std::ostream&
operator<<(std::ostream& os, const hinfo& hi) {
os << "hinfo:\n";
os << "total_qual: " << hi.total_qual << "\n";
os << "read: ";
for (unsigned i(0); i<hap_cand::HAP_SIZE; ++i) { os << id_to_base(hi.hseq[i]); }
os << "\n";
return os;
}
std::ostream&
operator<<(std::ostream& os, const hap_cand& hc) {
os << "hap_cand:\n";
os << "total_qual: " << hc.total_qual() << "\n";
os << "read: ";
for (unsigned i(0); i<hap_cand::HAP_SIZE; ++i) { os << id_to_base(hc.base_id(i)); }
os << "\n";
os << "qual: ";
for (unsigned i(0); i<hap_cand::HAP_SIZE; ++i) { os << static_cast<char>(33+hc.qual(i)); }
os << "\n";
return os;
}
void
write_alt_alleles(const DDIGT_SGRID::index_t dgt,
const unsigned ref_gt,
std::ostream& os) {
unsigned normal_gt;
unsigned tumor_gt;
DDIGT_SGRID::get_digt_grid_states(dgt,normal_gt,tumor_gt);
unsigned normal_digt(DIGT_SGRID::get_digt_state(normal_gt,ref_gt));
unsigned tumor_digt(DIGT_SGRID::get_digt_state(tumor_gt,ref_gt));
bool is_print(false);
for(unsigned b(0); b<N_BASE; ++b) {
if(b==ref_gt) continue;
if(DIGT::expect2(b,normal_digt) ||
DIGT::expect2(b,tumor_digt)) {
if(is_print) os << ",";
os << id_to_base(b);
is_print=true;
}
}
if(! is_print) os << ".";
}
void
write_nonref_2allele_test(const blt_options& opt,
const snp_pos_info& pi,
const nonref_test_call& nrc,
std::ostream& os) {
os << nrc.snp_qphred
<< '\t' << NR2TEST::label(static_cast<NR2TEST::index_t>(nrc.max_gt)) << "_" << id_to_base(nrc.nonref_id)
<< '\t' << nrc.max_gt_qphred;
//if(opt.is_print_used_allele_counts) {
pi.print_known_counts(os,opt.used_allele_count_min_qscore);
pi.print_known_qscore(os,opt.used_allele_count_min_qscore);
//}
#if 0
if (opt.is_print_all_poly_gt) {
for (unsigned gt(0); gt<DIGT::SIZE; ++gt) {
#if 1
// print GT as prob:
os << '\t' << po.pprob[gt];
#else
// print GT as qval:
os << '\t' << error_prob_to_qphred(prob_comp(po.pprob,po.pprob+DIGT::SIZE,gt));
#endif
}
}
const result_set& ge(dgt.genome);
const result_set& po(dgt.poly);
#endif
#if 0
if (nrc.is_freq) {
os << std::setprecision(8) << std::fixed;
for (unsigned i(0); i<N_BASE; ++i) {
os << '\t' << nrc.allele_freq[i];
}
os.unsetf(std::ios::fixed);
}
#endif
}
