diff --git a/docs/DualBarcodesWithDiagnostics_8hpp.html b/docs/DualBarcodesPairedEndWithDiagnostics_8hpp.html similarity index 89% rename from docs/DualBarcodesWithDiagnostics_8hpp.html rename to docs/DualBarcodesPairedEndWithDiagnostics_8hpp.html index 8411228..1cf457f 100644 --- a/docs/DualBarcodesWithDiagnostics_8hpp.html +++ b/docs/DualBarcodesPairedEndWithDiagnostics_8hpp.html @@ -5,7 +5,7 @@ -kaori: kaori/handlers/DualBarcodesWithDiagnostics.hpp File Reference +kaori: kaori/handlers/DualBarcodesPairedEndWithDiagnostics.hpp File Reference @@ -78,19 +78,19 @@
Classes | Namespaces
-
DualBarcodesWithDiagnostics.hpp File Reference
+
DualBarcodesPairedEndWithDiagnostics.hpp File Reference

Process dual barcodes with extra diagnostics. More...

-

Go to the source code of this file.

+

Go to the source code of this file.

- - + +

Classes

class  kaori::DualBarcodesWithDiagnostics< max_size >
 Handler for dual barcodes with extra diagnostics. More...
class  kaori::DualBarcodesPairedEndWithDiagnostics< max_size >
 Handler for dual barcodes with extra diagnostics. More...
 
