added "const" to bcf_p1_cal()

[samtools.git] / bcftools / prob1.c

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 176a0fc96d4e0b12f14172bc7c0d68297e01a50a..9d418c55acdb5d0b276bda0d718a23708bf24f6a 100644 (file)
--- 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];
@@ -356,7 +365,7 @@ long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
        return pd;
 }
 
-int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
+int bcf_p1_cal(const bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 {
        int i, k;
        long double sum = 0.;
@@ -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];