#define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; }
#define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; }
int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float *_qual,
const ka_probpar_t *c, int *state, uint8_t *q)
{
int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float *_qual,
const ka_probpar_t *c, int *state, uint8_t *q)
{
- double **f, **b, m[9], f_sink, sI, sM, pf, pb, pD;
+ double **f, **b, *s, m[9], sI, sM, pb;
float *qual;
uint8_t *ref, *query;
int bw, bw2, i, k, is_diff = 0;
float *qual;
uint8_t *ref, *query;
int bw, bw2, i, k, is_diff = 0;
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));
}
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));
}
// 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);
// 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);
- int beg = 1, end = l_ref, x;
+ int beg = 1, end = l_ref, x, _beg, _end;
+ double sum;
int u, v01;
set_u(u, bw, 0, k); set_u(v01, bw, 0, k-1);
int u, v01;
set_u(u, bw, 0, k); set_u(v01, bw, 0, k-1);
+ // 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;
- double *fi = f[i], *fi1 = f[i-1];
- int beg = 0, end = l_ref, x;
+ double *fi = f[i], *fi1 = f[i-1], sum;
+ int beg = 0, end = l_ref, x, _beg, _end;
e = (ref[k] > 3 || query[i] > 3)? 1. : ref[k] == query[i]? 1. - qual[i] : qual[i] / 3.;
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];
e = (ref[k] > 3 || query[i] > 3)? 1. : ref[k] == query[i]? 1. - qual[i] : qual[i] / 3.;
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, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG
}
// fprintf(stderr, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG
}
+ // rescale
+ s[i] = sum;
+ set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
+ for (k = _beg; k <= _end; ++k) fi[k] /= sum;
- // 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;
+ { // sink (actually f[l_query+1])
+ double sum;
+ for (k = 0, sum = 0.; k <= l_ref; ++k) {
+ int u;
+ set_u(u, bw, l_query, k);
+ if (u < 3 || u >= bw2*3+3) continue;
+ sum += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
+ }
+ s[l_query+1] = sum; // the last scaling factor
for (k = 0; k <= l_ref; ++k) {
int u;
double *bi = b[l_query];
set_u(u, bw, l_query, k);
if (u < 3 || u >= bw2*3+3) continue;
for (k = 0; k <= l_ref; ++k) {
int u;
double *bi = b[l_query];
set_u(u, bw, l_query, k);
if (u < 3 || u >= bw2*3+3) continue;
- int beg = 0, end = l_ref, x;
+ int beg = 0, end = l_ref, x, _beg, _end;
double *bi = b[i], *bi1 = b[i+1];
x = i - bw; beg = beg > x? beg : x;
x = i + bw; end = end < x? end : x;
for (k = end; k >= beg; --k) {
int u, v11, v01, v10;
double e;
double *bi = b[i], *bi1 = b[i+1];
x = i - bw; beg = beg > x? beg : x;
x = i + bw; end = end < x? end : x;
for (k = end; k >= beg; --k) {
int u, v11, v01, v10;
double e;
e = k >= l_ref? 0 : (ref[k+1] > 3 || query[i+1] > 3)? 1. : ref[k+1] == query[i+1]? 1. - qual[i+1] : qual[i+1] / 3.;
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);
bi[u+0] = e * m[0] * bi1[v11+0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2];
e = k >= l_ref? 0 : (ref[k+1] > 3 || query[i+1] > 3)? 1. : ref[k+1] == query[i+1]? 1. - qual[i+1] : qual[i+1] / 3.;
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);
bi[u+0] = e * m[0] * bi1[v11+0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2];
bi[u+2] = e * m[6] * bi1[v11+0] + m[8] * bi[v01+2];
// fprintf(stderr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG
}
bi[u+2] = e * m[6] * bi1[v11+0] + m[8] * bi[v01+2];
// fprintf(stderr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG
}
+ // rescale
+ set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
+ for (k = _beg; k <= _end; ++k) bi[k] /= s[i];
/*** MAP ***/
for (i = 1; i <= l_query; ++i) {
double sum = 0., *fi = f[i], *bi = b[i], max = 0.;
/*** MAP ***/
for (i = 1; i <= l_query; ++i) {
double sum = 0., *fi = f[i], *bi = b[i], max = 0.;
z = fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = k<<2 | 0; sum += z;
z = fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = k<<2 | 1; sum += z;
}
z = fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = k<<2 | 0; sum += z;
z = fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = k<<2 | 1; sum += z;
}
- fprintf(stderr, "[%d,%.10lg,%.10lg],%d,%lg,%d:%d,%lg\n", is_diff, pf, pb, i, sum, max_k>>2, max_k&3, max);
+ fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%d)~%lg\n", pb, sum, i, max_k>>2, max_k&3, max); // DEBUG
-// uint8_t *query = (uint8_t*)"\0\3\3\1";
- uint8_t *query = (uint8_t*)"\1\3\3\1"; // FIXME: the output is not so right given this input!!!
+ uint8_t *query = (uint8_t*)"\0\3\3\1";
+// uint8_t *query = (uint8_t*)"\1\3\3\1"; // FIXME: the output is not so right given this input!!!
static float qual[4] = {.01, .01, .01, .01};
ka_prob_extend(ref, l_ref, query, l_query, qual, &ka_probpar_def, 0, 0);
return 0;
static float qual[4] = {.01, .01, .01, .01};
ka_prob_extend(ref, l_ref, query, l_query, qual, &ka_probpar_def, 0, 0);
return 0;