1#ifndef KAORI_SINGLE_BARCODE_SINGLE_END_HPP
2#define KAORI_SINGLE_BARCODE_SINGLE_END_HPP
24template<SeqLength max_size_>
75 my_counts(barcode_pool.size()),
76 my_use_first(options.use_first)
85 State(
typename SimpleSingleMatch<max_size_>::State s,
typename std::vector<Count>::size_type nvar) : search(std::move(s)), counts(nvar) {}
87 typename SimpleSingleMatch<max_size_>::State search;
88 std::vector<Count> counts;
92 void process(State& state,
const std::pair<const char*, const char*>& x)
const {
95 found = my_matcher.search_first(x.first, x.second - x.first, state.search);
97 found = my_matcher.search_best(x.first, x.second - x.first, state.search);
100 ++(state.counts[state.search.index]);
105 static constexpr bool use_names =
false;
114 State initialize()
const {
115 return State(my_matcher.initialize(), my_counts.size());
118 void reduce(State& s) {
119 my_matcher.reduce(s.search);
120 for (
decltype(my_counts.size()) i = 0, end = my_counts.size(); i < end; ++i) {
121 my_counts[i] += s.counts[i];
130 SimpleSingleMatch<max_size_> my_matcher;
131 std::vector<Count> my_counts;
Defines the SimpleSingleMatch class.
Pool of barcode sequences.
Definition BarcodePool.hpp:24
Handler for single-end single barcodes.
Definition SingleBarcodeSingleEnd.hpp:25
const std::vector< Count > & get_counts() const
Definition SingleBarcodeSingleEnd.hpp:140
SingleBarcodeSingleEnd(const char *template_seq, SeqLength template_length, const BarcodePool &barcode_pool, const Options &options)
Definition SingleBarcodeSingleEnd.hpp:62
Count get_total() const
Definition SingleBarcodeSingleEnd.hpp:147
Namespace for the kaori barcode-matching library.
Definition BarcodePool.hpp:16
std::size_t SeqLength
Definition utils.hpp:37
SearchStrand
Definition utils.hpp:31
DuplicateAction
Definition utils.hpp:26
unsigned long long Count
Definition utils.hpp:67
Optional parameters for SimpleSingleMatch.
Definition SimpleSingleMatch.hpp:36
DuplicateAction duplicates
Definition SimpleSingleMatch.hpp:45
int max_mismatches
Definition SimpleSingleMatch.hpp:40
SearchStrand strand
Definition SimpleSingleMatch.hpp:50
Optional parameters for SingleBarcodeSingleEnd.
Definition SingleBarcodeSingleEnd.hpp:30
DuplicateAction duplicates
Definition SingleBarcodeSingleEnd.hpp:50
SearchStrand strand
Definition SingleBarcodeSingleEnd.hpp:45
int max_mismatches
Definition SingleBarcodeSingleEnd.hpp:34
bool use_first
Definition SingleBarcodeSingleEnd.hpp:40