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Searched refs:DNASeq4 (Results 1 – 18 of 18) sorted by relevance

/dports/biology/stacks/stacks-2.4/src/
H A DDNASeq4.h71 class DNASeq4 {
78 DNASeq4() : l_(0), v_() {}
79 explicit DNASeq4(const DNASeq4& other) : l_(other.l_), v_(other.v_) {}
80 DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();}
81 DNASeq4(const char* s, size_t len);
83 DNASeq4(const string& s) : DNASeq4(s.c_str(), s.size()) {}
85 DNASeq4& operator= (const DNASeq4& other) {l_ = other.l_; v_ = other.v_; return *this;}
86 …DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *t…
97 DNASeq4 rev_compl() const;
106 friend struct std::hash<DNASeq4>;
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H A DDNASeq4.cc3 DNASeq4::DNASeq4(const char* s, size_t len) : l_(len), v_() { in DNASeq4() function in DNASeq4
9 string DNASeq4::str() const { in str()
17 DNASeq4 DNASeq4::rev_compl() const { in rev_compl()
18 DNASeq4 rev; in rev_compl()
38 void DNASeq4::resize(size_t len) { in resize()
52 void DNASeq4::append(iterator first, iterator past) { in append()
79 void DNASeq4::remove_Ns() { in remove_Ns()
86 DNASeq4 seq; in remove_Ns()
99 void DNASeq4::shift_Ns_towards_the_end() { in shift_Ns_towards_the_end()
H A Ddebruijn.h32 Kmer(size_t km_len, DNASeq4::iterator& first, DNASeq4::iterator past);
63 const DNASeq4* seq_;
64 DNASeq4::iterator next_nt_;
68 …Kmerizer(size_t km_len, const DNASeq4& seq) : km_len_(km_len), seq_(&seq), next_nt_(seq_->begin())…
219 void rebuild(const vector<const DNASeq4*>& reads, size_t min_kmer_count);
272 Kmer::Kmer(size_t km_len, DNASeq4::iterator& first, DNASeq4::iterator past)
280 DNASeq4::iterator km_start = first;
H A DAlignment.h10 const DNASeq4* seq_;
14 Alignment(const DNASeq4& seq, const Cigar& cigar) : seq_(&seq), cig_(&cigar) { in Alignment()
37 DNASeq4::iterator seq_it_;
38 DNASeq4::iterator seq_past_; // For debugging purposes; only used in assert's.
184 DNASeq4 seq; in merger_of()
H A Dtsv2bam.cc274 map<DNASeq4, vector<string>> pe_reads; in run()
334 map<DNASeq4, vector<string> >& loc_stacks = loc_it->second->pe_reads; in run()
335 …pair<const DNASeq4,vector<string>>& stack = *loc_stacks.insert({DNASeq4(seq.seq), vector<string>()… in run()
393 DNASeq4(seq, seq_len), in run()
402 for (const pair<const DNASeq4, vector<string>>& stack : loc.second.pe_reads) { in run()
411 … dbg_reversed_pe_reads ? stack.first : (const DNASeq4&) stack.first.rev_compl(), in run()
435 DNASeq4(seq, seq_len), in run()
H A DSuffixTree.h112 DNASeq4 seq_;
118 SuffixTree(const DNASeq4& s): seq_(s), seq_str_(seq_.str()) { this->root = new STNode(1); } in SuffixTree()
126 const DNASeq4& seq() { return this->seq_; }; in seq()
H A Dlocus.h230 DNASeq4 ref_;
245 const DNASeq4& ref() const {return ref_;} in ref()
251 void ref(DNASeq4&& s) {ref_ = move(s);} in ref()
273 DNASeq4::iterator ref_it_;
274 DNASeq4::iterator ref_past_;
H A Dgstacks.h260 DNASeq4 assemble_locus_contig(
271 …bool align_reads_to_contig(SuffixTree *st, GappedAln *g_aln, DNASeq4 &query, AlignRes &aln_res) co…
273 …size_t find_locus_overlap(SuffixTree *st, GappedAln *g_aln, const DNASeq4 &se_consensus, string &o…
H A DBamI.h75 DNASeq4 seq() const {return DNASeq4((uchar*) bam_get_seq(r_), r_->core.l_qseq);} in seq()
94 const DNASeq4& seq,
H A Dgstacks.cc1002 DNASeq4 new_ctg; in process()
1584 DNASeq4
1619 return DNASeq4(); in assemble_locus_contig()
1653 return DNASeq4(); in assemble_locus_contig()
1657 DNASeq4 contig = DNASeq4(SPath::contig_str(best_path.begin(), best_path.end(), km_length)); in assemble_locus_contig()
1698 return DNASeq4(); in assemble_locus_contig()
1740 DNASeq4 fw_contig, pe_contig; in assemble_locus_contig()
1741 DNASeq4* todo_contig; in assemble_locus_contig()
1759 return DNASeq4(); in assemble_locus_contig()
1772 return DNASeq4(); in assemble_locus_contig()
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H A Dstacks.h264 DNASeq4 seq;
268 Read(DNASeq4&& s, string&& n) in Read()
H A Ddebruijn.cc109 void Graph::rebuild(const vector<const DNASeq4*>& reads, size_t min_kmer_count) { in rebuild()
119 for (const DNASeq4* s : reads) { in rebuild()
H A Dlocus_readers.h852 DNASeq4 seq = r.seq(); in build_one_locus()
938 DNASeq4 seq = pe_rec.seq(); in build_one_locus()
960 aln_loc.ref(DNASeq4(max_ref_span)); in build_one_locus()
H A Dlocus.cc369 ref_ = DNASeq4(); in clear()
416 DNASeq4::iterator nt = ref_.end(); in hard_clip_right_Ns()
H A DBamI.cc29 const DNASeq4& seq, in assign()
H A Dexport_formats.cc2407 rec.append_allele(DNASeq4(sorted_haps[i].first).rev_compl().str()); in write_batch()
/dports/biology/stacks/stacks-2.4/
H A DMakefile.am23 src/DNASeq4.h src/DNASeq4.cc \
H A DMakefile.in125 src/DNASeq4.$(OBJEXT) src/DNASeq.$(OBJEXT) \
635 src/DNASeq4.h src/DNASeq4.cc \
785 src/DNASeq4.$(OBJEXT): src/$(am__dirstamp) \
988 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/DNASeq4.Po@am__quote@