- +

diff --git a/docs/DualBarcodesWithDiagnostics_8hpp_source.html b/docs/DualBarcodesPairedEndWithDiagnostics_8hpp_source.html similarity index 58% rename from docs/DualBarcodesWithDiagnostics_8hpp_source.html rename to docs/DualBarcodesPairedEndWithDiagnostics_8hpp_source.html index 707eede..a23ce89 100644 --- a/docs/DualBarcodesWithDiagnostics_8hpp_source.html +++ b/docs/DualBarcodesPairedEndWithDiagnostics_8hpp_source.html @@ -5,7 +5,7 @@ -kaori: kaori/handlers/DualBarcodesWithDiagnostics.hpp Source File +kaori: kaori/handlers/DualBarcodesPairedEndWithDiagnostics.hpp Source File @@ -75,25 +75,25 @@
-
DualBarcodesWithDiagnostics.hpp
+
DualBarcodesPairedEndWithDiagnostics.hpp
-Go to the documentation of this file.
1#ifndef KAORI_DUAL_BARCODES_WITH_DIAGNOSTICS_HPP
-
2#define KAORI_DUAL_BARCODES_WITH_DIAGNOSTICS_HPP
+Go to the documentation of this file.
1#ifndef KAORI_DUAL_BARCODES_PAIRED_END_WITH_DIAGNOSTICS_HPP
+
2#define KAORI_DUAL_BARCODES_PAIRED_END_WITH_DIAGNOSTICS_HPP
3
-
4#include "DualBarcodes.hpp"
+
4#include "DualBarcodesPairedEnd.hpp"
5#include "CombinatorialBarcodesPairedEnd.hpp"
6#include "../utils.hpp"
7
14namespace kaori {
15
25template<size_t max_size>
-
26class DualBarcodesWithDiagnostics {
+
26class DualBarcodesPairedEndWithDiagnostics {
27public:
-
44 DualBarcodesWithDiagnostics(
+
44 DualBarcodesPairedEndWithDiagnostics(
45 const char* template_seq1, size_t template_length1, const BarcodePool& barcode_pool1,
46 const char* template_seq2, size_t template_length2, const BarcodePool& barcode_pool2,
-
47 const typename DualBarcodes<max_size>::Options& options
+
47 const typename DualBarcodesPairedEnd<max_size>::Options& options
48 ) :
49 dual_handler(template_seq1, template_length1, barcode_pool1, template_seq2, template_length2, barcode_pool2, options),
50
@@ -106,31 +106,31 @@
57 barcode_pool2,
58 [&]{
59 typename CombinatorialBarcodesPairedEnd<max_size>::Options combopt;
-
60 combopt.use_first = options.use_first;
+
60 combopt.use_first = options.use_first;
61
-
62 combopt.max_mismatches1 = options.max_mismatches1;
-
63 combopt.strand1 = options.strand1;
-
64 combopt.max_mismatches2 = options.max_mismatches2;
-
65 combopt.strand2 = options.strand2;
+
62 combopt.max_mismatches1 = options.max_mismatches1;
+
63 combopt.strand1 = options.strand1;
+
64 combopt.max_mismatches2 = options.max_mismatches2;
+
65 combopt.strand2 = options.strand2;
66
67 // we allow duplicates in the trie for each individual barcode, as only the pairs are unique in the dual barcode setup.
68 combopt.duplicates = DuplicateAction::FIRST;
-
69 combopt.random = options.random;
+
69 combopt.random = options.random;
70 return combopt;
71 }()
72 )
73 {}
74
75private:
-
76 DualBarcodes<max_size> dual_handler;
+
76 DualBarcodesPairedEnd<max_size> dual_handler;
77 CombinatorialBarcodesPairedEnd<max_size> combo_handler;
78
79public:
83 struct State {
84 State() {}
-
85 State(typename DualBarcodes<max_size>::State ds, typename CombinatorialBarcodesPairedEnd<max_size>::State cs) : dual_state(std::move(ds)), combo_state(std::move(cs)) {}
+
85 State(typename DualBarcodesPairedEnd<max_size>::State ds, typename CombinatorialBarcodesPairedEnd<max_size>::State cs) : dual_state(std::move(ds)), combo_state(std::move(cs)) {}
86
-
90 typename DualBarcodes<max_size>::State dual_state;
+
90 typename DualBarcodesPairedEnd<max_size>::State dual_state;
91 typename CombinatorialBarcodesPairedEnd<max_size>::State combo_state;
95 };
96
@@ -152,54 +152,57 @@
119 }
120 }
125public:
-
130 void sort() {
+
130 void sort() {
131 combo_handler.sort();
132 }
133
-
139 const std::vector<int>& get_counts() const {
+
139 const std::vector<int>& get_counts() const {
140 return dual_handler.get_counts();
141 }
142
-
147 const std::vector<std::array<int, 2> >& get_combinations() const {
+
147 const std::vector<std::array<int, 2> >& get_combinations() const {
148 return combo_handler.get_combinations();
149 }
150
-
154 int get_total() const {
+
154 int get_total() const {
155 return dual_handler.get_total();
156 }
157
-
161 int get_barcode1_only() const {
+
161 int get_barcode1_only() const {
162 return combo_handler.get_barcode1_only();
163 }
164
-
168 int get_barcode2_only() const {
+
168 int get_barcode2_only() const {
169 return combo_handler.get_barcode2_only();
170 }
171};
172
-
173}
-
174
-
175#endif
+
176// Soft-deprecated back-compatible aliases.
+
177template<size_t max_size>
+
178using DualBarcodesWithDiagnostics = DualBarcodesPairedEndWithDiagnostics<max_size>;
+
183}
+
184
+
185#endif
CombinatorialBarcodesPairedEnd.hpp
Process paired-end combinatorial barcodes.
-
DualBarcodes.hpp
Process dual barcodes.
+
DualBarcodesPairedEnd.hpp
Process dual barcodes.
kaori::CombinatorialBarcodesPairedEnd
Handler for paired-end combinatorial barcodes.
Definition: CombinatorialBarcodesPairedEnd.hpp:29
-
kaori::DualBarcodesWithDiagnostics
Handler for dual barcodes with extra diagnostics.
Definition: DualBarcodesWithDiagnostics.hpp:26
-
kaori::DualBarcodesWithDiagnostics::get_barcode1_only
int get_barcode1_only() const
Definition: DualBarcodesWithDiagnostics.hpp:161
-
kaori::DualBarcodesWithDiagnostics::get_counts
const std::vector< int > & get_counts() const
Definition: DualBarcodesWithDiagnostics.hpp:139
-
kaori::DualBarcodesWithDiagnostics::get_total
int get_total() const
Definition: DualBarcodesWithDiagnostics.hpp:154
-
kaori::DualBarcodesWithDiagnostics::get_combinations
const std::vector< std::array< int, 2 > > & get_combinations() const
Definition: DualBarcodesWithDiagnostics.hpp:147
-
kaori::DualBarcodesWithDiagnostics::get_barcode2_only
int get_barcode2_only() const
Definition: DualBarcodesWithDiagnostics.hpp:168
-
kaori::DualBarcodesWithDiagnostics::DualBarcodesWithDiagnostics
DualBarcodesWithDiagnostics(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const typename DualBarcodes< max_size >::Options &options)
Definition: DualBarcodesWithDiagnostics.hpp:44
-
kaori::DualBarcodesWithDiagnostics::sort
void sort()
Definition: DualBarcodesWithDiagnostics.hpp:130
+
kaori::DualBarcodesPairedEndWithDiagnostics
Handler for dual barcodes with extra diagnostics.
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:26
+
kaori::DualBarcodesPairedEndWithDiagnostics::get_combinations
const std::vector< std::array< int, 2 > > & get_combinations() const
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:147
+
kaori::DualBarcodesPairedEndWithDiagnostics::get_counts
const std::vector< int > & get_counts() const
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:139
+
kaori::DualBarcodesPairedEndWithDiagnostics::DualBarcodesPairedEndWithDiagnostics
DualBarcodesPairedEndWithDiagnostics(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const typename DualBarcodesPairedEnd< max_size >::Options &options)
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:44
+
kaori::DualBarcodesPairedEndWithDiagnostics::get_barcode2_only
int get_barcode2_only() const
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:168
+
kaori::DualBarcodesPairedEndWithDiagnostics::sort
void sort()
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:130
+
kaori::DualBarcodesPairedEndWithDiagnostics::get_barcode1_only
int get_barcode1_only() const
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:161
+
kaori::DualBarcodesPairedEndWithDiagnostics::get_total
int get_total() const
Definition: DualBarcodesPairedEndWithDiagnostics.hpp:154
kaori
Namespace for the kaori barcode-matching library.
Definition: BarcodePool.hpp:13
kaori::BarcodePool
Pool of barcode sequences for a variable region.
Definition: BarcodePool.hpp:21
-
kaori::DualBarcodes::Options
Optional parameters for SingleBarcodeSingleEnd.
Definition: DualBarcodes.hpp:32
-
kaori::DualBarcodes::Options::strand1
SearchStrand strand1
Definition: DualBarcodes.hpp:48
-
kaori::DualBarcodes::Options::random
bool random
Definition: DualBarcodes.hpp:71
-
kaori::DualBarcodes::Options::use_first
bool use_first
Definition: DualBarcodes.hpp:37
-
kaori::DualBarcodes::Options::strand2
SearchStrand strand2
Definition: DualBarcodes.hpp:59
-
kaori::DualBarcodes::Options::max_mismatches1
int max_mismatches1
Definition: DualBarcodes.hpp:42
-
kaori::DualBarcodes::Options::max_mismatches2
int max_mismatches2
Definition: DualBarcodes.hpp:53
+
kaori::DualBarcodesPairedEnd::Options
Optional parameters for DualBarcodesPairedEnd.
Definition: DualBarcodesPairedEnd.hpp:32
+
kaori::DualBarcodesPairedEnd::Options::max_mismatches1
int max_mismatches1
Definition: DualBarcodesPairedEnd.hpp:42
+
kaori::DualBarcodesPairedEnd::Options::random
bool random
Definition: DualBarcodesPairedEnd.hpp:71
+
kaori::DualBarcodesPairedEnd::Options::max_mismatches2
int max_mismatches2
Definition: DualBarcodesPairedEnd.hpp:53
+
kaori::DualBarcodesPairedEnd::Options::strand2
SearchStrand strand2
Definition: DualBarcodesPairedEnd.hpp:59
+
kaori::DualBarcodesPairedEnd::Options::use_first
bool use_first
Definition: DualBarcodesPairedEnd.hpp:37
+
kaori::DualBarcodesPairedEnd::Options::strand1
SearchStrand strand1
Definition: DualBarcodesPairedEnd.hpp:48
diff --git a/docs/DualBarcodes_8hpp.html b/docs/DualBarcodesPairedEnd_8hpp.html similarity index 86% rename from docs/DualBarcodes_8hpp.html rename to docs/DualBarcodesPairedEnd_8hpp.html index 01ddfcd..585b474 100644 --- a/docs/DualBarcodes_8hpp.html +++ b/docs/DualBarcodesPairedEnd_8hpp.html @@ -5,7 +5,7 @@ -kaori: kaori/handlers/DualBarcodes.hpp File Reference +kaori: kaori/handlers/DualBarcodesPairedEnd.hpp File Reference @@ -78,22 +78,22 @@
Classes | Namespaces
-
DualBarcodes.hpp File Reference
+
DualBarcodesPairedEnd.hpp File Reference

Process dual barcodes. More...

