/*
P(<b1,b2>) = \theta \sum_{i=1}^{N-1} 1/i
P(D|<b1,b2>) = \sum_{k=1}^{N-1} p_k 1/2 [(k/N)^n_2(1-k/N)^n_1 + (k/N)^n1(1-k/N)^n_2]
- p_k = i/k / \sum_{i=1}^{N-1} 1/i
+ p_k = 1/k / \sum_{i=1}^{N-1} 1/i
*/
static void cal_het(bam_maqcns_t *aa)
{
int k, n1, n2;
double sum_harmo; // harmonic sum
double poly_rate;
- double p1 = 0.0, p3 = 0.0; // just for testing
free(aa->lhet);
aa->lhet = (double*)calloc(256 * 256, sizeof(double));
for (n1 = 0; n1 < 256; ++n1) {
for (n2 = 0; n2 < 256; ++n2) {
long double sum = 0.0;
- double lC = lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1); // \binom{n1+n2}{n1}
+ double lC = aa->is_soap? 0 : lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1); // \binom{n1+n2}{n1}
for (k = 1; k <= aa->n_hap - 1; ++k) {
double pk = 1.0 / k / sum_harmo;
double log1 = log((double)k/aa->n_hap);
sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2));
}
aa->lhet[n1<<8|n2] = lC + logl(sum);
- if (n1 == 17 && n2 == 3) p3 = lC + logl(expl(logl(0.5) * 20));
- if (n1 == 19 && n2 == 1) p1 = lC + logl(expl(logl(0.5) * 20));
}
}
poly_rate = aa->het_rate * sum_harmo;
long double sum_a[257], b[256], q_c[256], tmp[256], fk2[256];
double *lC;
- lC = (double*)calloc(256 * 256, sizeof(double));
// aa->lhet will be allocated and initialized
free(aa->fk); free(aa->coef);
+ aa->coef = 0;
aa->fk = (double*)calloc(256, sizeof(double));
- aa->coef = (double*)calloc(256*256*64, sizeof(double));
aa->fk[0] = fk2[0] = 1.0;
for (n = 1; n != 256; ++n) {
aa->fk[n] = pow(aa->theta, n) * (1.0 - aa->eta) + aa->eta;
fk2[n] = aa->fk[n>>1]; // this is an approximation, assuming reads equally likely come from both strands
}
+ if (aa->is_soap) return;
+ aa->coef = (double*)calloc(256*256*64, sizeof(double));
+ lC = (double*)calloc(256 * 256, sizeof(double));
for (n = 1; n != 256; ++n)
for (k = 1; k <= n; ++k)
lC[n<<8|k] = lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
for (j = 0; j != 4; ++j) b->c[j] = (int)(254.0 * b->c[j] / c + 0.5);
for (j = c = 0; j != 4; ++j) c += b->c[j];
}
- // generate likelihood
- for (j = 0; j != 4; ++j) {
- // homozygous
- float tmp1, tmp3;
- int tmp2, bar_e;
- for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != 4; ++k) {
- if (j == k) continue;
- tmp1 += b->esum[k]; tmp2 += b->c[k]; tmp3 += b->fsum[k];
- }
- if (tmp2) {
- bar_e = (int)(tmp1 / tmp3 + 0.5);
- if (bar_e < 4) bar_e = 4; // should not happen
- if (bar_e > 63) bar_e = 63;
- p[j<<2|j] = tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
- } else p[j<<2|j] = 0.0; // all the bases are j
- // heterozygous
- for (k = j + 1; k < 4; ++k) {
- for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i != 4; ++i) {
- if (i == j || i == k) continue;
- tmp1 += b->esum[i]; tmp2 += b->c[i]; tmp3 += b->fsum[i];
+ if (!bm->is_soap) {
+ // generate likelihood
+ for (j = 0; j != 4; ++j) {
+ // homozygous
+ float tmp1, tmp3;
+ int tmp2, bar_e;
+ for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != 4; ++k) {
+ if (j == k) continue;
+ tmp1 += b->esum[k]; tmp2 += b->c[k]; tmp3 += b->fsum[k];
}
if (tmp2) {
bar_e = (int)(tmp1 / tmp3 + 0.5);
- if (bar_e < 4) bar_e = 4;
+ if (bar_e < 4) bar_e = 4; // should not happen
if (bar_e > 63) bar_e = 63;
- p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
- } else p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]]; // all the bases are either j or k
+ p[j<<2|j] = tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
+ } else p[j<<2|j] = 0.0; // all the bases are j
+ // heterozygous
+ for (k = j + 1; k < 4; ++k) {
+ for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i != 4; ++i) {
+ if (i == j || i == k) continue;
+ tmp1 += b->esum[i]; tmp2 += b->c[i]; tmp3 += b->fsum[i];
+ }
+ if (tmp2) {
+ bar_e = (int)(tmp1 / tmp3 + 0.5);
+ if (bar_e < 4) bar_e = 4;
+ if (bar_e > 63) bar_e = 63;
+ p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
+ } else p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]]; // all the bases are either j or k
+ }
+ //
+ for (k = 0; k != 4; ++k)
+ if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
}
- //
- for (k = 0; k != 4; ++k)
- if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
- }
- { // fix p[k<<2|k]
- float max1, max2, min1, min2;
- int max_k, min_k;
- max_k = min_k = -1;
- max1 = max2 = -1.0; min1 = min2 = 1e30;
- for (k = 0; k < 4; ++k) {
- if (b->esum[k] > max1) {
- max2 = max1; max1 = b->esum[k]; max_k = k;
- } else if (b->esum[k] > max2) max2 = b->esum[k];
+ { // fix p[k<<2|k]
+ float max1, max2, min1, min2;
+ int max_k, min_k;
+ max_k = min_k = -1;
+ max1 = max2 = -1.0; min1 = min2 = 1e30;
+ for (k = 0; k < 4; ++k) {
+ if (b->esum[k] > max1) {
+ max2 = max1; max1 = b->esum[k]; max_k = k;
+ } else if (b->esum[k] > max2) max2 = b->esum[k];
+ }
+ for (k = 0; k < 4; ++k) {
+ if (p[k<<2|k] < min1) {
+ min2 = min1; min1 = p[k<<2|k]; min_k = k;
+ } else if (p[k<<2|k] < min2) min2 = p[k<<2|k];
+ }
+ if (max1 > max2 && (min_k != max_k || min1 + 1.0 > min2))
+ p[max_k<<2|max_k] = min1 > 1.0? min1 - 1.0 : 0.0;
}
- for (k = 0; k < 4; ++k) {
- if (p[k<<2|k] < min1) {
- min2 = min1; min1 = p[k<<2|k]; min_k = k;
- } else if (p[k<<2|k] < min2) min2 = p[k<<2|k];
+ } else { // apply the SOAP model
+ // generate likelihood
+ for (j = 0; j != 4; ++j) {
+ float tmp;
+ // homozygous
+ for (k = 0, tmp = 0.0; k != 4; ++k)
+ if (j != k) tmp += b->esum[k];
+ p[j<<2|j] = tmp;
+ // heterozygous
+ for (k = j + 1; k < 4; ++k) {
+ for (i = 0, tmp = 0.0; i != 4; ++i)
+ if (i != j && i != k) tmp += b->esum[i];
+ p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp;
+ }
}
- if (max1 > max2 && (min_k != max_k || min1 + 1.0 > min2))
- p[max_k<<2|max_k] = min1 > 1.0? min1 - 1.0 : 0.0;
}
// convert necessary information to glf1_t
projects / samtools.git / blobdiff