+// calculate z_{nr}^{(k)}
+static void mc_cal_z(mc_aux_t *ma, int k)
+{
+ double *z[2], *tmp, *bk, *pdg;
+ int i, j;
+ z[0] = ma->z;
+ z[1] = ma->zswap;
+ bk = ma->beta + k * 3; pdg = ma->pdg;
+ z[0][0] = 1.; z[0][1] = z[0][2] = 0.;
+ for (j = 0; j < ma->n; ++j) {
+ int max = (j + 1) * 2;
+ double p[3];
+ pdg = ma->pdg + j * 3;
+ p[0] = bk[0] * pdg[0]; p[1] = bk[1] * pdg[1]; p[2] = bk[2] * pdg[2];
+ z[1][0] = p[0] * z[0][0];
+ z[1][1] = p[0] * z[0][1] + p[1] * z[0][0];
+ for (i = 2; i <= max; ++i)
+ z[1][i] = p[0] * z[0][i] + p[1] * z[0][i-1] + p[2] * z[0][i-2];
+ if (j < ma->n - 1) z[1][max+1] = z[1][max+2] = 0.;
+ tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+ }
+ if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (2 * ma->n + 1));
+}
+// Warning: this is cubic in ma->n, very sloooooow
+static void mc_add_afs(mc_aux_t *ma, double PD, double *f_map, double *p_map)
+{
+ int k, l;
+ double sum = 0.;
+ memset(ma->afs1, 0, sizeof(double) * (2 * ma->n + 1));
+ for (k = 0; k <= 2 * ma->n; ++k) {
+ mc_cal_z(ma, k);
+ for (l = 0; l <= 2 * ma->n; ++l)
+ ma->afs1[l] += ma->alpha[k] * ma->z[l] / PD;
+ }
+ for (k = 0; k <= 2 * ma->n; ++k) {
+ ma->afs[k] += ma->afs1[k];
+ sum += ma->afs1[k];
+ }
+ {
+ int max_k = 0;
+ double max = -1., e = 0.;
+ for (k = 0; k <= 2 * ma->n; ++k) {
+ if (ma->afs1[k] > max) max = ma->afs1[k], max_k = k;
+ e += k * ma->afs1[k];
+ }
+ *f_map = .5 * max_k / ma->n; *p_map = max;
+ printf(" * %.3lg:%.3lg:%.3lg:%.3lg * ", sum, 1.-.5*max_k/ma->n, max, 1.-.5*e/ma->n);
+ }
+}
+
+int mc_cal(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, mc_rst_t *rst, int level)
+{
+ int i, tot;
+ memset(rst, 0, sizeof(mc_rst_t));
+ rst->f_em = rst->f_exp = -1.; rst->ref = rst->alt = -1;
+ // precalculation
+ tot = sum_err(n, plp, ma);
+ if (tot == 0) return 0; // no good bases
+ set_allele(ref, ma);
+ cal_pdg(ma);
+ // set ref/major allele
+ rst->ref = ma->ref; rst->alt = ma->alt;
+ // calculate naive and Nielsen's freq
+ rst->f_naive = mc_freq0(ma, &rst->f_nielsen);
+ { // calculate f_em
+ double flast = rst->f_naive;
+ for (i = 0; i < MC_MAX_EM_ITER; ++i) {
+ rst->f_em = mc_freq_iter(flast, ma);
+ if (fabs(rst->f_em - flast) < MC_EM_EPS) break;
+ flast = rst->f_em;
+ }
+ }
+ if (level >= 2) // quadratic-time calculations; necessary for genotyping
+ rst->p_ref = mc_ref_prob(ma, &rst->PD, &rst->f_exp);
+ if (level >= 3)
+ mc_add_afs(ma, rst->PD, &rst->f_map, &rst->p_map);
+ return tot;
+}