void
somatic_indel_caller::
get_somatic_indel(const strelka_options& opt,
const strelka_deriv_options& dopt,
const double indel_error_prob,
const double ref_error_prob,
const indel_key& ik,
const indel_data& normal_id,
const indel_data& tumor_id,
const bool is_use_alt_indel,
somatic_indel_call& sindel) const {
// for now, lhood calculation of tumor and normal are independent:
// get likelihood of each genotype
static const bool is_normal_het_bias(false);
static const bool is_tumor_het_bias(true);
static const double normal_het_bias(0.0);
static const double tumor_het_bias(0.4);
double normal_lhood[STAR_DIINDEL::SIZE];
double tumor_lhood[STAR_DIINDEL::SIZE];
static const unsigned n_tier(2);
result_set tier_rs[n_tier];
for (unsigned i(0); i<n_tier; ++i) {
const bool is_include_tier2(i==1);
if (is_include_tier2) {
if (not opt.is_tier2()) continue;
if (tier_rs[0].sindel_qphred==0) {
tier_rs[1].sindel_qphred=0;
continue;
}
}
indel_digt_caller::get_indel_digt_lhood(opt,dopt,indel_error_prob,ref_error_prob,ik,normal_id,
is_normal_het_bias,normal_het_bias,
is_include_tier2,is_use_alt_indel,
normal_lhood);
indel_digt_caller::get_indel_digt_lhood(opt,dopt,indel_error_prob,ref_error_prob,ik,tumor_id,
is_tumor_het_bias,tumor_het_bias,
is_include_tier2,is_use_alt_indel,
tumor_lhood);
calculate_result_set(opt,normal_lnprior(),
_ln_som_match,_ln_som_mismatch,
normal_lhood,tumor_lhood,tier_rs[i]);
}
sindel.tier=0;
if (opt.is_tier2()) {
if (tier_rs[0].sindel_qphred > tier_rs[1].sindel_qphred) {
sindel.tier=1;
}
}
sindel.rs=tier_rs[sindel.tier];
sindel.is_indel=(sindel.rs.sindel_qphred != 0);
}
void
somatic_snv_caller_strand_grid::
position_somatic_snv_call(const extended_pos_info& normal_epi,
const extended_pos_info& tumor_epi,
const extended_pos_info* normal_epi_t2_ptr,
const extended_pos_info* tumor_epi_t2_ptr,
somatic_snv_genotype_grid& sgt) const {
static const bool is_always_test(false);
{
const snp_pos_info& normal_pi(normal_epi.pi);
const snp_pos_info& tumor_pi(tumor_epi.pi);
if(normal_pi.ref_base=='N') return;
sgt.ref_gt=base_to_id(normal_pi.ref_base);
// check that a non-reference call meeting quality criteria even
// exists:
if(not is_always_test) {
if(is_spi_allref(normal_pi,sgt.ref_gt) and is_spi_allref(tumor_pi,sgt.ref_gt)) return;
}
}
// strawman model treats normal and tumor as independent, so
// calculate separate lhoods:
blt_float_t normal_lhood[DIGT_SGRID::SIZE];
blt_float_t tumor_lhood[DIGT_SGRID::SIZE];
const bool is_tier2(NULL != normal_epi_t2_ptr);
static const unsigned n_tier(2);
result_set tier_rs[n_tier];
for(unsigned i(0); i<n_tier; ++i) {
const bool is_include_tier2(i==1);
if(is_include_tier2) {
if(! is_tier2) continue;
if(tier_rs[0].snv_qphred==0) {
tier_rs[1].snv_qphred=0;
continue;
}
}
// get likelihood of each genotype
//
static const bool is_normal_het_bias(false);
static const blt_float_t normal_het_bias(0.0);
static const bool is_tumor_het_bias(false);
static const blt_float_t tumor_het_bias(0.0);
const extended_pos_info& nepi(is_include_tier2 ? *normal_epi_t2_ptr : normal_epi );
const extended_pos_info& tepi(is_include_tier2 ? *tumor_epi_t2_ptr : tumor_epi );
get_diploid_gt_lhood_spi(_opt,nepi.pi,is_normal_het_bias,normal_het_bias,normal_lhood);
get_diploid_gt_lhood_spi(_opt,tepi.pi,is_tumor_het_bias,tumor_het_bias,tumor_lhood);
