| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/ |
| H A D | kmercounts.cpp | 89 while (index + kmer_len - 1 < sv.size() && i < kmer_len) { in InitPosBits()
103 if (i < kmer_len) { in InitPosBits()
186 if (m_SeqLength < kmer_len) { in Reset()
313 i += kmer_len - 1; in Reset()
526 if (m_SeqLength < kmer_len) { in Reset()
541 AutoArray<double> base(kmer_len); in Reset()
542 for (Uint4 i=0;i < kmer_len;i++) { in Reset()
557 for (unsigned j=0;j < kmer_len && i < seq_len - kmer_len + 1;j++) { in Reset()
560 i += kmer_len; in Reset()
578 i += kmer_len; in Reset()
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| /dports/biology/stacks/stacks-2.4/src/ |
| H A D | kmers.cc | 27 int kmer_len, span, min_matches; in determine_kmer_length() local
40 for (kmer_len = 7; kmer_len < read_len; kmer_len += 2) { in determine_kmer_length()
48 if (kmer_len >= read_len) { in determine_kmer_length()
53 kmer_len -= 2; in determine_kmer_length()
55 return kmer_len; in determine_kmer_length()
61 span = (kmer_len * (dist + 1)) - 1; in calc_min_kmer_matches()
85 kmer = new char[kmer_len + 1]; in initialize_kmers()
109 strncpy(kmer, k, kmer_len); in generate_kmers_lazily()
110 kmer[kmer_len] = '\0'; in generate_kmers_lazily()
125 strncpy(kmer, k, kmer_len); in generate_kmers()
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| H A D | kmer_filter.cc | 48 int kmer_len = 15; variable
337 char *kmer = new char[kmer_len + 1]; in process_paired_reads()
501 char *kmer = new char[kmer_len + 1]; in process_reads()
727 char *kmer = new char[kmer_len + 1]; in normalize_paired_reads()
895 char *kmer = new char[kmer_len + 1]; in normalize_reads()
1107 char *kmer = new char [kmer_len + 1]; in process_file_kmers()
1118 kmer[kmer_len] = '\0'; in process_file_kmers()
1225 kmer[kmer_len] = '\0'; in normalize_kmer_lookup()
1262 kmer[kmer_len] = '\0'; in normalize_kmer_lookup()
1294 kmer[kmer_len] = '\0'; in kmer_lookup()
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| H A D | ustacks.cc | 529 … uint min_hits = (round((double) con_len * min_match_len) - (kmer_len * max_gaps)) - kmer_len + 1; in search_for_gaps()
541 size_t num_kmers = con_len - kmer_len + 1; in search_for_gaps()
559 if (tag_1->len < kmer_len) continue; in search_for_gaps()
560 num_kmers = tag_1->len - kmer_len + 1; in search_for_gaps()
734 if (r->seq->size() < kmer_len) continue; in merge_remainders()
735 num_kmers = r->seq->size() - kmer_len + 1; in merge_remainders()
867 int min_hits = (round((double) con_len * min_match_len) - (kmer_len * max_gaps)) - kmer_len + 1; in search_for_gapped_remainders()
897 if (r->seq->size() < kmer_len) continue; in search_for_gapped_remainders()
2061 size_t num_kmers = con_len - kmer_len + 1; in calc_kmer_distance()
2071 if (tag_1->len < kmer_len) continue; in calc_kmer_distance()
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| H A D | cstacks.cc | 35 int kmer_len = 0; variable
643 int num_kmers = con_len - kmer_len + 1; in find_kmer_matches_by_sequence()
645 initialize_kmers(kmer_len, num_kmers, kmers); in find_kmer_matches_by_sequence()
652 assert(size_t(kmer_len) <= allele->second.length()); in find_kmer_matches_by_sequence()
654 num_kmers = allele->second.length() - kmer_len + 1; in find_kmer_matches_by_sequence()
790 int kmer_len = 19; in search_for_gaps() local
