X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fprob1.c;h=c820f71ae5f018ab6cd1515bf95ed5f8879b9641;hb=c8e59c53055a63e697e98a5942a2d811eb4db5b9;hp=04a0e1555a16832d9237c1a47b9168931717997a;hpb=e561d6e1a3c58df4de0e2856c2cfb9b2b68e7f11;p=samtools.git

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 04a0e15..c820f71 100644
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -310,19 +310,28 @@ static void contrast(bcf_p1aux_t *ma, double pc[4]) // mc_cal_y() must be called
 	pc[1] = pc[1] == 1.? 99 : (int)(-4.343 * log(1. - pc[1]) + .499);
 }
 
-static double mc_cal_afs(bcf_p1aux_t *ma)
+static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
 {
 	int k;
-	long double sum = 0.;
+	long double sum = 0., sum2;
 	double *phi = ma->is_indel? ma->phi_indel : ma->phi;
 	memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
 	mc_cal_y(ma);
+	// compute AFS
 	for (k = 0, sum = 0.; k <= ma->M; ++k)
 		sum += (long double)phi[k] * ma->z[k];
 	for (k = 0; k <= ma->M; ++k) {
 		ma->afs1[k] = phi[k] * ma->z[k] / sum;
 		if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
 	}
+	// compute folded variant probability
+	for (k = 0, sum = 0.; k <= ma->M; ++k)
+		sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+	for (k = 1, sum2 = 0.; k < ma->M; ++k)
+		sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+	*p_var_folded = sum2 / sum;
+	*p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
+	// the expected frequency
 	for (k = 0, sum = 0.; k <= ma->M; ++k) {
 		ma->afs[k] += ma->afs1[k];
 		sum += k * ma->afs1[k];
@@ -372,8 +381,11 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 	if (b->n_alleles < 2) return -1; // FIXME: find a better solution
 	// 
 	rst->rank0 = cal_pdg(b, ma);
-	rst->f_exp = mc_cal_afs(ma);
+	rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded);
 	rst->p_ref = ma->afs1[ma->M];
+	for (k = 0, sum = 0.; k < ma->M; ++k)
+		sum += ma->afs1[k];
+	rst->p_var = (double)sum;
 	// calculate f_flat and f_em
 	for (k = 0, sum = 0.; k <= ma->M; ++k)
 		sum += (long double)ma->z[k];
@@ -391,6 +403,19 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 			flast = rst->f_em;
 		}
 	}
+	{ // estimate equal-tail credible interval (95% level)
+		int l, h;
+		double p;
+		for (i = 0, p = 0.; i < ma->M; ++i)
+			if (p + ma->afs1[i] > 0.025) break;
+			else p += ma->afs1[i];
+		l = i;
+		for (i = ma->M-1, p = 0.; i >= 0; --i)
+			if (p + ma->afs1[i] > 0.025) break;
+			else p += ma->afs1[i];
+		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.;
 	contrast(ma, rst->pc);
 	return 0;