get_diploid_het_grid_lhood_spi(nepi.pi,normal_lhood+DIGT::SIZE);
get_diploid_het_grid_lhood_spi(tepi.pi,tumor_lhood+DIGT::SIZE);
get_diploid_strand_grid_lhood_spi(nepi.pi,sgt.ref_gt,normal_lhood+DIGT_SGRID::PRESTRAND_SIZE);
get_diploid_strand_grid_lhood_spi(tepi.pi,sgt.ref_gt,tumor_lhood+DIGT_SGRID::PRESTRAND_SIZE);
// genomic site results:
calculate_result_set_grid(normal_lhood,
tumor_lhood,
get_prior_set(sgt.ref_gt),
_ln_som_match,_ln_som_mismatch,
sgt.ref_gt,
tier_rs[i]);
#if 0
#ifdef ENABLE_POLY
// polymorphic site results:
assert(0); // still needs to be adapted for 2-tier system:
calculate_result_set(normal_lhood,tumor_lhood,
lnprior_polymorphic(sgt.ref_gt),sgt.ref_gt,sgt.poly);
#else
sgt.poly.snv_qphred = 0;
#endif
#endif
#ifdef SOMATIC_DEBUG
if((i==0) && (tier_rs[i].snv_qphred > 0)) {
const somatic_snv_caller_strand_grid::prior_set& pset(get_prior_set(sgt.ref_gt));
const blt_float_t lnmatch(_ln_som_match);
const blt_float_t lnmismatch(_ln_som_mismatch);
log_os << "DUMP ON\n";
log_os << "tier1_qphred: " << tier_rs[0].snv_qphred << "\n";
// instead of dumping the entire distribution, we sort the lhood,prior,and prob to print out the N top values of each:
std::vector<double> lhood(DDIGT_SGRID::SIZE);
std::vector<double> prior(DDIGT_SGRID::SIZE);
std::vector<double> post(DDIGT_SGRID::SIZE);
// first get raw lhood:
//
for(unsigned ngt(0); ngt<DIGT_SGRID::PRESTRAND_SIZE; ++ngt) {
for(unsigned tgt(0); tgt<DIGT_SGRID::PRESTRAND_SIZE; ++tgt) {
const unsigned dgt(DDIGT_SGRID::get_state(ngt,tgt));
// unorm takes the role of the normal prior for the somatic case:
// static const blt_float_t unorm(std::log(static_cast<blt_float_t>(DIGT_SGRID::PRESTRAND_SIZE)));
//blt_float_t prior;
//if(tgt==ngt) { prior=pset.normal[ngt]+lnmatch; }
//else { prior=pset.somatic_marginal[ngt]+lnmismatch; }
blt_float_t pr;
if(tgt==ngt) { pr=pset.normal[ngt]+lnmatch; }
else { pr=pset.somatic_marginal[ngt]+lnmismatch; }
prior[dgt] = pr;
lhood[dgt] = normal_lhood[ngt]+tumor_lhood[tgt];
post[dgt] = lhood[dgt] + prior[dgt];
}
}
for(unsigned gt(DIGT_SGRID::PRESTRAND_SIZE); gt<DIGT_SGRID::SIZE; ++gt) {
const unsigned dgt(DDIGT_SGRID::get_state(gt,gt));
lhood[dgt] = normal_lhood[gt]+tumor_lhood[gt];
prior[dgt] = pset.normal[gt]+lnmatch;
post[dgt] = lhood[dgt] + prior[dgt];
}
std::vector<double> lhood2(lhood);
sort_n_dump("lhood_prior",lhood,prior,sgt.ref_gt);
sort_n_dump("post_lhood",post,lhood2,sgt.ref_gt);
log_os << "DUMP OFF\n";
}
#endif
}
if((tier_rs[0].snv_qphred==0) ||
(is_tier2 && (tier_rs[1].snv_qphred==0))) return;
sgt.snv_tier=0;
sgt.snv_from_ntype_tier=0;
if(is_tier2) {
if(tier_rs[0].snv_qphred > tier_rs[1].snv_qphred) {
sgt.snv_tier=1;
}
if(tier_rs[0].snv_from_ntype_qphred > tier_rs[1].snv_from_ntype_qphred) {
sgt.snv_from_ntype_tier=1;
}
}
sgt.rs=tier_rs[sgt.snv_from_ntype_tier];
if(is_tier2 && (tier_rs[0].ntype != tier_rs[1].ntype)) {
// catch NTYPE conflict states:
sgt.rs.ntype = NTYPE::CONFLICT;
sgt.rs.snv_from_ntype_qphred = 0;
} else {
// classify NTYPE:
//
// convert diploid genotype into more limited ntype set:
//
if (sgt.rs.ntype==sgt.ref_gt) {
sgt.rs.ntype=NTYPE::REF;
} else if(DIGT::is_het(sgt.rs.ntype)) {
sgt.rs.ntype=NTYPE::HET;
} else {
sgt.rs.ntype=NTYPE::HOM;
}
}
sgt.rs.snv_qphred = tier_rs[sgt.snv_tier].snv_qphred;
sgt.is_snv=((sgt.rs.snv_qphred != 0));
}