allocate query profile in one memory block

diff --git a/ksw.c b/ksw.c
index c49b2dfd9479a783e73ea2a6ff8a3f6e67df7378..ff59a0df265cf31bd83d150da9271f65c2942bb8 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -17,7 +17,6 @@ struct _ksw_query_t {
        int slen;
        uint8_t shift;
        __m128i *qp, *H0, *H1, *E;
-       uint8_t *mem;
 };
 
 ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat)
@@ -25,17 +24,16 @@ ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_
        ksw_query_t *q;
        uint8_t *aligned;
        int8_t *t;
-       int qlenp, slen, a, tmp;
+       int qlen16, slen, a, tmp;
 
-       q = calloc(1, sizeof(ksw_query_t));
-       q->slen = slen = (qlen + p - 1) / p; // length of segment
-       qlenp = slen * p; // qlenp can be divided by p
-       q->mem = malloc(64 + qlenp * (m + 2));
-       aligned = (uint8_t*)(((size_t)q->mem + 15) & ~0xful); // align memory
-       q->qp = (__m128i*)aligned;
-       q->H0 = q->qp + qlenp * m;
-       q->H1 = q->H0 + qlenp;
-       q->E  = q->H1 + qlenp;
+       slen = (qlen + p - 1) / p;
+       qlen16 = (qlen + 15) >> 4 << 4;
+       q = malloc(sizeof(ksw_query_t) + 256 + qlen16 * (m + 2)); // a single block of memory
+       q->slen = slen;
+       q->qp = (__m128i*)(((size_t)q + sizeof(ksw_query_t) + 15) >> 4 << 4);
+       q->H0 = q->qp + qlen16 * m;
+       q->H1 = q->H0 + qlen16;
+       q->E  = q->H1 + qlen16;
        // compute shift
        tmp = m * m;
        for (a = 0, q->shift = 127; a < tmp; ++a) // find the minimum score (should be negative)
@@ -48,7 +46,7 @@ ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_
                int i, k;
                const int8_t *ma = mat + a * m;
                for (i = 0; i < slen; ++i)
-                       for (k = i; k < qlenp; k += slen) { // p iterations
+                       for (k = i; k < qlen16; k += slen) { // p iterations
                                *t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
                                //printf("%d,%d,%d,%d\n", a, i, k, *(t-1));
                        }
@@ -56,12 +54,6 @@ ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_
        return q;
 }
 
-void ksw_qdestroy(ksw_query_t *q)
-{
-       if (!q) return;
-       free(q->mem); free(q);
-}
-
 int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, unsigned _e) // the first gap costs -(_o+_e)
 {
        int slen, i, score;
@@ -151,7 +143,7 @@ int main()
        uint8_t *q = (uint8_t*)"\1\1";
        ksw_query_t *qq = ksw_qinit(2, q, 16, 2, mat);
        int s = ksw_sse2_16(qq, 6, t, 5, 2);
-       ksw_qdestroy(qq);
+       free(qq);
        printf("%d\n", s);
        return 0;
 }

diff --git a/ksw.h b/ksw.h
index a3e858079e003b74fefb7c788be69d6cc4c591f9..95254919eb5f34f35c7ab904940069c4ea0a39ce 100644 (file)
--- a/ksw.h
+++ b/ksw.h
@@ -9,7 +9,6 @@ extern "C" {
 #endif
 
 ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat);
-void ksw_qdestroy(ksw_query_t *q);
 int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned o, unsigned e); // first gap costs -(o+e)
 
 #ifdef __cplusplus