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Searched refs:CLocAlnSet (Results 1 – 5 of 5) sorted by relevance

/dports/biology/stacks/stacks-2.4/src/
H A Dlocus.h227 class CLocAlnSet {
236 CLocAlnSet() in CLocAlnSet() function
239 CLocAlnSet(CLocAlnSet&&) = default;
240 CLocAlnSet& operator= (CLocAlnSet&&) = default;
265 static CLocAlnSet juxtapose(CLocAlnSet&& left, CLocAlnSet&& right, long offset);
272 const CLocAlnSet& loc_aln_;
280 site_iterator(const CLocAlnSet& loc_aln) in site_iterator()
311 void CLocAlnSet::add(SAlnRead&& r) { in add()
318 CLocAlnSet::site_iterator& CLocAlnSet::site_iterator::operator++ () {
336 void CLocAlnSet::site_iterator::counts(Counts<Nt4>& counts) const { in counts()
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H A Dlocus.cc366 CLocAlnSet::clear() { in clear()
394 void CLocAlnSet::recompute_consensus() { in recompute_consensus()
408 void CLocAlnSet::hard_clip_right_Ns() { in hard_clip_right_Ns()
432 CLocAlnSet::sort_by_read_name() in sort_by_read_name()
445 CLocAlnSet::sort_by_alignment_offset() in sort_by_alignment_offset()
474 CLocAlnSet::merge_paired_reads() in merge_paired_reads()
527 ostream& operator<< (ostream& os, const CLocAlnSet& loc) { in operator <<()
535 CLocAlnSet::remove_unmerged_reads(ostream* log) in remove_unmerged_reads()
643 CLocAlnSet
644 CLocAlnSet::juxtapose(CLocAlnSet&& left, CLocAlnSet&& right, long offset) in juxtapose()
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H A Dgstacks.h240 void process(CLocAlnSet& aln_loc);
264 CLocAlnSet& aln_loc,
279 const CLocAlnSet& aln_loc,
287 const CLocAlnSet& aln_loc,
299 const CLocAlnSet& aln_loc,
331 const CLocAlnSet& aln_loc,
352 void using_true_reference(CLocAlnSet& aln_loc, CLocReadSet&& loc);
H A Dgstacks.cc263 CLocAlnSet aln_loc; // For ref-based. in main()
955 CLocAlnSet aln_loc; in process()
1135 LocusProcessor::process(CLocAlnSet& aln_loc) in process()
1203 for (CLocAlnSet::site_iterator site (aln_loc); bool(site); ++site) { in process()
1825 CLocAlnSet& aln_loc, in add_read_to_aln()
1849 const CLocAlnSet& aln_loc, in phase_hets()
1988 const CLocAlnSet& aln_loc, in phase_sample_hets()
2196 const CLocAlnSet& aln_loc, in count_pairwise_cooccurrences()
2382 const CLocAlnSet& aln_loc, in write_one_locus()
H A Dlocus_readers.h102 bool build_one_locus(CLocAlnSet& readset);
770 bool BamCLocBuilder::build_one_locus(CLocAlnSet& aln_loc) in build_one_locus()