si128(vWH, 1);
            vNH = _mm_insert_epi8_rpl(vNH, H_pr[j], 15);
            vF = _mm_srli_si128(vF, 1);
            vF = _mm_insert_epi8_rpl(vF, F_pr[j], 15);
            vF = _mm_max_epi8_rpl(
                    _mm_subs_epi8(vNH, vOpen),
                    _mm_subs_epi8(vF, vGap));
            vE = _mm_max_epi8_rpl(
                    _mm_subs_epi8(vWH, vOpen),
                    _mm_subs_epi8(vE, vGap));
            vMat = _mm_set_epi8(
                    matrow0[s2[j-0]],
                    matrow1[s2[j-1]],
                    matrow2[s2[j-2]],
                    matrow3[s2[j-3]],
                    matrow4[s2[j-4]],
                    matrow5[s2[j-5]],
                    matrow6[s2[j-6]],
                    matrow7[s2[j-7]],
                    matrow8[s2[j-8]],
                    matrow9[s2[j-9]],
                    matrow10[s2[j-10]],
                    matrow11[s2[j-11]],
                    matrow12[s2[j-12]],
                    matrow13[s2[j-13]],
                    matrow14[s2[j-14]],
                    matrow15[s2[j-15]]
                    );
            vNWH = _mm_adds_epi8(vNWH, vMat);
            vWH = _mm_max_epi8_rpl(vNWH, vE);
            vWH = _mm_max_epi8_rpl(vWH, vF);
            vWH = _mm_max_epi8_rpl(vWH, vZero);
            /* as minor diagonal vector passes across the j=-1 boundary,
             * assign the appropriate boundary conditions */
            {
                __m128i cond = _mm_packs_epi16(
                        _mm_cmpeq_epi16(vJLo16,vNegOne16),
                        _mm_cmpeq_epi16(vJHi16,vNegOne16));
                vWH = _mm_andnot_si128(cond, vWH);
                vF = _mm_blendv_epi8_rpl(vF, vNegInf, cond);
                vE = _mm_blendv_epi8_rpl(vE, vNegInf, cond);
            }
            /* cannot start checking sat until after J clears boundary */
            if (j > PAD) {
                vSaturationCheckMin = _mm_min_epi8_rpl(vSaturationCheckMin, vWH);
                vSaturationCheckMax = _mm_max_epi8_rpl(vSaturationCheckMax, vWH);
            }
#ifdef PARASAIL_TABLE
            arr_store_si128(result->tables->score_table, vWH, i, s1Len, j, s2Len);
#endif
#ifdef PARASAIL_ROWCOL
            arr_store_rowcol(result->rowcols->score_row, result->rowcols->score_col, vWH, i, s1Len, j, s2Len);
#endif
            H_pr[j-15] = (int8_t)_mm_extract_epi8_rpl(vWH,0);
            F_pr[j-15] = (int8_t)_mm_extract_epi8_rpl(vF,0);
            /* as minor diagonal vector passes across table, extract
             * max values within the i,j bounds */
            {
                __m128i cond_valid_J = _mm_and_si128(
                        _mm_packs_epi16(
                            _mm_cmpgt_epi16(vJLo16, vNegOne16),
                            _mm_cmpgt_epi16(vJHi16, vNegOne16)),
                        _mm_packs_epi16(
                            _mm_cmplt_epi16(vJLo16, vJLimit16),
                            _mm_cmplt_epi16(vJHi16, vJLimit16)));
                __m128i cond_valid_IJ = _mm_and_si128(cond_valid_J, vIltLimit);
                __m128i cond_eq = _mm_cmpeq_epi8(vWH, vMaxH);
                __m128i cond_max = _mm_cmpgt_epi8(vWH, vMaxH);
                __m128i cond_all = _mm_and_si128(cond_max, cond_valid_IJ);
                __m128i cond_Jlt = _mm_packs_epi16(
                        _mm_cmplt_epi16(vJLo16, vEndJLo),
                        _mm_cmplt_epi16(vJHi16, vEndJHi));
                __m128i cond_lo = _mm_unpacklo_epi8(cond_all, cond_all);
                __m128i cond_hi = _mm_unpackhi_epi8(cond_all, cond_all);
                vMaxH = _mm_blendv_epi8_rpl(vMaxH, vWH, cond_all);
                vEndILo = _mm_blendv_epi8_rpl(vEndILo, vILo16, cond_lo);
                vEndIHi = _mm_blendv_epi8_rpl(vEndIHi, vIHi16, cond_hi);
                vEndJLo = _mm_blendv_epi8_rpl(vEndJLo, vJLo16, cond_lo);
                vEndJHi = _mm_blendv_epi8_rpl(vEndJHi, vJHi16, cond_hi);
                cond_all = _mm_and_si128(cond_Jlt, cond_eq);
                cond_all = _mm_and_si128(cond_all, cond_valid_IJ);
                cond_lo = _mm_unpacklo_epi8(cond_all, cond_all);
                cond_hi = _mm_unpackhi_epi8(cond_all, cond_all);
                vEndILo = _mm_blendv_epi8_rpl(vEndILo, vILo16, cond_lo);
                vEndIHi = _mm_blendv_epi8_rpl(vEndIHi, vIHi16, cond_hi);
                vEndJLo = _mm_blendv_epi8_rpl(vEndJLo, vJLo16, cond_lo);
                vEndJHi = _mm_blendv_epi8_rpl(vEndJHi, vJHi16, cond_hi);
            }
            vJLo16 = _mm_add_epi16(vJLo16, vOne16);
            vJHi16 = _mm_add_epi16(vJHi16, vOne16);
        }
        vILo16 = _mm_add_epi16(vILo16, vN16);
        vIHi16 = _mm_add_epi16(vIHi16, vN16);
    }

    /* alignment ending position */
    {
        int8_t *t = (int8_t*)&vMaxH;
        int16_t *ilo = (int16_t*)&vEndILo;
        int16_t *jlo = (int16_t*)&vEndJLo;
        int16_t *ihi = (int16_t*)&vEndIHi;
        int16_t *jhi = (int16_t*)&vEndJHi;
        int32_t k;
        for (k=0; k<N/2; ++k, ++t, ++ilo, ++jlo) {
            if (*t > score) {
                score = *t;
                end_query = *ilo;
                end_ref = *jlo;
            }
            else if (*t == score) {
                if (*jlo < end_ref) {
                    end_query = *ilo;
                    end_ref = *jlo;
                }
                else if (*jlo == end_ref && *ilo < end_query) {
                    end_query = *ilo;
                    end_ref = *jlo;
                }
            }
        }
        for (k=N/2; k<N; ++k, ++t, ++ihi, ++jhi) {
            if (*t > score) {
                score = *t;
                end_query = *ihi;
                end_ref = *jhi;
            }
            else if (*t == score) {
                if (*jhi < end_ref) {
                    end_query = *ihi;
                    end_ref = *jhi;
                }
                else if (*jhi == end_ref && *ihi < end_query) {
                    end_query = *ihi;
                    end_ref = *jhi;
                }
            }
        }
    }

    if (_mm_movemask_epi8(_mm_or_si128(
            _mm_cmplt_epi8(vSaturationCheckMin, vNegLimit),
            _mm_cmpgt_epi8(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;

    parasail_free(_F_pr);
    parasail_free(_H_pr);
    parasail_free(s2B);
    if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
        parasail_free(s1);
    }

    return result;
}