calculate posterior allele frequency

[samtools.git] / bam_mcns.c

diff --git a/bam_mcns.c b/bam_mcns.c
index dee2016507100888faf053163ec47a8b8b474828..c1cdb9077ff7b9278f631c5da3915348114ae5c9 100644 (file)
--- a/bam_mcns.c
+++ b/bam_mcns.c
@@ -39,7 +39,7 @@ mc_aux_t *mc_init(int n) // FIXME: assuming diploid
        ma->beta = calloc((2 * ma->n + 1) * 3, sizeof(double));
        for (i = 0; i <= MC_MAX_SUMQ; ++i)
                ma->q2p[i] = pow(10., -i / 10.);
-       for (i = 0; i <= 2 * ma->n; ++i) {
+       for (i = 0; i <= 2 * ma->n; ++i) { // beta[k][g]=P(g|k/M)
                double *bi = ma->beta + 3 * i;
                double f = (double)i / (2 * ma->n);
                bi[0] = (1. - f) * (1. - f);
@@ -153,18 +153,44 @@ double mc_freq_iter(double f0, mc_aux_t *ma)
        return f;
 }
 
+double mc_freq_post(mc_aux_t *ma)
+{
+       int i, k;
+       long double f = 0.;
+       for (i = 0; i < ma->n; ++i) {
+               double *pdg = ma->pdg + i * 3;
+               long double y = 0., z = 0.;
+               for (k = 0; k <= ma->n * 2; ++k) {
+                       double *bk = ma->beta + k * 3;
+/*
+                       int g;
+                       double yk = 0., zk = 0.;
+                       for (g = 0; g < 3; ++g) {
+                               yk += g * pdg[g] * bk[g];
+                               zk += pdg[g] * bk[g];
+                       }
+                       y += yk * ma->alpha[k];
+                       z += zk * ma->alpha[k];
+*/
+                       y += (pdg[1] * bk[1] + 2. * pdg[2] * bk[2]) * ma->alpha[k];
+                       z += (pdg[0] * bk[0] + pdg[1] * bk[1] + pdg[2] * bk[2]) * ma->alpha[k];
+               }
+               f += y / z;
+       }
+       return f / ma->n / 2;
+}
+
 double mc_ref_prob(mc_aux_t *ma)
 {
-       int k, i, g;
+       int k, i;
        long double PD = 0., Pref = 0.;
        for (k = 0; k <= ma->n * 2; ++k) {
                long double x = 1.;
                double *bk = ma->beta + k * 3;
                for (i = 0; i < ma->n; ++i) {
-                       double y = 0., *pdg = ma->pdg + i * 3;
-                       for (g = 0; g < 3; ++g)
-                               y += pdg[g] * bk[g];
-                       x *= y;
+                       double *pdg = ma->pdg + i * 3;
+//                     int g; double y=0.; for (g = 0; g < 3; ++g) y += pdg[g] * bk[g];
+                       x *= pdg[0] * bk[0] + pdg[1] * bk[1] + pdg[2] * bk[2];
                }
                PD += x * ma->alpha[k];
        }
@@ -189,6 +215,7 @@ int mc_call_gt(const mc_aux_t *ma, double f0, int k)
                g[i] /= sum;
                if (g[i] > max) max = g[i], max_i = i;
        }
+//     printf("***%lg,%lg,%lg,%lg,%lg,%lg\n", g[0], g[1], g[2], pdg[0], pdg[1], pdg[2]);
        max = 1. - max;
        if (max < 1e-308) max = 1e-308;
        q = (int)(-3.434 * log(max) + .499);