/**
* Sets the prior. Must not change the label argument if one is set already.
*/
void prior(const F& prior) {
check_prior(prior);
if (prior_.empty() || prior_.arguments() == prior.arguments()) {
prior_ = prior;
} else {
throw std::invalid_argument("attempt to change the label argument");
}
}
//! Creates a naive Bayes model with the given label and uniform prior.
explicit naive_bayes(argument_type label)
: prior_({label}, result_type(1)) {
check_prior(prior_);
}
//! Creates a naive Bayes model with given prior distribution and CPDs.
explicit naive_bayes(const LabelF& prior)
: prior_(prior) {
check_prior(prior_);
}
static
void
calculate_result_set(const strelka_options& opt,
const double* normal_lnprior,
const double lnmatch,
const double lnmismatch,
const double* normal_lhood,
const double* tumor_lhood,
result_set& rs) {
#ifdef SOMATIC_DEBUG
std::vector<double> check_prior(DDIINDEL::SIZE);
for (unsigned ngt(0); ngt<STAR_DIINDEL::SIZE; ++ngt) {
const double base_prior(normal_lnprior[ngt]);
for (unsigned tgt(0); tgt<STAR_DIINDEL::SIZE; ++tgt) {
const unsigned dgt(DDIINDEL::get_state(ngt,tgt));
check_prior[dgt] =
base_prior+
((tgt==ngt) ? lnmatch : lnmismatch);
}
}
check_ln_distro(check_prior.begin(),
check_prior.end(),
"somatic indel full prior");
#endif
// get unnormalized posterior:
std::vector<double> pprob(DDIINDEL::SIZE);
for (unsigned ngt(0); ngt<STAR_DIINDEL::SIZE; ++ngt) {
const double base_prior(normal_lnprior[ngt]);
for (unsigned tgt(0); tgt<STAR_DIINDEL::SIZE; ++tgt) {
const unsigned dgt(DDIINDEL::get_state(ngt,tgt));
pprob[dgt] =
normal_lhood[ngt]+
tumor_lhood[tgt]+
base_prior+
((tgt==ngt) ? lnmatch : lnmismatch);
}
}
normalize_ln_distro(pprob.begin(),pprob.end(),rs.max_gt);
#ifdef DEBUG_INDEL_CALL
log_os << "INDEL_CALL pprob(noindel),pprob(hom),pprob(het): " << pprob[STAR_DIINDEL::NOINDEL] << " " << pprob[STAR_DIINDEL::HOM] << " " << pprob[STAR_DIINDEL::HET] << "\n";
#endif
double nonsomatic_sum(0);
for (unsigned gt(0); gt<STAR_DIINDEL::SIZE; ++gt) {
nonsomatic_sum += pprob[DDIINDEL::get_state(gt,gt)];
}
rs.sindel_qphred=error_prob_to_qphred(nonsomatic_sum);
double not_somfrom_sum[STAR_DIINDEL::SIZE];
for (unsigned sgt(0); sgt<STAR_DIINDEL::SIZE; ++sgt) {
not_somfrom_sum[sgt]=nonsomatic_sum;
for (unsigned ngt(0); ngt<STAR_DIINDEL::SIZE; ++ngt) {
if (sgt==ngt) continue;
for (unsigned tgt(0); tgt<STAR_DIINDEL::SIZE; ++tgt) {
if (tgt==ngt) continue;
not_somfrom_sum[sgt] += pprob[DDIINDEL::get_state(ngt,tgt)];
}
}
}
rs.sindel_from_ref_qphred=error_prob_to_qphred(not_somfrom_sum[STAR_DIINDEL::NOINDEL]);
rs.sindel_from_het_qphred=error_prob_to_qphred(not_somfrom_sum[STAR_DIINDEL::HET]);
rs.sindel_from_hom_qphred=error_prob_to_qphred(not_somfrom_sum[STAR_DIINDEL::HOM]);
double not_somfromanyhom_sum(nonsomatic_sum);
for (unsigned ngt(0); ngt<STAR_DIINDEL::SIZE; ++ngt) {
if (STAR_DIINDEL::HET != ngt) continue;
for (unsigned tgt(0); tgt<STAR_DIINDEL::SIZE; ++tgt) {
if (tgt==ngt) continue;
not_somfromanyhom_sum += pprob[DDIINDEL::get_state(ngt,tgt)];
}
}
rs.sindel_from_anyhom_qphred=error_prob_to_qphred(not_somfromanyhom_sum);
rs.max_gt_qphred=error_prob_to_qphred(prob_comp(pprob.begin(),pprob.end(),rs.max_gt));
}