-

Go to the source code of this file.

+

Go to the source code of this file.

- - + + - - + +

Classes

class  kaori::DualBarcodes< max_size >
 Handler for dual barcodes. More...
class  kaori::DualBarcodesPairedEnd< max_size >
 Handler for dual barcodes. More...
 
struct  kaori::DualBarcodes< max_size >::Options
 Optional parameters for SingleBarcodeSingleEnd. More...
struct  kaori::DualBarcodesPairedEnd< max_size >::Options
 Optional parameters for DualBarcodesPairedEnd. More...
 
- - - + + + diff --git a/docs/classes.html b/docs/classes.html index e196582..607aeb8 100644 --- a/docs/classes.html +++ b/docs/classes.html @@ -87,7 +87,7 @@
CombinatorialBarcodesPairedEnd (kaori)
CombinatorialBarcodesSingleEnd (kaori)
D
-
DualBarcodes (kaori)
DualBarcodesWithDiagnostics (kaori)
+
DualBarcodesPairedEnd (kaori)
DualBarcodesPairedEndWithDiagnostics (kaori)
F
FastqReader (kaori)
@@ -96,7 +96,7 @@
MismatchTrie (kaori)
O
-
CombinatorialBarcodesSingleEnd::Options (kaori)
DualBarcodes::Options (kaori)
RandomBarcodeSingleEnd::Options (kaori)
SegmentedBarcodeSearch::Options (kaori)
SimpleBarcodeSearch::Options (kaori)
SimpleSingleMatch::Options (kaori)
SingleBarcodePairedEnd::Options (kaori)
SingleBarcodeSingleEnd::Options (kaori)
+
CombinatorialBarcodesSingleEnd::Options (kaori)
DualBarcodesPairedEnd::Options (kaori)
RandomBarcodeSingleEnd::Options (kaori)
SegmentedBarcodeSearch::Options (kaori)
SimpleBarcodeSearch::Options (kaori)
SimpleSingleMatch::Options (kaori)
SingleBarcodePairedEnd::Options (kaori)
SingleBarcodeSingleEnd::Options (kaori)
R
RandomBarcodeSingleEnd (kaori)
SegmentedMismatches::Result (kaori)
diff --git a/docs/classkaori_1_1DualBarcodes-members.html b/docs/classkaori_1_1DualBarcodesPairedEnd-members.html similarity index 72% rename from docs/classkaori_1_1DualBarcodes-members.html rename to docs/classkaori_1_1DualBarcodesPairedEnd-members.html index efa1c6a..aaaba66 100644 --- a/docs/classkaori_1_1DualBarcodes-members.html +++ b/docs/classkaori_1_1DualBarcodesPairedEnd-members.html @@ -71,19 +71,19 @@
-
kaori::DualBarcodes< max_size > Member List
+
kaori::DualBarcodesPairedEnd< max_size > Member List
-

This is the complete list of members for kaori::DualBarcodes< max_size >, including all inherited members.

+

This is the complete list of members for kaori::DualBarcodesPairedEnd< max_size >, including all inherited members.

