KSTREAM_INIT(gzFile, gzread, 16384)
#define MC_MAX_EM_ITER 16
-#define MC_EM_EPS 1e-4
+#define MC_EM_EPS 1e-5
#define MC_DEF_INDEL 0.15
unsigned char seq_nt4_table[256] = {
return i;
}
// f0 is the reference allele frequency
-static double mc_freq_iter(double f0, const bcf_p1aux_t *ma)
+static double mc_freq_iter(double f0, const bcf_p1aux_t *ma, int beg, int end)
{
double f, f3[3];
int i;
f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
- for (i = 0, f = 0.; i < ma->n; ++i) {
+ for (i = beg, f = 0.; i < end; ++i) {
double *pdg;
pdg = ma->pdg + i * 3;
f += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
/ (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
}
- f /= ma->n * 2.;
+ f /= (end - beg) * 2.;
return f;
}
+static double mc_gtfreq_iter(double g[3], const bcf_p1aux_t *ma, int beg, int end)
+{
+ double err, gg[3];
+ int i;
+ gg[0] = gg[1] = gg[2] = 0.;
+ for (i = beg; i < end; ++i) {
+ double *pdg, sum, tmp[3];
+ pdg = ma->pdg + i * 3;
+ tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2];
+ sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg);
+ gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum;
+ }
+ err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]);
+ err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]);
+ g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2];
+ return err;
+}
+
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
{
double sum, g[3];
for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1)
for (k2 = 0; k2 <= 2*n2; ++k2)
if ((y = contrast2_aux(p1, sum, n1, n2, k1, k2, ret)) >= 0) z += y;
+ if (ret[0] + ret[1] + ret[2] < 0.99) // It seems that this may be caused by floating point errors. I do not really understand why...
+ z = 1.0, ret[0] = ret[1] = ret[2] = 1./3;
}
return (double)z;
}
{ // calculate f_em
double flast = rst->f_flat;
for (i = 0; i < MC_MAX_EM_ITER; ++i) {
- rst->f_em = mc_freq_iter(flast, ma);
+ rst->f_em = mc_freq_iter(flast, ma, 0, ma->n);
if (fabs(rst->f_em - flast) < MC_EM_EPS) break;
flast = rst->f_em;
}
+ if (ma->n1 > 0 && ma->n1 < ma->n) {
+ for (k = 0; k < 2; ++k) {
+ flast = rst->f_em;
+ for (i = 0; i < MC_MAX_EM_ITER; ++i) {
+ rst->f_em2[k] = k? mc_freq_iter(flast, ma, ma->n1, ma->n) : mc_freq_iter(flast, ma, 0, ma->n1);
+ if (fabs(rst->f_em2[k] - flast) < MC_EM_EPS) break;
+ flast = rst->f_em2[k];
+ }
+ }
+ }
+ }
+ { // compute g[3]
+ rst->g[0] = (1. - rst->f_em) * (1. - rst->f_em);
+ rst->g[1] = 2. * rst->f_em * (1. - rst->f_em);
+ rst->g[2] = rst->f_em * rst->f_em;
+ for (i = 0; i < MC_MAX_EM_ITER; ++i)
+ if (mc_gtfreq_iter(rst->g, ma, 0, ma->n) < MC_EM_EPS) break;
}
{ // estimate equal-tail credible interval (95% level)
int l, h;
h = i;
rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
}
- rst->g[0] = rst->g[1] = rst->g[2] = -1.;
rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
if (rst->p_var > 0.1) // skip contrast2() if the locus is a strong non-variant
rst->p_chi2 = contrast2(ma, rst->cmp);