struct __mc_aux_t {
int n, M;
- int ref, alt;
+ int ref, alt, alt2;
double *q2p, *pdg; // pdg -> P(D|g)
- double *alpha, *beta;
+ double *phi, *CMk; // CMk=\binom{M}{k}
double *z, *zswap; // aux for afs
double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
int *qsum, *bcnt;
int i;
if (type == MC_PTYPE_COND2) {
for (i = 0; i <= 2 * ma->n; ++i)
- ma->alpha[i] = 2. * (i + 1) / (2 * ma->n + 1) / (2 * ma->n + 2);
+ ma->phi[i] = 2. * (i + 1) / (2 * ma->n + 1) / (2 * ma->n + 2);
+ } else if (type == MC_PTYPE_FLAT) {
+ for (i = 0; i <= ma->M; ++i)
+ ma->phi[i] = 1. / (ma->M + 1);
} else {
double sum;
for (i = 0, sum = 0.; i < 2 * ma->n; ++i)
- sum += (ma->alpha[i] = theta / (2 * ma->n - i));
- ma->alpha[2 * ma->n] = 1. - sum;
+ sum += (ma->phi[i] = theta / (2 * ma->n - i));
+ ma->phi[2 * ma->n] = 1. - sum;
}
}
ma->qsum = calloc(4 * ma->n, sizeof(int));
ma->bcnt = calloc(4 * ma->n, sizeof(int));
ma->pdg = calloc(3 * ma->n, sizeof(double));
- ma->alpha = calloc(2 * ma->n + 1, sizeof(double));
- ma->beta = calloc((2 * ma->n + 1) * 3, sizeof(double));
+ ma->phi = calloc(ma->M + 1, sizeof(double));
+ ma->CMk = calloc(ma->M + 1, sizeof(double));
ma->z = calloc(2 * ma->n + 1, sizeof(double));
ma->zswap = calloc(2 * ma->n + 1, sizeof(double));
ma->afs = calloc(2 * ma->n + 1, sizeof(double));
ma->afs1 = calloc(2 * ma->n + 1, sizeof(double));
for (i = 0; i <= MC_MAX_SUMQ; ++i)
ma->q2p[i] = pow(10., -i / 10.);
- for (i = 0; i <= ma->M; ++i) { // beta[k][g]=P(g|k/M)
- double *bi = ma->beta + 3 * i;
- double f = (double)i / ma->M;
- bi[0] = (1. - f) * (1. - f);
- bi[1] = 2 * f * (1. - f);
- bi[2] = f * f;
- }
+ for (i = 0; i <= ma->M; ++i)
+ ma->CMk[i] = exp(lgamma(ma->M + 1) - lgamma(i + 1) - lgamma(ma->M - i + 1));
mc_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
return ma;
}
if (ma) {
free(ma->qsum); free(ma->bcnt);
free(ma->q2p); free(ma->pdg);
- free(ma->alpha); free(ma->beta);
+ free(ma->phi); free(ma->CMk);
free(ma->z); free(ma->zswap);
free(ma->afs); free(ma->afs1);
free(ma);
for (i = 1; i < 4; ++i) // insertion sort
for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
- ma->ref = sum[3]&3; ma->alt = sum[2]&3;
- if (ref == ma->alt) tmp = ma->ref, ma->ref = ma->alt, ma->alt = tmp;
- // note that ma->ref might not be ref in case of triallele
+ ma->ref = sum[3]&3; ma->alt = sum[2]&3; ma->alt2 = -1;
+ if (ma->ref != ref) { // the best base is not ref
+ if (ref >= 0 && ref <= 3) { // ref is not N
+ if (ma->alt == ref) tmp = ma->ref, ma->ref = ma->alt, ma->alt = tmp; // then switch alt and ref
+ else ma->alt2 = ma->alt, ma->alt = ma->ref, ma->ref = ref; // then set ref as ref
+ } else ma->alt2 = ma->alt, ma->alt = ma->ref, ma->ref = sum[0]&3; // then set the weakest as ref
+ }
}
static void cal_pdg(mc_aux_t *ma)
return f;
}
-static double mc_ref_prob(const mc_aux_t *ma, double *_PD, double *f_exp)
-{
- int k, i;
- long double PD = 0., Pref = 0., Ef = 0.;
- for (k = 0; k <= ma->M; ++k) {
- long double x = 1., y = 0.;
- double *bk = ma->beta + k * 3;
- for (i = 0; i < ma->n; ++i) {
- double *pdg = ma->pdg + i * 3;
- double z = pdg[0] * bk[0] + pdg[1] * bk[1] + pdg[2] * bk[2];
- x *= z;
- y += (pdg[1] * bk[1] + 2. * pdg[2] * bk[2]) / z;
- }
- PD += x * ma->alpha[k];
- Ef += x * y * ma->alpha[k];
- }
- for (k = 0; k <= ma->n * 2; ++k) {
- long double x = 1.0;
- for (i = 0; i < ma->n; ++i)
- x *= ma->pdg[i * 3 + 2] * ma->beta[k * 3 + 2];
- Pref += x * ma->alpha[k];
- }
- *f_exp = (double)(Ef / PD / ma->M);
- *_PD = PD;
- return Pref / PD;
-}
-
int mc_call_gt(const mc_aux_t *ma, double f0, int k)
{
double sum, g[3];
if (q > 99) q = 99;
return q<<2|max_i;
}
-// calculate z_{nr}^{(k)}
-static void mc_cal_z(mc_aux_t *ma, int k)
+
+static void mc_cal_z(mc_aux_t *ma)
{
- double *z[2], *tmp, *bk, *pdg;
+ double *z[2], *tmp, *pdg;
int i, j;
z[0] = ma->z;
z[1] = ma->zswap;
- bk = ma->beta + k * 3; pdg = ma->pdg;
+ 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];
+ p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[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.;
+// int k; for (k = 0; k <= max; ++k) printf("%d:%.3lg ", k, z[1][k]); putchar('\n');
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)
+
+static double mc_add_afs(mc_aux_t *ma)
{
- 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;
+ int k;
+ long double sum = 0.;
+ memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
+ mc_cal_z(ma);
+ for (k = 0, sum = 0.; k <= ma->M; ++k)
+ sum += (long double)ma->phi[k] * ma->z[k] / ma->CMk[k];
+ for (k = 0; k <= ma->M; ++k) {
+ ma->afs1[k] = ma->phi[k] * ma->z[k] / ma->CMk[k] / sum;
+ if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
}
- for (k = 0; k <= 2 * ma->n; ++k) {
+ for (k = 0, sum = 0.; k <= ma->M; ++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; // e should equal mc_rst_t::f_exp
-// printf(" * %.3lg:%.3lg:%.3lg:%.3lg * ", sum, 1.-.5*max_k/ma->n, max, 1.-.5*e/ma->n);
+ sum += k * ma->afs1[k];
}
+ return sum / ma->M;
}
int mc_cal(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, mc_rst_t *rst, int level)
set_allele(ref, ma);
cal_pdg(ma);
// set ref/major allele
- rst->ref = ma->ref; rst->alt = ma->alt;
+ rst->ref = ma->ref; rst->alt = ma->alt; rst->alt2 = ma->alt2;
// calculate naive and Nielsen's freq
rst->f_naive = mc_freq0(ma, &rst->f_nielsen);
{ // calculate f_em
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);
+ if (level >= 2) {
+ rst->f_exp = mc_add_afs(ma);
+ rst->p_ref = ma->afs1[ma->M];
+ }
return tot;
}
projects / samtools.git / blobdiff