simplify a bit

diff --git a/ksw.c b/ksw.c
index 24c9e8c814fd2db93b74b17dee2da1d2b1dd5e24..fe83a119b6e409b4d87200eba6af698dfc7bfad5 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -38,7 +38,7 @@
 
 struct _ksw_query_t {
        int slen;
-       uint8_t shift;
+       uint8_t shift, mdiff;
        __m128i *qp, *H0, *H1, *E;
 };
 
@@ -58,9 +58,12 @@ ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_
        q->slen = slen;
        // compute shift
        tmp = m * m;
-       for (a = 0, q->shift = 127; a < tmp; ++a) // find the minimum score (should be negative)
+       for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score
                if (mat[a] < (int8_t)q->shift) q->shift = mat[a];
+               if (mat[a] > (int8_t)q->mdiff) q->mdiff = mat[a];
+       }
        q->shift = 256 - q->shift; // NB: q->shift is uint8_t
+       q->mdiff += q->shift; // this is the difference between the min and max scores
        // An example: p=8, qlen=19, slen=3 and segmentation:
        //  {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}
        t = (int8_t*)q->qp;
@@ -79,13 +82,6 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
        int slen, i, score;
        __m128i zero, gapo, gape, shift, gmax, *H0, *H1, *E;
 
-#define __set_16(ret, xx) do { \
-               uint16_t t16 = ((uint16_t)(xx) << 8) | ((uint16_t)(xx) & 0x00ff); \
-               (ret) = _mm_insert_epi16((ret), t16, 0); \
-               (ret) = _mm_shufflelo_epi16((ret), 0); \
-               (ret) = _mm_shuffle_epi32((ret), 0); \
-       } while (0)
-
 #define __max_16(ret, xx) do { \
                (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
                (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 4)); \
@@ -95,11 +91,10 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
        } while (0)
 
        // initialization
-       zero = _mm_set1_epi32(0);
-       shift = gmax = gapo = gape = zero; // only to avoid gcc warnings
-       __set_16(gapo, _o + _e);
-       __set_16(gape, _e);
-       __set_16(shift, q->shift);
+       gmax = zero = _mm_set1_epi32(0);
+       gapo = _mm_set1_epi8(_o + _e);
+       gape = _mm_set1_epi8(_e);
+       shift = _mm_set1_epi8(q->shift);
        H0 = q->H0; H1 = q->H1; E = q->E;
        slen = q->slen;
        for (i = 0; i < slen; ++i) {