diff --git a/docs/DualBarcodes_8hpp_source.html b/docs/DualBarcodesPairedEnd_8hpp_source.html similarity index 84% rename from docs/DualBarcodes_8hpp_source.html rename to docs/DualBarcodesPairedEnd_8hpp_source.html index b7d95b6..b0dabac 100644 --- a/docs/DualBarcodes_8hpp_source.html +++ b/docs/DualBarcodesPairedEnd_8hpp_source.html @@ -5,7 +5,7 @@ -kaori: kaori/handlers/DualBarcodes.hpp Source File +kaori: kaori/handlers/DualBarcodesPairedEnd.hpp Source File @@ -75,10 +75,10 @@
-
DualBarcodes.hpp
+
DualBarcodesPairedEnd.hpp
-Go to the documentation of this file.
1#ifndef KAORI_DUAL_BARCODES_HPP
+Go to the documentation of this file.
1#ifndef KAORI_DUAL_BARCODES_HPP
2#define KAORI_DUAL_BARCODES_HPP
3
4#include "../ScanTemplate.hpp"
@@ -88,29 +88,29 @@
14namespace kaori {
15
26template<size_t max_size>
-
27class DualBarcodes {
+
27class DualBarcodesPairedEnd {
28public:
-
32 struct Options {
-
37 bool use_first = true;
+
32 struct Options {
+
37 bool use_first = true;
38
-
42 int max_mismatches1 = 0;
+
42 int max_mismatches1 = 0;
43
-
48 SearchStrand strand1 = SearchStrand::FORWARD;
+
48 SearchStrand strand1 = SearchStrand::FORWARD;
49
-
53 int max_mismatches2 = 0;
+
53 int max_mismatches2 = 0;
54
-
59 SearchStrand strand2 = SearchStrand::FORWARD;
+
59 SearchStrand strand2 = SearchStrand::FORWARD;
60
-
64 DuplicateAction duplicates = DuplicateAction::ERROR;
+
64 DuplicateAction duplicates = DuplicateAction::ERROR;
65
-
71 bool random = false;
+
71 bool random = false;
72 };
73
74public:
-
92 DualBarcodes(
+
92 DualBarcodesPairedEnd(
93 const char* template_seq1, size_t template_length1, const BarcodePool& barcode_pool1,
94 const char* template_seq2, size_t template_length2, const BarcodePool& barcode_pool2,
-
95 const Options& options
+
95 const Options& options
96 ) :
97 search_reverse1(search_reverse(options.strand1)),
98 search_reverse2(search_reverse(options.strand2)),
@@ -189,7 +189,7 @@
171 [&]{
172 typename SegmentedBarcodeSearch<2>::Options bopt;
173 bopt.max_mismatches = { max_mm1, max_mm2 };
-
174 bopt.duplicates = options.duplicates;
+
174 bopt.duplicates = options.duplicates;
175 bopt.reverse = false; // we already handle strandedness when creating 'combined_set'.
176 return bopt;
177 }()
@@ -392,22 +392,25 @@
388 int total = 0;
389
390public:
-
396 const std::vector<int>& get_counts() const {
+
396 const std::vector<int>& get_counts() const {
397 return counts;
398 }
399
-
403 int get_total() const {
+
403 int get_total() const {
404 return total;
405 }
406};
407
-
408}
-
409
-
410#endif
-
kaori::DualBarcodes
Handler for dual barcodes.
Definition: DualBarcodes.hpp:27
-
kaori::DualBarcodes::DualBarcodes
DualBarcodes(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const Options &options)
Definition: DualBarcodes.hpp:92
-
kaori::DualBarcodes::get_counts
const std::vector< int > & get_counts() const
Definition: DualBarcodes.hpp:396
-
kaori::DualBarcodes::get_total
int get_total() const
Definition: DualBarcodes.hpp:403
+
411// Soft-deprecated back-compatible aliases.
+
412template<size_t max_size>
+
413using DualBarcodes = DualBarcodesPairedEnd<max_size>;
+
418}
+
419
+
420#endif
+
kaori::DualBarcodesPairedEnd
Handler for dual barcodes.
Definition: DualBarcodesPairedEnd.hpp:27
+
kaori::DualBarcodesPairedEnd::get_counts
const std::vector< int > & get_counts() const
Definition: DualBarcodesPairedEnd.hpp:396
+
kaori::DualBarcodesPairedEnd::DualBarcodesPairedEnd
DualBarcodesPairedEnd(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const Options &options)
Definition: DualBarcodesPairedEnd.hpp:92
+
kaori::DualBarcodesPairedEnd::get_total
int get_total() const
Definition: DualBarcodesPairedEnd.hpp:403
kaori::SegmentedBarcodeSearch
Search for known barcode sequences with segmented mismatches.
Definition: BarcodeSearch.hpp:290
kaori::SegmentedBarcodeSearch::reduce
void reduce(State &state)
Definition: BarcodeSearch.hpp:423
kaori::SegmentedBarcodeSearch::search
void search(const std::string &search_seq, State &state) const
Definition: BarcodeSearch.hpp:461
@@ -415,14 +418,14 @@
kaori::BarcodePool
Pool of barcode sequences for a variable region.
Definition: BarcodePool.hpp:21
kaori::BarcodePool::length
size_t length
Definition: BarcodePool.hpp:59
kaori::BarcodePool::size
size_t size() const
Definition: BarcodePool.hpp:64
-
kaori::DualBarcodes::Options
Optional parameters for SingleBarcodeSingleEnd.
Definition: DualBarcodes.hpp:32
-
kaori::DualBarcodes::Options::strand1
SearchStrand strand1
Definition: DualBarcodes.hpp:48
-
kaori::DualBarcodes::Options::random
bool random
Definition: DualBarcodes.hpp:71
-
kaori::DualBarcodes::Options::use_first
bool use_first
Definition: DualBarcodes.hpp:37
-
kaori::DualBarcodes::Options::strand2
SearchStrand strand2
Definition: DualBarcodes.hpp:59
-
kaori::DualBarcodes::Options::max_mismatches1
int max_mismatches1
Definition: DualBarcodes.hpp:42
-
kaori::DualBarcodes::Options::duplicates
DuplicateAction duplicates
Definition: DualBarcodes.hpp:64
-
kaori::DualBarcodes::Options::max_mismatches2
int max_mismatches2
Definition: DualBarcodes.hpp:53
+
kaori::DualBarcodesPairedEnd::Options
Optional parameters for DualBarcodesPairedEnd.
Definition: DualBarcodesPairedEnd.hpp:32
+
kaori::DualBarcodesPairedEnd::Options::max_mismatches1
int max_mismatches1
Definition: DualBarcodesPairedEnd.hpp:42
+
kaori::DualBarcodesPairedEnd::Options::random
bool random
Definition: DualBarcodesPairedEnd.hpp:71
+
kaori::DualBarcodesPairedEnd::Options::max_mismatches2
int max_mismatches2
Definition: DualBarcodesPairedEnd.hpp:53
+
kaori::DualBarcodesPairedEnd::Options::strand2
SearchStrand strand2
Definition: DualBarcodesPairedEnd.hpp:59
+
kaori::DualBarcodesPairedEnd::Options::duplicates
DuplicateAction duplicates
Definition: DualBarcodesPairedEnd.hpp:64
+
kaori::DualBarcodesPairedEnd::Options::use_first
bool use_first
Definition: DualBarcodesPairedEnd.hpp:37
+
kaori::DualBarcodesPairedEnd::Options::strand1
SearchStrand strand1
Definition: DualBarcodesPairedEnd.hpp:48
kaori::SegmentedBarcodeSearch::Options
Optional parameters for a SegmentedBarcodeSearch.
Definition: BarcodeSearch.hpp:295
kaori::SegmentedBarcodeSearch::Options::max_mismatches
std::array< int, num_segments > max_mismatches
Definition: BarcodeSearch.hpp:309
kaori::SegmentedBarcodeSearch::Options::reverse
bool reverse
Definition: BarcodeSearch.hpp:315
diff --git a/docs/annotated.html b/docs/annotated.html index a01c355..e2e6567 100644 --- a/docs/annotated.html +++ b/docs/annotated.html @@ -82,9 +82,9 @@

 CCombinatorialBarcodesPairedEndHandler for paired-end combinatorial barcodes
 ▼CCombinatorialBarcodesSingleEndHandler for single-end combinatorial barcodes
 COptionsOptional parameters for CombinatorialBarcodeSingleEnd
 ▼CDualBarcodesHandler for dual barcodes
 COptionsOptional parameters for SingleBarcodeSingleEnd
 CDualBarcodesWithDiagnosticsHandler for dual barcodes with extra diagnostics
 ▼CDualBarcodesPairedEndHandler for dual barcodes
 COptionsOptional parameters for DualBarcodesPairedEnd
 CDualBarcodesPairedEndWithDiagnosticsHandler for dual barcodes with extra diagnostics
 CFastqReaderStream reads from a FASTQ file
 ▼CMismatchTrieBase class for the mismatch search
 CAddStatusStatus of the barcode sequence addition
- - - + + +
DualBarcodes(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const Options &options)kaori::DualBarcodes< max_size >inline
get_counts() constkaori::DualBarcodes< max_size >inline
get_total() constkaori::DualBarcodes< max_size >inline
DualBarcodesPairedEnd(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const Options &options)kaori::DualBarcodesPairedEnd< max_size >inline
get_counts() constkaori::DualBarcodesPairedEnd< max_size >inline
get_total() constkaori::DualBarcodesPairedEnd< max_size >inline
diff --git a/docs/classkaori_1_1DualBarcodes.html b/docs/classkaori_1_1DualBarcodesPairedEnd.html similarity index 77% rename from docs/classkaori_1_1DualBarcodes.html rename to docs/classkaori_1_1DualBarcodesPairedEnd.html index 235afca..089e76e 100644 --- a/docs/classkaori_1_1DualBarcodes.html +++ b/docs/classkaori_1_1DualBarcodesPairedEnd.html @@ -5,7 +5,7 @@ -kaori: kaori::DualBarcodes< max_size > Class Template Reference +kaori: kaori::DualBarcodesPairedEnd< max_size > Class Template Reference @@ -71,41 +71,41 @@
Classes | Public Member Functions | -List of all members
-
kaori::DualBarcodes< max_size > Class Template Reference
+List of all members
+
kaori::DualBarcodesPairedEnd< max_size > Class Template Reference

