- double **f, **b, *s, m[9], sI, sM, pb;
- float *qual;
- uint8_t *ref, *query;
- int bw, bw2, i, k, is_diff = 0;
-
- /*** initialization ***/
- ref = _ref - 1; // change to 1-based coordinate
- query = _query - 1;
- qual = _qual - 1;
- bw = c->bw;
- bw2 = c->bw * 2 + 1;
- // allocate forward and backward matrices f[][] and b[][]
- 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)); // FIXME: this is over-allocated for very short seqs
- b[i] = calloc(bw2 * 3 + 6, sizeof(double));
- }
- s = calloc(l_query+2, sizeof(double)); // s[] is the scaling factor to avoid underflow
- // initialize transition probability
- sM = sI = 1. / (2 * l_query + 2); // the value here seems not to affect results; FIXME: need proof
- 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.;
- { // write D cells
- int beg = 1, end = l_ref, x, _beg, _end;
- double sum;
- x = 0 - bw; beg = beg > x? beg : x;
- x = 0 + bw; end = end < x? end : x;
- for (k = beg, sum = 0.; k <= end; ++k) {
- int u, v01;
- set_u(u, bw, 0, k); set_u(v01, bw, 0, k-1);
- sum += (f[0][u+2] = m[2] * f[0][v01+0] + m[8] * f[0][v01+2]);
- }
- // rescale to avoid floating point underflow
- s[0] = sum;
- set_u(_beg, bw, 0, 0); set_u(_end, bw, 0, end); _end += 2;
- for (k = _beg; k <= _end; ++k) f[0][k] /= sum;
+
+#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; \