807 int num_kmers = con_len - kmer_len + 1; in search_for_gaps()
811 initialize_kmers(kmer_len, num_kmers, kmers); in search_for_gaps()
825 num_kmers = allele->second.length() - kmer_len + 1; in search_for_gaps()
1850 kmer_len = is_integer(optarg); in parse_command_line()
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| /dports/biology/canu/canu-2.2/src/overlapErrorAdjustment/ |
| H A D | computeDiff.C | 62 CollectKmerStat(const char* seq, int32 reg_len, int32 kmer_len, int32 *stats) { in CollectKmerStat() argument
63 assert(kmer_len > 0); in CollectKmerStat()
65 memset(stats, 0, sizeof(int32) * (1 << (2 * kmer_len))); in CollectKmerStat()
67 for (int32 i = 0; (i + kmer_len) <= reg_len; i = i + kmer_len) { in CollectKmerStat()
68 stats[Convert2Int(seq + i, kmer_len)]++; in CollectKmerStat()
71 for (int32 i = 0; (i + kmer_len) <= -reg_len; i = i + kmer_len) { in CollectKmerStat()
72 stats[Convert2Int(seq - i, -kmer_len)]++; in CollectKmerStat()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/cobalt/ |
| H A D | kmercounts.hpp | 234 Uint4 kmer_len);
446 static void SetParams(unsigned kmer_len, unsigned alphabet_size) in SetParams() argument
448 TKmerCounts::SetKmerLength(kmer_len); in SetParams()
498 static void SetParams(unsigned kmer_len, ECompressedAlphabet alph) { in SetParams() argument
499 TKmerCounts::SetKmerLength(kmer_len); in SetParams()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/demo/ |
| H A D | clusterer_app.cpp | 146 unsigned int kmer_len = (unsigned int)args["k"].AsInteger(); in x_RunBinary() local
164 TKMethods::SetParams(kmer_len, alph); in x_RunBinary()
231 unsigned int kmer_len = (unsigned int)args["k"].AsInteger(); in x_RunSparse() local
249 TKMethods::SetParams(kmer_len, alph); in x_RunSparse()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/debruijn/ |
| H A D | Integer.hpp | 76 IntegerTemplate(int kmer_len, uint64_t n) { in IntegerTemplate() argument
77 int p = (kmer_len+31)/32; in IntegerTemplate()
304 cast_from_other(int kl) : kmer_len(kl) {} in cast_from_other()
313 int partial_part_bits = 2*(kmer_len%32); in operator ()()
319 int kmer_len; member
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| H A D | DBGraph.hpp | 23 CKmerCountTemplate(int kmer_len = 0) : m_kmer_len(kmer_len) { in CKmerCountTemplate() argument
255 CKmerMapTemplate(int kmer_len = 0) : m_kmer_len(kmer_len) { in CKmerMapTemplate() argument
615 size_t KmerNum(unsigned kmer_len) const { in KmerNum()
620 if(l >= kmer_len) in KmerNum()
621 num += l-kmer_len+1; in KmerNum()
643 …iterator(int kmer_len, const CReadHolder& rholder, size_t position = 0, size_t position_in_read = … in kmer_iterator() argument
688 kmer_iterator kbegin(int kmer_len) const { return kmer_iterator(kmer_len, *this); } in kbegin()
712 kmer_iterator KmersForRead(int kmer_len) const { in KmersForRead()
713 if(kmer_len <= (int)m_readholder.m_read_length[m_read]) in KmersForRead()
714 return kmer_iterator(kmer_len, m_readholder, m_position, 0, m_read); in KmersForRead()
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | repeat_builder.cpp | 2731 const size_t kmer_len = 12; in merge() local
2733 build_kmer_table(consensus_, kmer_table, kmer_len); in merge()
2740 kmer_len, in merge()
2797 kmer_len, in merge()
2829 kmer_len, in merge()
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