Handler for dual barcodes. - More...

+ More...

-

#include <DualBarcodes.hpp>

+

#include <DualBarcodesPairedEnd.hpp>

- - + +

Classes

struct  Options
 Optional parameters for SingleBarcodeSingleEnd. More...
struct  Options
 Optional parameters for DualBarcodesPairedEnd. More...
 
- - - - - - + + + + + +

Public Member Functions

 DualBarcodes (const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const Options &options)
 
const std::vector< int > & get_counts () const
 
int get_total () const
 
 DualBarcodesPairedEnd (const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const Options &options)
 
const std::vector< int > & get_counts () const
 
int get_total () const
 

Detailed Description

template<size_t max_size>
-class kaori::DualBarcodes< max_size >

Handler for dual barcodes.

+class kaori::DualBarcodesPairedEnd< max_size >

Handler for dual barcodes.

In this design, each read contains a barcoding element created from a template with a single variable region. For one read, the barcode is drawn from one pool of options, while the other read contains a barcode from another pool. However, unlike CombinatorialBarcodesPairedEnd, the combinations are not random but are specifically assembled, typically corresponding to specific pairs of genes. This handler will capture the frequencies of each barcode combination.

Template Parameters
@@ -114,8 +114,8 @@

Constructor & Destructor Documentation

- -

◆ DualBarcodes()

+ +

◆ DualBarcodesPairedEnd()

@@ -126,7 +126,7 @@

- + @@ -164,7 +164,7 @@

- + @@ -191,13 +191,13 @@

Options::duplicates.

+

barcode_pool1 and barcode_pool2 are expected to have the same number of barcodes. Corresponding values across the two pools define a particular combination of dual barcodes. Duplication of sequences within each pool is allowed; only pairs of the same barcodes are considered to be duplicates with respect to Options::duplicates.

Member Function Documentation

- -

◆ get_counts()

+ +

◆ get_counts()

@@ -208,7 +208,7 @@

kaori::DualBarcodes< max_size >::DualBarcodes kaori::DualBarcodesPairedEnd< max_size >::DualBarcodesPairedEnd ( const char *  template_seq1, const Options & const Options &  options 
- + @@ -224,8 +224,8 @@

-

◆ get_total()

+ +

◆ get_total()

@@ -236,7 +236,7 @@

const std::vector< int > & kaori::DualBarcodes< max_size >::get_counts const std::vector< int > & kaori::DualBarcodesPairedEnd< max_size >::get_counts ( ) const
- + @@ -253,7 +253,7 @@

DualBarcodes.hpp +
  • kaori/handlers/DualBarcodesPairedEnd.hpp
    • diff --git a/docs/classkaori_1_1DualBarcodesWithDiagnostics-members.html b/docs/classkaori_1_1DualBarcodesPairedEndWithDiagnostics-members.html similarity index 56% rename from docs/classkaori_1_1DualBarcodesWithDiagnostics-members.html rename to docs/classkaori_1_1DualBarcodesPairedEndWithDiagnostics-members.html index dda644f..63ffef7 100644 --- a/docs/classkaori_1_1DualBarcodesWithDiagnostics-members.html +++ b/docs/classkaori_1_1DualBarcodesPairedEndWithDiagnostics-members.html @@ -71,23 +71,23 @@
    -
    kaori::DualBarcodesWithDiagnostics< max_size > Member List
    +
    kaori::DualBarcodesPairedEndWithDiagnostics< max_size > Member List
    -

    This is the complete list of members for kaori::DualBarcodesWithDiagnostics< max_size >, including all inherited members.

    +

    This is the complete list of members for kaori::DualBarcodesPairedEndWithDiagnostics< max_size >, including all inherited members.

    int kaori::DualBarcodes< max_size >::get_total int kaori::DualBarcodesPairedEnd< max_size >::get_total ( ) const
    - - - - - - - + + + + + + +
    DualBarcodesWithDiagnostics(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const typename DualBarcodes< max_size >::Options &options)kaori::DualBarcodesWithDiagnostics< max_size >inline
    get_barcode1_only() constkaori::DualBarcodesWithDiagnostics< max_size >inline
    get_barcode2_only() constkaori::DualBarcodesWithDiagnostics< max_size >inline
    get_combinations() constkaori::DualBarcodesWithDiagnostics< max_size >inline
    get_counts() constkaori::DualBarcodesWithDiagnostics< max_size >inline
    get_total() constkaori::DualBarcodesWithDiagnostics< max_size >inline
    sort()kaori::DualBarcodesWithDiagnostics< max_size >inline
    DualBarcodesPairedEndWithDiagnostics(const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const typename DualBarcodesPairedEnd< max_size >::Options &options)kaori::DualBarcodesPairedEndWithDiagnostics< max_size >inline
    get_barcode1_only() constkaori::DualBarcodesPairedEndWithDiagnostics< max_size >inline
    get_barcode2_only() constkaori::DualBarcodesPairedEndWithDiagnostics< max_size >inline
    get_combinations() constkaori::DualBarcodesPairedEndWithDiagnostics< max_size >inline
    get_counts() constkaori::DualBarcodesPairedEndWithDiagnostics< max_size >inline
    get_total() constkaori::DualBarcodesPairedEndWithDiagnostics< max_size >inline
    sort()kaori::DualBarcodesPairedEndWithDiagnostics< max_size >inline
    diff --git a/docs/classkaori_1_1DualBarcodesWithDiagnostics.html b/docs/classkaori_1_1DualBarcodesPairedEndWithDiagnostics.html similarity index 69% rename from docs/classkaori_1_1DualBarcodesWithDiagnostics.html rename to docs/classkaori_1_1DualBarcodesPairedEndWithDiagnostics.html index e817f1e..1e81b08 100644 --- a/docs/classkaori_1_1DualBarcodesWithDiagnostics.html +++ b/docs/classkaori_1_1DualBarcodesPairedEndWithDiagnostics.html @@ -5,7 +5,7 @@ -kaori: kaori::DualBarcodesWithDiagnostics< max_size > Class Template Reference +kaori: kaori::DualBarcodesPairedEndWithDiagnostics< max_size > Class Template Reference @@ -71,43 +71,43 @@
    Public Member Functions | -List of all members
    -
    kaori::DualBarcodesWithDiagnostics< max_size > Class Template Reference
    +List of all members
    +
    kaori::DualBarcodesPairedEndWithDiagnostics< max_size > Class Template Reference

