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Functions74 in github.com/DerrickWood/kraken

⨍ Functions 74 ◇ Types & classes 9

↓ 15 callersMethodsize

src/quickfile.cpp:111

↓ 10 callersMethodptr

src/quickfile.cpp:107

↓ 9 callersFunctionusage

src/classify.cpp:590

↓ 5 callersMethodget_k

Simple accessors/convenience methods

src/krakendb.cpp:121

↓ 5 callersMethodis_valid

src/seqreader.cpp:83

↓ 4 callersMethodat

Convenience method, allows for testing guard

src/krakendb.cpp:312

↓ 4 callersMethodclose_file

src/quickfile.cpp:123

↓ 4 callersMethodnext_sequence

src/seqreader.cpp:34

↓ 4 callersFunctionusage

src/set_lcas.cpp:259

↓ 3 callersMethodambig_kmer

src/krakenutil.cpp:178

↓ 3 callersMethodnext_kmer

src/krakenutil.cpp:147

↓ 3 callersFunctionusage

src/db_shrink.cpp:158

↓ 3 callersFunctionusage

src/db_sort.cpp:176

↓ 3 callersFunctionusage

src/kmer_estimator.cpp:132

↓ 2 callersFunctionbuild_parent_map

Build a node->parent map from NCBI Taxonomy nodes.dmp file

src/krakenutil.cpp:27

↓ 2 callersMethodcanonical_representation

Lexicographically smallest of k-mer and reverse comp. of k-mer

src/krakendb.cpp:188

↓ 2 callersMethodget_key_ct

src/krakendb.cpp:125

↓ 2 callersMethodget_key_len

src/krakendb.cpp:123

↓ 2 callersMethodget_val_len

src/krakendb.cpp:124

↓ 2 callersMethodheader_size

src/krakendb.cpp:127

↓ 2 callersMethodindexed_nt

How long are bin keys (i.e., what is minimizer length in bp?)

src/krakendb.cpp:302

↓ 2 callersMethodkmer_query

perform search over last range to speed up queries NOTE: retry_on_failure implies all pointer params are non-NULL

src/krakendb.cpp:200

↓ 2 callersFunctionlca

Return lowest common ancestor of a and b LCA(0,x) = LCA(x,0) = x Default ancestor is 1 (root of tree)

src/krakenutil.cpp:50

↓ 2 callersMethodload_file

src/quickfile.cpp:74

↓ 2 callersMethodopen_file

src/quickfile.cpp:38

↓ 2 callersMethodset_index

Associates the index with this database

src/krakendb.cpp:116

↓ 2 callersFunctionset_lcas

src/set_lcas.cpp:176

↓ 1 callersFunctionbin_and_sort_data

src/db_sort.cpp:77

↓ 1 callersMethodbin_key

Bin key: each k-mer is made of several overlapping m-mers, m < k The bin key is the m-mer whose canonical representation is "smallest" ("smallest" can

src/krakendb.cpp:132

↓ 1 callersFunctionclassify_sequence

src/classify.cpp:264

↓ 1 callersFunctionfill_request_map

src/make_seqid_to_taxid_map.cpp:92

↓ 1 callersMethodget_array

Return start of index array (skips header)

src/krakendb.cpp:307

↓ 1 callersFunctionhash_code

MurmurHash3 finalizer

src/kmer_estimator.cpp:38

↓ 1 callersFunctionhitlist_string

src/classify.cpp:432

↓ 1 callersMethodindex_type

Index version (v2 uses different minimizer sort order)

src/krakendb.cpp:297

↓ 1 callersMethodmake_index

Creates an index, indicating starting positions of each bin Bins contain k-mer/taxon pairs with k-mers that share a bin key

src/krakendb.cpp:73

↓ 1 callersFunctionobtain_estimated_kmer_ct

src/kmer_estimator.cpp:61

↓ 1 callersFunctionparse_command_line

src/classify.cpp:479

↓ 1 callersFunctionparse_command_line

src/db_shrink.cpp:122

↓ 1 callersFunctionparse_command_line

src/db_sort.cpp:125

↓ 1 callersFunctionparse_command_line

src/kmer_estimator.cpp:92

↓ 1 callersFunctionparse_command_line

src/set_lcas.cpp:197

↓ 1 callersFunctionprocess_file

src/classify.cpp:188

↓ 1 callersFunctionprocess_file

src/set_lcas.cpp:163

↓ 1 callersFunctionprocess_files

src/set_lcas.cpp:134

↓ 1 callersFunctionprocess_single_file

src/set_lcas.cpp:91

↓ 1 callersFunctionreport_stats

src/classify.cpp:163

↓ 1 callersFunctionreport_taxo_numbers

src/make_seqid_to_taxid_map.cpp:56

↓ 1 callersFunctionresolve_tree

Tree resolution: take all hit taxa (plus ancestors), then return leaf of highest weighted leaf-to-root path.

src/krakenutil.cpp:71

MethodFastaReader

src/seqreader.cpp:26

MethodFastqReader

src/seqreader.cpp:87

MethodKmerScanner

Create a scanner for the string over the interval [start, finish)

src/krakenutil.cpp:118

Basic constructor

src/krakendb.cpp:46

MethodKrakenDBIndex

src/krakendb.cpp:278

MethodQuickFile

src/quickfile.cpp:27

Functionget_ancestry

src/classify.cpp:469

Methodget_index

Simple accessor

src/krakendb.cpp:111

src/krakenutil.cpp:135

Methodget_key_bits

src/krakendb.cpp:122

Methodget_pair_ptr

Returns start of k-mer/taxon pair array (skips header)

src/krakendb.cpp:106

Simple accessor

src/krakendb.cpp:101

src/classify.cpp:68

src/db_shrink.cpp:35

src/db_sort.cpp:40

src/kmer_estimator.cpp:47

src/set_lcas.cpp:49

src/make_seqid_to_taxid_map.cpp:42

Functionpair_cmp

src/db_sort.cpp:113

Methodpair_size

src/krakendb.cpp:126

Methodreverse_complement

Code mostly from Jellyfish 1.6 source

src/krakendb.cpp:168

src/krakenutil.cpp:137

Methodsync_file

src/quickfile.cpp:119

Method~DNASequenceReader

src/seqreader.hpp:37

Method~QuickFile

src/quickfile.cpp:115