Functions — github.com/DerrickWood/kraken2

CodeHub MCPcopy Create free account

hub / github.com/DerrickWood/kraken2 / functions

Functions299 in github.com/DerrickWood/kraken2

⨍ Functions 299◇ Types & classes 37

↓ 107 callersMethodsize

src/hyperloglogplus.cc:790

↓ 42 callersFunctionasn1_indefinite_tag_end

src/blast_defline.c:82

↓ 30 callersFunctionget_explicit_tag

src/blast_defline.c:139

↓ 18 callersMethodnodes

src/taxonomy.h:70

↓ 17 callersMethodinsert

src/hyperloglogplus.cc:472

↓ 13 callersFunctionasn1_get_byte

src/blast_defline.c:49

↓ 12 callersFunctionalloc_memory

src/blast_utils.c:38

↓ 12 callersFunctionasn1_peek_byte

src/blast_defline.c:62

↓ 12 callersFunctionget_text_seq_id

src/blast_defline.c:244

↓ 11 callersFunctionasn1_sequence_start

src/blast_defline.c:71

↓ 11 callersFunctionstring_append_char

src/blast_to_fasta.c:96

↓ 10 callersFunctionasn1_get_optional_visible_string_field

src/blast_defline.c:146

↓ 9 callersMethodvalue

src/compact_hash.h:22

↓ 8 callersMethodGetInternalID

src/taxonomy.h:81

↓ 8 callersFunctionMurmurHash3

src/kv_store.h:23

↓ 8 callersFunctionasn1_get_optional_integer_field

src/blast_defline.c:156

↓ 7 callersMethodNextSequence

src/seqreader.h:113

↓ 7 callersMethodreadCount

src/readcounts.h:23

↓ 7 callersFunctionread_into_buffer

src/blast_utils.c:69

↓ 7 callersFunctionstring_append_str

src/blast_to_fasta.c:117

↓ 6 callersMethodLoadSequence

src/mmscanner.cc:98

↓ 6 callersMethodLowestCommonAncestor

Logic here depends on higher nodes having smaller IDs Idea: track two nodes, advance lower tracker up tree, trackers meet @ LCA

src/taxonomy.cc:262

↓ 6 callersFunctionasn1_get_integer

src/blast_defline.c:123

↓ 6 callersFunctionasn1_get_mandatory_visible_string_field

src/blast_defline.c:172

↓ 6 callersMethodfptr

src/mmap_file.cc:109

↓ 6 callersFunctionfree_string

src/blast_to_fasta.c:168

↓ 6 callersFunctionomp_get_max_threads

src/omp_hack.cc:20

↓ 6 callersFunctionomp_set_num_threads

src/omp_hack.cc:21

↓ 6 callersFunctionread_int

src/blast_to_fasta.c:192

↓ 6 callersFunctionstring_data

src/blast_to_fasta.c:87

↓ 6 callersFunctionusage

src/build_db.cc:587

↓ 5 callersMethodNextMinimizer

src/mmscanner.cc:114

↓ 5 callersFunctionOpenOutputStream

src/classify.cc:939

↓ 5 callersFunctiongetIndex

src/hyperloglogplus.cc:102

↓ 5 callersMethodpush

src/threadpool.h:24

↓ 4 callersFunctionRemoveBlocking

src/classify.cc:138

↓ 4 callersFunctionasn1_get_mandatory_integer_field

src/blast_defline.c:166

↓ 4 callersMethodclose

src/gzstream.h:98

↓ 4 callersMethodfilesize

src/mmap_file.cc:113

↓ 4 callersFunctiongetEncodedRank

src/hyperloglogplus.cc:138

↓ 4 callersFunctiongetRank

src/hyperloglogplus.cc:117

↓ 4 callersFunctionget_internal_taxid

src/libtax.cc:38

↓ 4 callersFunctioninit_string

src/blast_to_fasta.c:76

↓ 4 callersMethodis_ambiguous

src/mmscanner.h:47

↓ 4 callersFunctionlinearCounting

* Gives the estimated cardinality for m bins, v of which are non-zero * using linear counting of Whang et al., 1990: n_hat = -m ln(v) * @param m num