    Handler for dual barcodes with extra diagnostics. - More...

    + More...

    -

    #include <DualBarcodesWithDiagnostics.hpp>

    +

    #include <DualBarcodesPairedEndWithDiagnostics.hpp>

    - - - - - - - - - - - - - - + + + + + + + + + + + + + +

    Public Member Functions

     DualBarcodesWithDiagnostics (const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const typename DualBarcodes< max_size >::Options &options)
     
    void sort ()
     
    const std::vector< int > & get_counts () const
     
    const std::vector< std::array< int, 2 > > & get_combinations () const
     
    int get_total () const
     
    int get_barcode1_only () const
     
    int get_barcode2_only () const
     
     DualBarcodesPairedEndWithDiagnostics (const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const typename DualBarcodesPairedEnd< max_size >::Options &options)
     
    void sort ()
     
    const std::vector< int > & get_counts () const
     
    const std::vector< std::array< int, 2 > > & get_combinations () const
     
    int get_total () const
     
    int get_barcode1_only () const
     
    int get_barcode2_only () const
     

    Detailed Description

    template<size_t max_size>
    -class kaori::DualBarcodesWithDiagnostics< max_size >

    Handler for dual barcodes with extra diagnostics.

    -

    This provides the same information as DualBarcodes but also captures the frequency of the invalid combinations. These frequences can be helpful for diagnosing problems with library construction. The handler also counts the number of reads where only one barcode construct matches to a read.

    +class kaori::DualBarcodesPairedEndWithDiagnostics< max_size >

    Handler for dual barcodes with extra diagnostics.

    +

    This provides the same information as DualBarcodesPairedEnd but also captures the frequency of the invalid combinations. These frequences can be helpful for diagnosing problems with library construction. The handler also counts the number of reads where only one barcode construct matches to a read.

    Template Parameters
    @@ -115,8 +115,8 @@

    Constructor & Destructor Documentation

    - -

    ◆ DualBarcodesWithDiagnostics()

    + +

    ◆ DualBarcodesPairedEndWithDiagnostics()

    @@ -127,7 +127,7 @@

    max_sizeMaximum length of the template sequences on both reads.
    - + @@ -165,7 +165,7 @@

    - + @@ -197,8 +197,8 @@

    Member Function Documentation

    - -

    ◆ get_barcode1_only()

    + +

    ◆ get_barcode1_only()

    @@ -209,7 +209,7 @@

    kaori::DualBarcodesWithDiagnostics< max_size >::DualBarcodesWithDiagnostics kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::DualBarcodesPairedEndWithDiagnostics ( const char *  template_seq1, const typename DualBarcodes< max_size >::Options & const typename DualBarcodesPairedEnd< max_size >::Options &  options 
    - + @@ -225,8 +225,8 @@

    -

    ◆ get_barcode2_only()

    + +

    ◆ get_barcode2_only()

    @@ -237,7 +237,7 @@

    int kaori::DualBarcodesWithDiagnostics< max_size >::get_barcode1_only int kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_barcode1_only ( ) const
    - + @@ -253,8 +253,8 @@

    -

    ◆ get_combinations()

    + +

    ◆ get_combinations()

    @@ -265,7 +265,7 @@

    int kaori::DualBarcodesWithDiagnostics< max_size >::get_barcode2_only int kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_barcode2_only ( ) const
    - + @@ -281,8 +281,8 @@

    -

    ◆ get_counts()

    + +

    ◆ get_counts()

    @@ -293,7 +293,7 @@

    const std::vector< std::array< int, 2 > > & kaori::DualBarcodesWithDiagnostics< max_size >::get_combinations const std::vector< std::array< int, 2 > > & kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_combinations ( ) const
    - + @@ -309,8 +309,8 @@

    -

    ◆ get_total()

    + +

    ◆ get_total()

    @@ -321,7 +321,7 @@

    const std::vector< int > & kaori::DualBarcodesWithDiagnostics< max_size >::get_counts const std::vector< int > & kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_counts ( ) const
    - + @@ -337,8 +337,8 @@

    -

    ◆ sort()

    + +

    ◆ sort()

    @@ -349,7 +349,7 @@

    int kaori::DualBarcodesWithDiagnostics< max_size >::get_total int kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_total ( ) const
    - + @@ -366,7 +366,7 @@

    DualBarcodesWithDiagnostics.hpp +
  • kaori/handlers/DualBarcodesPairedEndWithDiagnostics.hpp
    • diff --git a/docs/dir_adbc8be79025c4dda6c0625b930b2946.html b/docs/dir_adbc8be79025c4dda6c0625b930b2946.html index 8d3f2dd..aa056d8 100644 --- a/docs/dir_adbc8be79025c4dda6c0625b930b2946.html +++ b/docs/dir_adbc8be79025c4dda6c0625b930b2946.html @@ -96,11 +96,11 @@

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    - c -

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    -
    kaori::DualBarcodes< max_size >::Options Member List
    +
    kaori::DualBarcodesPairedEnd< max_size >::Options Member List
    -

    This is the complete list of members for kaori::DualBarcodes< max_size >::Options, including all inherited members.

