Searched refs:snp_i (Results 1 – 3 of 3) sorted by relevance
| /dports/biology/stacks/stacks-2.4/src/ |
| H A D | PopMap.h | 251 size_t snp_i = 0; in populate_internal() local
252 --snp_i; in populate_internal()
267 ++snp_i; in populate_internal()
342 d->obshap[0][snp_i] = char(rec_alleles.at(gt.first)); in populate_internal()
343 d->obshap[1][snp_i] = char(rec_alleles.at(gt.second)); in populate_internal()
345 Datum::SNPData& s = d->snpdata[snp_i]; in populate_internal()
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| H A D | gstacks.cc | 2006 for(size_t snp_i=0; snp_i<snp_cols.size(); ++snp_i) in phase_sample_hets() local
2007 if (calls[snp_cols[snp_i]].sample_calls()[sample].call() == snp_type_het) in phase_sample_hets()
2008 het_snps.push_back(snp_i); in phase_sample_hets()
2258 size_t snp_i = het_snps[het_i]; in assemble_phase_sets() local
2268 size_t n = cooccurrences.at(snp_i, nti, snp_j, ntj); in assemble_phase_sets()
2682 for (size_t snp_i : het_snps) in write_sample_hapgraph() local
2683 het_cols.push_back(snp_cols[snp_i]); in write_sample_hapgraph()
2701 size_t snp_i = het_snps[het_i]; in write_sample_hapgraph() local
2707 size_t n = cooccurrences.at(snp_i, nti, snp_j, ntj); in write_sample_hapgraph()
2710 os << "\t\t" << nodeid(snp_cols[snp_i],nti) in write_sample_hapgraph()
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| H A D | populations.cc | 1269 for (auto snp_i=cloc->snps.size(); snp_i!=0; ) { in keep_random_snp() local
1270 --snp_i; in keep_random_snp()
1271 if (snp_i != kept_snp_i) in keep_random_snp()
1272 erase_snp(cloc, d, n_samples, snp_i); in keep_random_snp()
1422 size_t snp_i = snps_n_samples.back().second; in filter_haps() local
1423 this->erase_snp(cloc, d, mpopi.n_samples(), snp_i); in filter_haps()
1427 if (snp.second > snp_i) in filter_haps()
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