- double **f, **b, m[9], f_sink, sI, sM, pf, pb;
- float *qual;
- uint8_t *ref, *query;
- int bw, bw2, i, k;
- /*** initialization ***/
- ref = _ref - 1;
- query = _query - 1;
- qual = _qual - 1;
- bw = c->bw;
- bw2 = c->bw * 2 + 1;
- f = calloc(l_query+1, sizeof(void*));
- b = calloc(l_query+1, sizeof(void*));
- for (i = 0; i <= l_query; ++i) {
- f[i] = calloc(bw2 * 3 + 6, sizeof(double));
- b[i] = calloc(bw2 * 3 + 6, sizeof(double));
- }
- // initialize m
- sM = sI = 1. / (2 * l_query + 1);
- m[0*3+0] = (1 - c->d - c->d) * (1 - sM);
- m[0*3+1] = m[0*3+2] = c->d * (1 - sM);
- m[1*3+0] = (1 - c->e) * (1 - sI);
- m[1*3+1] = c->e * (1 - sI);
- m[1*3+2] = 0.;
- m[2*3+0] = 1 - c->e;
- m[2*3+1] = 0.;
- m[2*3+2] = c->e;
- /*** forward ***/
- // f[0]
- set_u(k, bw, 0, 0);
- f[0][k] = 1.;
- // f[1..l_query]; core loop
- for (i = 1; i <= l_query; ++i) {
- double *fi = f[i], *fi1 = f[i-1];
- int beg = 0, end = l_ref, x;
- x = i - bw; beg = beg > x? beg : x;
- x = i + bw; end = end < x? end : x;
- for (k = beg; k <= end; ++k) {
- int u, v11, v01, v10;
- double e;
- e = (ref[k] == 4 || query[i] == 4)? 1. : ref[k] == query[i]? 1. - qual[i] : qual[i]; // FIXME: can be better
- set_u(u, bw, i, k);
- set_u(v11, bw, i-1, k-1);
- set_u(v10, bw, i-1, k);
- set_u(v01, bw, i, k-1);
- fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]);
- fi[u+1] = .25 * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
- fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
- fprintf(stderr, "{%d,%d}@%d %.10lg,%.10lg,%.10lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]);
- }
- }
- // sink
- for (k = 0, f_sink = 0.; k <= l_ref; ++k) {
- int u;
- set_u(u, bw, l_query, k);
- if (u < 3 || u >= bw2*3+3) continue;
- f_sink += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
+
+#define __score_aux(_p, _q0, _sc, _io, _ie, _do, _de) { \
+ int t1, t2; \
+ score_aux_t *_q; \
+ _q = _q0; \
+ _p->M = _q->M >= _q->I? _q->M : _q->I; \
+ _p->M = _p->M >= _q->D? _p->M : _q->D; \
+ _p->M += (_sc); \
+ ++_q; t1 = _q->M - _io - _ie; t2 = _q->I - _ie; _p->I = t1 >= t2? t1 : t2; \
+ _q = _p-1; t1 = _q->M - _do - _de; t2 = _q->D - _de; _p->D = t1 >= t2? t1 : t2; \