    +

    This is the complete list of members for kaori::DualBarcodesPairedEnd< max_size >::Options, including all inherited members.

    void kaori::DualBarcodesWithDiagnostics< max_size >::sort void kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::sort ( )
    file  CombinatorialBarcodesSingleEnd.hpp [code]
     Process single-end combinatorial barcodes.
     
    file  DualBarcodes.hpp [code]
     Process dual barcodes.
    file  DualBarcodesPairedEnd.hpp [code]
     Process dual barcodes.
     
    file  DualBarcodesWithDiagnostics.hpp [code]
     Process dual barcodes with extra diagnostics.
    file  DualBarcodesPairedEndWithDiagnostics.hpp [code]
     Process dual barcodes with extra diagnostics.
     
    file  RandomBarcodeSingleEnd.hpp [code]
     Process single-end random barcodes.
     ▼ handlers
     CombinatorialBarcodesPairedEnd.hppProcess paired-end combinatorial barcodes
     CombinatorialBarcodesSingleEnd.hppProcess single-end combinatorial barcodes
     DualBarcodes.hppProcess dual barcodes
     DualBarcodesWithDiagnostics.hppProcess dual barcodes with extra diagnostics
     DualBarcodesPairedEnd.hppProcess dual barcodes
     DualBarcodesPairedEndWithDiagnostics.hppProcess dual barcodes with extra diagnostics
     RandomBarcodeSingleEnd.hppProcess single-end random barcodes
     SingleBarcodePairedEnd.hppProcess paired-end single barcodes
     SingleBarcodeSingleEnd.hppProcess single-end single barcodes
     Ckaori::BarcodePoolPool of barcode sequences for a variable region
     Ckaori::CombinatorialBarcodesPairedEnd< max_size >Handler for paired-end combinatorial barcodes
     Ckaori::CombinatorialBarcodesSingleEnd< max_size, num_variable >Handler for single-end combinatorial barcodes
     Ckaori::DualBarcodes< max_size >Handler for dual barcodes
     Ckaori::DualBarcodesWithDiagnostics< max_size >Handler for dual barcodes with extra diagnostics
     Ckaori::DualBarcodesPairedEnd< max_size >Handler for dual barcodes
     Ckaori::DualBarcodesPairedEndWithDiagnostics< max_size >Handler for dual barcodes with extra diagnostics
     Ckaori::FastqReaderStream reads from a FASTQ file
     ▼Ckaori::MismatchTrieBase class for the mismatch search
     Ckaori::AnyMismatchesSearch for barcodes with mismatches anywhere
     Ckaori::SegmentedMismatches< num_segments >Search for barcodes with segmented mismatches
     Ckaori::CombinatorialBarcodesSingleEnd< max_size, num_variable >::OptionsOptional parameters for CombinatorialBarcodeSingleEnd
     Ckaori::DualBarcodes< max_size >::OptionsOptional parameters for SingleBarcodeSingleEnd
     Ckaori::DualBarcodesPairedEnd< max_size >::OptionsOptional parameters for DualBarcodesPairedEnd
     Ckaori::RandomBarcodeSingleEnd< max_size >::OptionsOptional parameters for SingleBarcodeSingleEnd
     Ckaori::SegmentedBarcodeSearch< num_segments >::OptionsOptional parameters for a SegmentedBarcodeSearch
     Ckaori::SimpleBarcodeSearch::OptionsOptional parameters for SimpleBarcodeSearch
    - - +
    + +
    - - +
    + +
    - - +
    + +
    diff --git a/docs/kaori_8hpp_source.html b/docs/kaori_8hpp_source.html index b583a8c..6e61cf6 100644 --- a/docs/kaori_8hpp_source.html +++ b/docs/kaori_8hpp_source.html @@ -83,8 +83,8 @@
    3
    4#include "handlers/CombinatorialBarcodesPairedEnd.hpp"
    5#include "handlers/CombinatorialBarcodesSingleEnd.hpp"
    -
    6#include "handlers/DualBarcodes.hpp"
    -
    7#include "handlers/DualBarcodesWithDiagnostics.hpp"
    +
    6#include "handlers/DualBarcodesPairedEnd.hpp"
    +
    7#include "handlers/DualBarcodesPairedEndWithDiagnostics.hpp"
    8#include "handlers/RandomBarcodeSingleEnd.hpp"
    9#include "handlers/SingleBarcodePairedEnd.hpp"
    10#include "handlers/SingleBarcodeSingleEnd.hpp"
    @@ -95,8 +95,8 @@
    24#endif
    CombinatorialBarcodesPairedEnd.hpp
    Process paired-end combinatorial barcodes.
    CombinatorialBarcodesSingleEnd.hpp
    Process single-end combinatorial barcodes.
    -
    DualBarcodesWithDiagnostics.hpp
    Process dual barcodes with extra diagnostics.
    -
    DualBarcodes.hpp
    Process dual barcodes.
    +
    DualBarcodesPairedEndWithDiagnostics.hpp
    Process dual barcodes with extra diagnostics.
    +
    DualBarcodesPairedEnd.hpp
    Process dual barcodes.
    RandomBarcodeSingleEnd.hpp
    Process single-end random barcodes.
    SingleBarcodePairedEnd.hpp
    Process paired-end single barcodes.
    SingleBarcodeSingleEnd.hpp
    Process single-end single barcodes.
    diff --git a/docs/namespacekaori.html b/docs/namespacekaori.html index 90234bf..e196906 100644 --- a/docs/namespacekaori.html +++ b/docs/namespacekaori.html @@ -95,11 +95,11 @@
    class  CombinatorialBarcodesSingleEnd
     Handler for single-end combinatorial barcodes. More...
     
    class  DualBarcodes
     Handler for dual barcodes. More...
    class  DualBarcodesPairedEnd
     Handler for dual barcodes. More...
     
    class  DualBarcodesWithDiagnostics
     Handler for dual barcodes with extra diagnostics. More...
    class  DualBarcodesPairedEndWithDiagnostics
     Handler for dual barcodes with extra diagnostics. More...
     
