keep the ending position

diff --git a/ksw.c b/ksw.c
index 7cb5d89f1804ed3b319bd75a1d0e36e6dcd390fa..0c78f9e6148fce35f3ea657cf54c0b011164c0cb 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -37,9 +37,9 @@
 #endif
 
 struct _ksw_query_t {
-       int slen;
+       int qlen, slen;
        uint8_t shift, mdiff;
-       __m128i *qp, *H0, *H1, *E;
+       __m128i *qp, *H0, *H1, *E, *Hmax;
 };
 
 ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_t *mat)
@@ -50,12 +50,13 @@ ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_
 
        slen = (qlen + p - 1) / p;
        qlen16 = (qlen + 15) >> 4 << 4;
-       q = malloc(sizeof(ksw_query_t) + 256 + qlen16 * (m + 3)); // a single block of memory
+       q = malloc(sizeof(ksw_query_t) + 256 + qlen16 * (m + 4)); // a single block of memory
        q->qp = (__m128i*)(((size_t)q + sizeof(ksw_query_t) + 15) >> 4 << 4); // align memory
        q->H0 = q->qp + (qlen16 * m) / 16;
        q->H1 = q->H0 + qlen16 / 16;
        q->E  = q->H1 + qlen16 / 16;
-       q->slen = slen;
+       q->Hmax = q->E + qlen16 / 16;
+       q->slen = slen; q->qlen = qlen;
        // compute shift
        tmp = m * m;
        for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score
@@ -77,10 +78,10 @@ ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_
        return 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 ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a) // the first gap costs -(_o+_e)
 {
        int slen, i, sum, score;
-       __m128i zero, gapo, gape, shift, gmax, reduce, thres, *H0, *H1, *E;
+       __m128i zero, gapoe, gape, shift, gmax, reduce, thres, *H0, *H1, *E, *Hmax;
 
 #define __max_16(ret, xx) do { \
                (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
@@ -91,13 +92,14 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
        } while (0)
 
        // initialization
+       a->te = -1;
        gmax = zero = _mm_set1_epi32(0);
-       gapo = _mm_set1_epi8(_o + _e);
-       gape = _mm_set1_epi8(_e);
+       gapoe = _mm_set1_epi8(a->gapo + a->gape);
+       gape = _mm_set1_epi8(a->gape);
        shift = _mm_set1_epi8(q->shift);
        thres = _mm_set1_epi8(254 - q->mdiff); // when max score exceeds this, shift all scores by "reduce" below
        reduce = _mm_set1_epi8(127);
-       H0 = q->H0; H1 = q->H1; E = q->E;
+       H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
        slen = q->slen;
        for (i = 0; i < slen; ++i) {
                _mm_store_si128(E + i, zero);
@@ -124,7 +126,7 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
                        max = _mm_max_epu8(max, h); // set max
                        _mm_store_si128(H1 + j, h); // save to H'(i,j)
                        // now compute E'(i+1,j)
-                       h = _mm_subs_epu8(h, gapo); // h=H'(i,j)-gapo
+                       h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo
                        e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape
                        e = _mm_max_epu8(e, h); // e=E'(i+1,j)
                        _mm_store_si128(E + j, e); // save to E'(i+1,j)
@@ -134,38 +136,55 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
                        // get H'(i-1,j) and prepare for the next j
                        h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
                }
-               gmax = _mm_max_epu8(gmax, max); // NB: H(i,j) updated in the lazy-F loop cannot exceed max
                // NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
-               for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3
+               for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3; NB: H(i,j) updated in the lazy-F loop cannot exceed max
                        f = _mm_slli_si128(f, 1);
                        for (j = 0; LIKELY(j < slen); ++j) {
                                h = _mm_load_si128(H1 + j);
                                h = _mm_max_epu8(h, f); // h=H'(i,j)
                                _mm_store_si128(H1 + j, h);
-                               h = _mm_subs_epu8(h, gapo);
+                               h = _mm_subs_epu8(h, gapoe);
                                f = _mm_subs_epu8(f, gape);
                                cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
                                if (UNLIKELY(cmp == 0xffff)) goto end_loop;
                        }
                }
 end_loop:
-               if (_mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(gmax, thres), zero)) != 0xffff) { // reduce
-                       /* When overflow is going to happen, subtract 127 from all scores. This heuristic
-                        * may miss the best alignment, but in practice this should happen very rarely. */
-                       sum += 127;
-                       gmax = _mm_subs_epu8(gmax, reduce);
-                       //int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&thres)[k]);printf("\n");
-                       for (j = 0; LIKELY(j < slen); ++j) {
-                               h = _mm_subs_epu8(_mm_load_si128(H1 + j), reduce);
-                               _mm_store_si128(H1 + j, h);
-                               e = _mm_subs_epu8(_mm_load_si128(E + j), reduce);
-                               _mm_store_si128(E + j, e);
+               if (_mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(max, gmax), zero)) != 0xffff) { // if max > gmax at any position
+                       int imax, igmax;
+                       __max_16(imax, max);   // maximum in max
+                       __max_16(igmax, gmax); // maximum in gmax
+                       if (imax > igmax) { // if the max has been updated
+                               a->te = i; // the end position on the target
+                               for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
+                                       _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
+                       }
+                       gmax = _mm_max_epu8(gmax, max); // update gmax
+                       if (_mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(gmax, thres), zero)) != 0xffff) { // reduce
+                               /* When overflow is going to happen, subtract 127 from all scores. This heuristic
+                                * may miss the best alignment, but in practice this should happen very rarely. */
+                               sum += 127;
+                               gmax = _mm_subs_epu8(gmax, reduce);
+                               //int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&thres)[k]);printf("\n");
+                               for (j = 0; LIKELY(j < slen); ++j) {
+                                       h = _mm_subs_epu8(_mm_load_si128(H1 + j), reduce);
+                                       _mm_store_si128(H1 + j, h);
+                                       e = _mm_subs_epu8(_mm_load_si128(E + j), reduce);
+                                       _mm_store_si128(E + j, e);
+                               }
                        }
                }
                S = H1; H1 = H0; H0 = S; // swap H0 and H1
        }
        __max_16(score, gmax);
-       return score + sum;
+       a->score = score + sum;
+       { // get a->qe, the end of query match
+               int max = -1;
+               uint8_t *t = (uint8_t*)Hmax;
+               for (i = 0, score = 0, a->qe = -1; i < q->qlen; ++i, ++t)
+                       if ((int)*t > max) max = *t, a->qe = i / 16 + i % 16 * slen;
+       }
+       return a->score;
 }
 
