struct __bcf_p1aux_t {
int n, M;
double *q2p, *pdg; // pdg -> P(D|g)
- double *phi, *CMk; // CMk=\binom{M}{k}
+ double *phi;
double *z, *zswap; // aux for afs
double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
const uint8_t *PL; // point to PL
ma->q2p = calloc(256, sizeof(double));
ma->pdg = calloc(3 * ma->n, sizeof(double));
ma->phi = calloc(ma->M + 1, sizeof(double));
- ma->CMk = calloc(ma->M + 1, sizeof(double));
ma->z = calloc(2 * ma->n + 1, sizeof(double));
ma->zswap = calloc(2 * ma->n + 1, sizeof(double));
ma->afs = calloc(2 * ma->n + 1, sizeof(double));
ma->afs1 = calloc(2 * ma->n + 1, sizeof(double));
for (i = 0; i < 256; ++i)
ma->q2p[i] = pow(10., -i / 10.);
- for (i = 0; i <= ma->M; ++i)
- ma->CMk[i] = exp(lgamma(ma->M + 1) - lgamma(i + 1) - lgamma(ma->M - i + 1));
bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
return ma;
}
{
if (ma) {
free(ma->q2p); free(ma->pdg);
- free(ma->phi); free(ma->CMk);
+ free(ma->phi);
free(ma->z); free(ma->zswap);
free(ma->afs); free(ma->afs1);
free(ma);
return q<<2|max_i;
}
-static void mc_cal_z(bcf_p1aux_t *ma)
+#define TINY 1e-20
+
+static void mc_cal_y(bcf_p1aux_t *ma)
{
- double *z[2], *tmp, *pdg;
- int i, j;
+ double *z[2], *tmp, *pdg, last_min, last_max;
+ int k, j;
z[0] = ma->z;
z[1] = ma->zswap;
pdg = ma->pdg;
z[0][0] = 1.; z[0][1] = z[0][2] = 0.;
+ last_min = last_max = 0;
for (j = 0; j < ma->n; ++j) {
- int max = (j + 1) * 2;
- double p[3];
+ int _min = last_min, _max = last_max;
+ double p[3], sum;
pdg = ma->pdg + j * 3;
p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
- z[1][0] = p[0] * z[0][0];
- z[1][1] = p[0] * z[0][1] + p[1] * z[0][0];
- for (i = 2; i <= max; ++i)
- z[1][i] = p[0] * z[0][i] + p[1] * z[0][i-1] + p[2] * z[0][i-2];
- if (j < ma->n - 1) z[1][max+1] = z[1][max+2] = 0.;
+// for (; _min < _max && z[0][_min] < TINY; ++_min) z[1][_min] = 0.;
+// for (; _max > _min && z[0][_max] < TINY; --_max) z[1][_max] = 0.;
+ _max += 2;
+ if (_min == 0)
+ k = 0, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k];
+ if (_min <= 1)
+ k = 1, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k] + k*(2*j+2-k) * p[1] * z[0][k-1];
+ for (k = _min < 2? 2 : _min; k <= _max; ++k)
+ z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k]
+ + k*(2*j+2-k) * p[1] * z[0][k-1]
+ + k*(k-1)* p[2] * z[0][k-2];
+ for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+ last_min = _min; last_max = _max;
}
if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
}
int k;
long double sum = 0.;
memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
- mc_cal_z(ma);
+ mc_cal_y(ma);
for (k = 0, sum = 0.; k <= ma->M; ++k)
- sum += (long double)ma->phi[k] * ma->z[k] / ma->CMk[k];
+ sum += (long double)ma->phi[k] * ma->z[k];
for (k = 0; k <= ma->M; ++k) {
- ma->afs1[k] = ma->phi[k] * ma->z[k] / ma->CMk[k] / sum;
+ ma->afs1[k] = ma->phi[k] * ma->z[k] / sum;
if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
}
for (k = 0, sum = 0.; k <= ma->M; ++k) {
rst->p_ref = ma->afs1[ma->M];
// calculate f_flat and f_em
for (k = 0, sum = 0.; k <= ma->M; ++k)
- sum += (long double)ma->z[k] / ma->CMk[k];
+ sum += (long double)ma->z[k];
rst->f_flat = 0.;
for (k = 0; k <= ma->M; ++k) {
- double p = ma->z[k] / ma->CMk[k] / sum;
+ double p = ma->z[k] / sum;
rst->f_flat += k * p;
}
rst->f_flat /= ma->M;