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Searched refs:num_kmers (Results 1 – 7 of 7) sorted by relevance

/dports/biology/stacks/stacks-2.4/src/
H A Dkmer_filter.cc725 int num_kmers; in normalize_paired_reads() local
893 int num_kmers; in normalize_reads() local
1106 int num_kmers; in process_file_kmers() local
1182 int num_kmers = kmers.size(); in calc_kmer_median() local
1184 freqs.reserve(num_kmers); in calc_kmer_median()
1194 (double) (freqs[num_kmers / 2 - 1] + freqs[num_kmers / 2]) / 2.0 : in calc_kmer_median()
1207 (double) (residuals[num_kmers / 2 - 1] + residuals[num_kmers / 2]) / 2.0 : in calc_kmer_median()
1250 (double) (sorted_cnts[num_kmers / 2 - 1] + sorted_cnts[num_kmers / 2]) / 2.0 : in normalize_kmer_lookup()
1286 int num_kmers, in kmer_lookup() argument
1298 cnts.reserve(num_kmers); in kmer_lookup()
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H A Dkmers.cc84 for (int i = 0; i < num_kmers; i++) { in initialize_kmers()
98 if (num_kmers > kmers.size()) { in generate_kmers_lazily()
99 int new_kmers = num_kmers - kmers.size(); in generate_kmers_lazily()
107 for (uint i = 0; i < num_kmers; i++) { in generate_kmers_lazily()
123 for (int i = 0; i < num_kmers; i++) { in generate_kmers()
215 for (int j = 0; j < num_kmers; j++) { in populate_kmer_hash()
242 int num_kmers; in populate_kmer_hash() local
262 for (int j = 0; j < num_kmers; j++) { in populate_kmer_hash()
297 int num_kmers; in populate_kmer_hash() local
318 for (int j = 0; j < num_kmers; j++) { in populate_kmer_hash()
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H A Dustacks.cc541 size_t num_kmers = con_len - kmer_len + 1; in search_for_gaps() local
560 num_kmers = tag_1->len - kmer_len + 1; in search_for_gaps()
563 assert(num_kmers > 0); in search_for_gaps()
566 for (uint j = 0; j < num_kmers; j++) in search_for_gaps()
723 size_t num_kmers = 0; in merge_remainders() local
738 assert(num_kmers > 0); in merge_remainders()
744 for (uint k = 0; k < num_kmers; k++) { in merge_remainders()
884 size_t num_kmers = 0; in search_for_gapped_remainders() local
902 for (uint j = 0; j < num_kmers; j++) in search_for_gapped_remainders()
905 assert(num_kmers > 0); in search_for_gapped_remainders()
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H A Dclean.cc597 int num_kmers = adp_len - kmer_size + 1; in init_adapter_seq() local
599 for (int i = 0; i < num_kmers; i++) { in init_adapter_seq()
613 int num_kmers = href->len - kmer_size + 1; in filter_adapter_seq() local
620 for (int i = 0; i < num_kmers; i++) { in filter_adapter_seq()
H A Dcstacks.cc643 int num_kmers = con_len - kmer_len + 1; in find_kmer_matches_by_sequence() local
645 initialize_kmers(kmer_len, num_kmers, kmers); in find_kmer_matches_by_sequence()
654 num_kmers = allele->second.length() - kmer_len + 1; in find_kmer_matches_by_sequence()
662 for (int j = 0; j < num_kmers; j++) in find_kmer_matches_by_sequence()
807 int num_kmers = con_len - kmer_len + 1; in search_for_gaps() local
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()
833 for (int j = 0; j < num_kmers; j++) in search_for_gaps()
1550 int num_kmers = strlen(catalog.begin()->second->con) - kmer_len + 1; in populate_kmer_hash() local
1562 generate_kmers(allele->second.c_str(), kmer_len, num_kmers, kmers); in populate_kmer_hash()
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H A Dsstacks.cc781 int num_kmers = con_len - gapped_kmer_len + 1; in search_for_gaps() local
812 initialize_kmers(gapped_kmer_len, num_kmers, kmers); in search_for_gaps()
837 generate_kmers_lazily(allele->second.c_str(), gapped_kmer_len, num_kmers, kmers); in search_for_gaps()
844 for (int j = 0; j < num_kmers; j++) in search_for_gaps()
/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/sequence/
H A D_sequence.py1967 num_kmers = len(self) - k + 1
1969 num_kmers = len(self) // k
1973 relative_freqs[kmer] = count / num_kmers