* remove "-f". Instead always compute consensus quality

[samtools.git] / bcftools / prob1.c

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 8bf968f6adffd6a7e22058d6c2c5886f33f7a5c1..c820f71ae5f018ab6cd1515bf95ed5f8879b9641 100644 (file)
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -32,7 +32,7 @@ unsigned char seq_nt4_table[256] = {
 };
 
 struct __bcf_p1aux_t {
-       int n, M, n1, is_indel, is_folded;
+       int n, M, n1, is_indel;
        double *q2p, *pdg; // pdg -> P(D|g)
        double *phi, *phi_indel;
        double *z, *zswap; // aux for afs
@@ -43,13 +43,6 @@ struct __bcf_p1aux_t {
        int PL_len;
 };
 
-static void fold_array(int M, double *x)
-{
-       int k;
-       for (k = 0; k < M/2; ++k)
-               x[k] = x[M-k] = (x[k] + x[M-k]) / 2.;
-}
-
 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
 {
        int i;
@@ -162,15 +155,6 @@ int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
        return 0;
 }
 
-void bcf_p1_set_folded(bcf_p1aux_t *p1a)
-{
-       if (p1a->n1 < 0) {
-               p1a->is_folded = 1;
-               fold_array(p1a->M, p1a->phi);
-               fold_array(p1a->M, p1a->phi_indel);
-       }
-}
-
 void bcf_p1_destroy(bcf_p1aux_t *ma)
 {
        if (ma) {
@@ -326,19 +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];
@@ -388,8 +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->p_ref = ma->is_folded? ma->afs1[ma->M] + ma->afs1[0] : ma->afs1[ma->M];
+       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];
@@ -428,7 +424,6 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 void bcf_p1_dump_afs(bcf_p1aux_t *ma)
 {
        int k;
-       if (ma->is_folded) fold_array(ma->M, ma->afs);
        fprintf(stderr, "[afs]");
        for (k = 0; k <= ma->M; ++k)
                fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);