if (b->info[0]) kputc(';', &s);
ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
- if (a.is_tested) ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
+ if (a.is_tested) {
+ if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%.2lg,%.2lg,%.2lg,%.2lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
+ ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
+ }
if (pr->g[0] >= 0. && p_hwe <= .2)
ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
kputc('\0', &s);
fprintf(stderr, " -L discard the PL genotype field\n");
fprintf(stderr, " -H perform Hardy-Weinberg test (slower)\n");
fprintf(stderr, " -v output potential variant sites only\n");
+ fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
fprintf(stderr, " -l FILE list of sites to output [all sites]\n");
fprintf(stderr, " -t FLOAT scaled mutation rate [%.4lg]\n", vc.theta);
fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
#define MC_MAX_EM_ITER 16
#define MC_EM_EPS 1e-4
+//#define _BCF_QUAD
+
unsigned char seq_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
double *z1, *z2; // only calculated when n1 is set
double t, t1, t2;
double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
+ double *k1k2;
const uint8_t *PL; // point to PL
int PL_len;
};
return 0;
}
-bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
+bcf_p1aux_t *bcf_p1_init(int n)
{
bcf_p1aux_t *ma;
int i;
return ma;
}
+#ifdef _BCF_QUAD
+static double lbinom(int n, int k)
+{
+ return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
+}
+#endif
+
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
{
if (n1 == 0 || n1 >= b->n) return -1;
b->n1 = n1;
+#ifdef _BCF_QUAD
+ {
+ int k1, k2, n2 = b->n - b->n1;
+ b->k1k2 = calloc((2*n1+1) * (2*n2+1), sizeof(double));
+ for (k1 = 0; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ b->k1k2[k1*(2*n2+1)+k2] = exp(lbinom(2*n1,k1) + lbinom(2*n2,k2) - lbinom(b->M,k1+k2));
+ }
+#endif
return 0;
}
free(ma->phi);
free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
free(ma->afs); free(ma->afs1);
+ free(ma->k1k2);
free(ma);
}
}
{
if (ma->n1 > 0 && ma->n1 < ma->n) {
int k;
- double x;
+ long double x;
memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
ma->t1 = ma->t2 = 0.;
memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
mc_cal_y_core(ma, 0);
// rescale z
- x = exp(ma->t - (ma->t1 + ma->t2));
+ x = expl(ma->t - (ma->t1 + ma->t2));
for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
} else mc_cal_y_core(ma, 0);
+#ifdef _BCF_QUAD
/*
- if (ma->n1 > 0 && ma->n1 < ma->n) {
- int i;
- double y[5];
- printf("*****\n");
- for (i = 0; i <= 2; ++i)
- printf("(%lf,%lf) ", ma->z1[i], ma->z2[i]);
- printf("\n");
- y[0] = ma->z1[0] * ma->z2[0];
- y[1] = 1./2. * (ma->z1[0] * ma->z2[1] + ma->z1[1] * ma->z2[0]);
- y[2] = 1./6. * (ma->z1[0] * ma->z2[2] + ma->z1[2] * ma->z2[0]) + 4./6. * ma->z1[1] * ma->z2[1];
- y[3] = 1./2. * (ma->z1[1] * ma->z2[2] + ma->z1[2] * ma->z2[1]);
- y[4] = ma->z1[2] * ma->z2[2];
- for (i = 0; i <= 4; ++i) printf("(%lf,%lf) ", ma->z[i], y[i]);
+ if (ma->n1 > 0 && ma->n1 < ma->n) { // DEBUG: consistency check; z[i] should equal y[i]
+ int i, k1, k2, n1 = ma->n1, n2 = ma->n - n1;
+ double *y;
+ printf("*** ");
+ y = calloc(ma->M + 1, sizeof(double));
+ for (k1 = 0; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ y[k1+k2] += ma->k1k2[k1*(2*n2+1)+k2] * ma->z1[k1] * ma->z2[k2];
+ for (i = 0; i <= ma->M; ++i) printf("(%lf,%lf) ", ma->z[i], y[i]);
printf("\n");
+ free(y);
}
*/
+#endif
+}
+
+static void contrast(bcf_p1aux_t *ma, double pc[4]) // mc_cal_y() must be called before hand
+{
+ int k, n1 = ma->n1, n2 = ma->n - ma->n1;
+ long double sum = -1., x, sum_alt;
+ double y;
+ pc[0] = pc[1] = pc[2] = pc[3] = -1.;
+ if (n1 <= 0 || n2 <= 0) return;
+#ifdef _BCF_QUAD
+ { // FIXME: can be improved by skipping zero cells
+ int k1, k2;
+ long double z[3];
+ z[0] = z[1] = z[2] = 0.;
+ for (k1 = 0; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2) {
+ double zz = ma->phi[k1+k2] * ma->z1[k1] * ma->z2[k2] * ma->k1k2[k1*(2*n2+1)+k2];
+ if ((double)k1/n1 < (double)k2/n2) z[0] += zz;
+ else if ((double)k1/n1 > (double)k2/n2) z[1] += zz;
+ else z[2] += zz;
+ }
+ sum = z[0] + z[1] + z[2];
+ pc[2] = z[0] / sum; pc[3] = z[1] / sum;
+ }
+#endif
+ for (k = 0, sum_alt = 0.; k <= ma->M; ++k)
+ sum_alt += (long double)ma->phi[k] * ma->z[k];
+// printf("* %lg, %lg *\n", (double)sum, (double)sum_alt); // DEBUG: sum should equal sum_alt
+ sum = sum_alt;
+ y = lgamma(2*n1 + 1) - lgamma(ma->M + 1);
+ for (k = 1, x = 0.; k <= 2 * n2; ++k)
+ x += ma->phi[k] * ma->z2[k] * exp(lgamma(ma->M - k + 1) - lgamma(2*n2 - k + 1) + y);
+ pc[0] = ma->z1[0] * x / sum;
+ y = lgamma(2*n2 + 1) - lgamma(ma->M + 1);
+ for (k = 1, x = 0.; k <= 2 * n1; ++k)
+ x += ma->phi[k] * ma->z1[k] * exp(lgamma(ma->M - k + 1) - lgamma(2*n1 - k + 1) + y);
+ pc[1] = ma->z2[0] * x / sum;
+ for (k = 0; k < 4; ++k) {
+ y = 1. - pc[k];
+ if (y <= 0.) y = 1e-100;
+ pc[k] = (int)(-3.434 * log(y) + .499);
+ if (pc[k] > 99.) pc[k] = 99.;
+ }
}
static double mc_cal_afs(bcf_p1aux_t *ma)
}
}
rst->g[0] = rst->g[1] = rst->g[2] = -1.;
+ contrast(ma, rst->pc);
// bcf_p1_cal_g3(ma, rst->g);
return 0;
}