src/hyperloglogplus.cc:260

↓ 4 callersFunctionload_more_data

src/blast_defline.c:32

↓ 4 callersMethodname_data

src/taxonomy.h:71

↓ 4 callersFunctionnext_power_of_2

src/blast_utils.c:34

↓ 4 callersFunctionomp_set_lock

src/omp_hack.cc:24

↓ 4 callersFunctionomp_unset_lock

src/omp_hack.cc:25

↓ 4 callersFunctionopen_file

src/blast_utils.c:56

↓ 4 callersMethodsize

src/threadpool.h:104

↓ 4 callersFunctionstring_reserve

src/blast_to_fasta.c:153

↓ 4 callersFunctionto_c_string

src/blast_to_fasta.c:89

↓ 3 callersMethodIsAAncestorOfB

Logic here depends on higher nodes having smaller IDs Idea: advance B tracker up tree, A is ancestor iff B tracker hits A

src/taxonomy.cc:251

↓ 3 callersMethodLoadBatch

src/seqreader.h:138

↓ 3 callersMethodLoadBlock

src/seqreader.h:93

↓ 3 callersMethodOpenFile

src/mmap_file.cc:20

↓ 3 callersFunctionProcessFiles

src/classify.cc:463

↓ 3 callersFunctionSplitString

src/utilities.cc:29

↓ 3 callersFunctionextractHighBits

src/hyperloglogplus.cc:93

↓ 3 callersFunctiongetEstimateBias

* Estimate the bias of raw estimate using empirically determined values. * Uses weighted average of the two cells between which the estimate falls.

src/hyperloglogplus.cc:291

↓ 3 callersFunctionget_ints

src/blast_defline.c:454

↓ 3 callersMethodhashed_key

src/compact_hash.h:18

↓ 3 callersFunctionload_index

src/classify.cc:243

↓ 3 callersFunctionomp_destroy_lock

src/omp_hack.cc:23

↓ 3 callersFunctionomp_init_lock

src/omp_hack.cc:22

↓ 3 callersMethodopen

src/gzstream.h:87

↓ 3 callersFunctionprintFasta

src/k2mask.cc:226

↓ 3 callersMethodrank_data

src/taxonomy.h:72

↓ 3 callersFunctionread_array

src/blast_to_fasta.c:219

↓ 3 callersFunctionread_string

src/blast_to_fasta.c:206

↓ 3 callersFunctionstring_append_int

src/blast_to_fasta.c:105

↓ 3 callersFunctionstring_clear

src/blast_to_fasta.c:85

↓ 3 callersFunctionusage

src/classify.cc:1116

↓ 3 callersFunctionusage

src/estimate_capacity.cc:170

↓ 3 callersFunctionusage

src/k2mask.cc:92

↓ 2 callersFunctionClassifySequence

src/classify.cc:757

↓ 2 callersMethodCompareAndSet

src/compact_hash.cc:151

↓ 2 callersMethodConvertToKrakenTaxonomy

src/taxonomy.cc:123

↓ 2 callersFunctionExpandSpacedSeedMask

src/utilities.cc:14

↓ 2 callersFunctionExtractNCBISequenceIDs

This function exists to deal with NCBI's use of \x01 characters to denote the start of a new FASTA header in the same line (for non-redundant DBs). We

src/build_db.cc:266

↓ 2 callersMethodGenerateExternalToInternalIDMap

src/taxonomy.cc:289

↓ 2 callersMethodMarkNode

Mark the given taxonomy node and all its unmarked ancestors

src/taxonomy.cc:116

↓ 2 callersFunctionMaskLowQualityBases

src/classify.cc:1007

↓ 2 callersFunctionParseCommandLine

src/classify.cc:1019

↓ 2 callersFunctionPrintKrakenStyleReportLine

src/reports.cc:130

↓ 2 callersFunctionReportKrakenStyle

src/reports.cc:241

↓ 2 callersFunctionReportMpaStyle

src/reports.cc:117

↓ 2 callersMethodWriteToDisk

Dump binary data to file

src/taxonomy.cc:275

↓ 2 callersFunctionasn1_backtrack

src/blast_defline.c:58

↓ 2 callersFunctionasn1_get_visible_string

src/blast_defline.c:97

↓ 2 callersFunctioncalculateRawEstimate

* calculate the raw estimate as harmonic mean of the ranks in the register */

src/hyperloglogplus.cc:271

↓ 2 callersFunctionclassify

src/classify.cc:264

↓ 2 callersFunctionclz

src/hyperloglogplus.cc:52

↓ 2 callersFunctioncountZeros

src/hyperloglogplus.cc:279

↓ 2 callersFunctiondefline_to_header

src/blast_to_fasta.c:352

↓ 2 callersFunctionget_object_id

src/blast_defline.c:268

↓ 2 callersFunctionks_getuntil

↓ 2 callersFunctionmask2str

src/dump_table.cc:36

next →1–100 of 299, ranked by callers