    class  FastqReader
     Stream reads from a FASTQ file. More...
     CCombinatorialBarcodesPairedEndHandler for paired-end combinatorial barcodes
     ▼CCombinatorialBarcodesSingleEndHandler for single-end combinatorial barcodes
     COptionsOptional parameters for CombinatorialBarcodeSingleEnd
     ▼CDualBarcodesHandler for dual barcodes
     COptionsOptional parameters for SingleBarcodeSingleEnd
     CDualBarcodesWithDiagnosticsHandler for dual barcodes with extra diagnostics
     ▼CDualBarcodesPairedEndHandler for dual barcodes
     COptionsOptional parameters for DualBarcodesPairedEnd
     CDualBarcodesPairedEndWithDiagnosticsHandler for dual barcodes with extra diagnostics
     CFastqReaderStream reads from a FASTQ file
     ▼CMismatchTrieBase class for the mismatch search
     CAddStatusStatus of the barcode sequence addition
    - - - - - - - + + + + + + +
    duplicateskaori::DualBarcodes< max_size >::Options
    max_mismatches1kaori::DualBarcodes< max_size >::Options
    max_mismatches2kaori::DualBarcodes< max_size >::Options
    randomkaori::DualBarcodes< max_size >::Options
    strand1kaori::DualBarcodes< max_size >::Options
    strand2kaori::DualBarcodes< max_size >::Options
    use_firstkaori::DualBarcodes< max_size >::Options
    duplicateskaori::DualBarcodesPairedEnd< max_size >::Options
    max_mismatches1kaori::DualBarcodesPairedEnd< max_size >::Options
    max_mismatches2kaori::DualBarcodesPairedEnd< max_size >::Options
    randomkaori::DualBarcodesPairedEnd< max_size >::Options
    strand1kaori::DualBarcodesPairedEnd< max_size >::Options
    strand2kaori::DualBarcodesPairedEnd< max_size >::Options
    use_firstkaori::DualBarcodesPairedEnd< max_size >::Options
    diff --git a/docs/structkaori_1_1DualBarcodes_1_1Options.html b/docs/structkaori_1_1DualBarcodesPairedEnd_1_1Options.html similarity index 60% rename from docs/structkaori_1_1DualBarcodes_1_1Options.html rename to docs/structkaori_1_1DualBarcodesPairedEnd_1_1Options.html index 2b649f3..c337616 100644 --- a/docs/structkaori_1_1DualBarcodes_1_1Options.html +++ b/docs/structkaori_1_1DualBarcodesPairedEnd_1_1Options.html @@ -5,7 +5,7 @@ -kaori: kaori::DualBarcodes< max_size >::Options Struct Reference +kaori: kaori::DualBarcodesPairedEnd< max_size >::Options Struct Reference @@ -71,45 +71,45 @@
    Public Attributes | -List of all members
    -
    kaori::DualBarcodes< max_size >::Options Struct Reference
    +List of all members
    +
    kaori::DualBarcodesPairedEnd< max_size >::Options Struct Reference
    -

    Optional parameters for SingleBarcodeSingleEnd. - More...

    +

    Optional parameters for DualBarcodesPairedEnd. + More...

    -

    #include <DualBarcodes.hpp>

    +

    #include <DualBarcodesPairedEnd.hpp>

    - - - - - - - - - - - - - - + + + + + + + + + + + + + +

    Public Attributes

    bool use_first = true
     
    int max_mismatches1 = 0
     
    SearchStrand strand1 = SearchStrand::FORWARD
     
    int max_mismatches2 = 0
     
    SearchStrand strand2 = SearchStrand::FORWARD
     
    DuplicateAction duplicates = DuplicateAction::ERROR
     
    bool random = false
     
    bool use_first = true
     
    int max_mismatches1 = 0
     
    SearchStrand strand1 = SearchStrand::FORWARD
     
    int max_mismatches2 = 0
     
    SearchStrand strand2 = SearchStrand::FORWARD
     
    DuplicateAction duplicates = DuplicateAction::ERROR
     
    bool random = false
     

    Detailed Description

    template<size_t max_size>
    -struct kaori::DualBarcodes< max_size >::Options

    Optional parameters for SingleBarcodeSingleEnd.

    +struct kaori::DualBarcodesPairedEnd< max_size >::Options

    Optional parameters for DualBarcodesPairedEnd.

    Member Data Documentation

    - -

    ◆ duplicates

    + +

    ◆ duplicates

    @@ -117,7 +117,7 @@

    DuplicateAction kaori::DualBarcodes< max_size >::Options::duplicates = DuplicateAction::ERRORDuplicateAction kaori::DualBarcodesPairedEnd< max_size >::Options::duplicates = DuplicateAction::ERROR
    @@ -125,8 +125,8 @@

    -

    ◆ max_mismatches1

    + +

    ◆ max_mismatches1

    @@ -134,7 +134,7 @@

    - int kaori::DualBarcodes< max_size >::Options::max_mismatches1 = 0 + int kaori::DualBarcodesPairedEnd< max_size >::Options::max_mismatches1 = 0

    @@ -142,8 +142,8 @@

    -

    ◆ max_mismatches2

    + +

    ◆ max_mismatches2

    @@ -151,7 +151,7 @@

    - int kaori::DualBarcodes< max_size >::Options::max_mismatches2 = 0 + int kaori::DualBarcodesPairedEnd< max_size >::Options::max_mismatches2 = 0

    @@ -159,8 +159,8 @@

    -

    ◆ random

    + +

    ◆ random

    @@ -168,7 +168,7 @@

    - bool kaori::DualBarcodes< max_size >::Options::random = false + bool kaori::DualBarcodesPairedEnd< max_size >::Options::random = false

    @@ -176,8 +176,8 @@

    -

    ◆ strand1

    + +

    ◆ strand1

    @@ -185,7 +185,7 @@

    - SearchStrand kaori::DualBarcodes< max_size >::Options::strand1 = SearchStrand::FORWARD + SearchStrand kaori::DualBarcodesPairedEnd< max_size >::Options::strand1 = SearchStrand::FORWARD

    @@ -193,8 +193,8 @@

    -

    ◆ strand2

    + +

    ◆ strand2

    @@ -202,7 +202,7 @@

    - SearchStrand kaori::DualBarcodes< max_size >::Options::strand2 = SearchStrand::FORWARD + SearchStrand kaori::DualBarcodesPairedEnd< max_size >::Options::strand2 = SearchStrand::FORWARD

    @@ -210,8 +210,8 @@

    -

    ◆ use_first

    + +

    ◆ use_first

    @@ -219,7 +219,7 @@

    - bool kaori::DualBarcodes< max_size >::Options::use_first = true + bool kaori::DualBarcodesPairedEnd< max_size >::Options::use_first = true

    @@ -228,7 +228,7 @@

    DualBarcodes.hpp +
  • kaori/handlers/DualBarcodesPairedEnd.hpp