 /*******************************************
@@ -201,22 +220,25 @@ unsigned char seq_nt4_table[256] = {
 
 int main(int argc, char *argv[])
 {
-       int c, sa = 1, sb = 3, sq = 5, sr = 2, i, j, k, forward_only = 0;
+       int c, sa = 1, sb = 3, i, j, k, forward_only = 0;
        int8_t mat[25];
+       ksw_aux_t a;
        gzFile fpt, fpq;
        kseq_t *kst, *ksq;
        // parse command line
-       while ((c = getopt(argc, argv, "a:b:q:r:f")) >= 0) {
+       a.gapo = 5; a.gape = 2; a.T = 20;
+       while ((c = getopt(argc, argv, "a:b:q:r:ft:")) >= 0) {
                switch (c) {
                        case 'a': sa = atoi(optarg); break;
                        case 'b': sb = atoi(optarg); break;
-                       case 'q': sq = atoi(optarg); break;
-                       case 'r': sr = atoi(optarg); break;
+                       case 'q': a.gapo = atoi(optarg); break;
+                       case 'r': a.gape = atoi(optarg); break;
+                       case 't': a.T = atoi(optarg); break;
                        case 'f': forward_only = 1; break;
                }
        }
        if (optind + 2 > argc) {
-               fprintf(stderr, "Usage: ksw [-a%d] [-b%d] [-q%d] [-r%d] <target.fa> <query.fa>\n", sa, sb, sq, sr);
+               fprintf(stderr, "Usage: ksw [-a%d] [-b%d] [-q%d] [-r%d] <target.fa> <query.fa>\n", sa, sb, a.gapo, a.gape);
                return 1;
        }
        // initialize scoring matrix
@@ -248,11 +270,11 @@ int main(int argc, char *argv[])
                while (kseq_read(kst) > 0) {
                        int s;
                        for (i = 0; i < kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];
-                       s = ksw_sse2_16(q[0], kst->seq.l, (uint8_t*)kst->seq.s, sq, sr);
-                       printf("%s\t%s\t+\t%d\n", ksq->name.s, kst->name.s, s);
+                       s = ksw_sse2_16(q[0], kst->seq.l, (uint8_t*)kst->seq.s, &a);
+                       printf("%s\t%s\t+\t%d\t%d\t%d\n", ksq->name.s, kst->name.s, s, a.te+1, a.qe+1);
                        if (q[1]) {
-                               s = ksw_sse2_16(q[1], kst->seq.l, (uint8_t*)kst->seq.s, sq, sr);
-                               printf("%s\t%s\t-\t%d\n", ksq->name.s, kst->name.s, s);
+                               s = ksw_sse2_16(q[1], kst->seq.l, (uint8_t*)kst->seq.s, &a);
+                               printf("%s\t%s\t-\t%d\t%d\t%d\n", ksq->name.s, kst->name.s, s, a.te+1, a.qe+1);
                        }
                }
                free(q[0]); free(q[1]);

diff --git a/ksw.h b/ksw.h
index 83fe224a6e5e9c5f95942e0cb4f1822974d59919..35ad212ec2c7ba261f3c2f04bf21e2607c883f6d 100644 (file)
--- a/ksw.h
+++ b/ksw.h
@@ -4,12 +4,20 @@
 struct _ksw_query_t;
 typedef struct _ksw_query_t ksw_query_t;
 
+typedef struct {
+       // input
+       unsigned gapo, gape; // the first gap costs gapo+gape
+       unsigned T; // threshold
+       // output
+       int score, te, qe;
+} ksw_aux_t;
+
 #ifdef __cplusplus
 extern "C" {
 #endif
 
 ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_t *mat); // to free, simply call free()
-int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned o, unsigned e); // first gap costs -(o+e)
+int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a);
 
 #ifdef __cplusplus
 }