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Functions299 in github.com/DerrickWood/kraken2

⨍ Functions 299◇ Types & classes 37

↓ 2 callersMethodnode_count

src/taxonomy.h:73

↓ 2 callersFunctionntoh_64

src/blast_to_fasta.c:176

↓ 2 callersFunctionomp_get_thread_num

src/omp_hack.cc:19

↓ 2 callersMethodpopulate

src/compact_hash.h:26

↓ 2 callersMethodreset

src/classify.cc:64

↓ 2 callersMethodreset

src/k2mask.cc:68

↓ 2 callersFunctionsaveMaskedRegions

src/k2mask.cc:145

↓ 2 callersFunctionsigma

* Ertl - calculation of sigma correction for 0-registers in M * x is the proportion of 0-registers, thus x \in [0, 1] * sigma := x + sum[from k=1

src/hyperloglogplus.cc:359

↓ 2 callersFunctionusage

src/blast_to_fasta.c:591

↓ 2 callersFunctionusage

src/dump_table.cc:144

↓ 2 callersFunctionwrite_sequence

src/blast_to_fasta.c:555

↓ 1 callersFunctionAddHitlistString

src/classify.cc:896

↓ 1 callersFunctionClassifyDaemon

src/classify.cc:333

↓ 1 callersMethodCloseFile

src/mmap_file.cc:125

↓ 1 callersMethodFindIndex

src/compact_hash.cc:130

↓ 1 callersFunctionGenerateTaxonomy

src/build_db.cc:452

↓ 1 callersMethodGet

src/compact_hash.cc:109

↓ 1 callersFunctionGetCladeCounters

src/reports.cc:32

↓ 1 callersFunctionGetCladeCounts

src/reports.cc:16

↓ 1 callersMethodGetValueCounts

src/compact_hash.cc:232

↓ 1 callersFunctionInitializeOutputs

src/classify.cc:954

↓ 1 callersFunctionKrakenReportDFS

Depth-first search of taxonomy tree, reporting info at each node

src/reports.cc:152

↓ 1 callersFunctionMpaReportDFS

src/reports.cc:51

↓ 1 callersFunctionOpenFifos

src/classify.cc:195

↓ 1 callersFunctionParseCommandLine

src/estimate_capacity.cc:102

↓ 1 callersFunctionParseCommandLine

src/build_db.cc:465

↓ 1 callersFunctionParseCommandLine

src/dump_table.cc:98

↓ 1 callersFunctionPrintMpaStyleReportLine

src/reports.cc:47

↓ 1 callersFunctionProcessSequence

src/estimate_capacity.cc:185

↓ 1 callersFunctionProcessSequence

src/build_db.cc:324

↓ 1 callersFunctionProcessSequenceFast

src/build_db.cc:305

↓ 1 callersFunctionProcessSequences

src/estimate_capacity.cc:66

↓ 1 callersFunctionProcessSequences

Slightly slower but deterministic when multithreaded

src/build_db.cc:217

↓ 1 callersFunctionProcessSequencesFast

A quick but nondeterministic build

src/build_db.cc:154

↓ 1 callersFunctionReadIDToTaxonMap

src/libtax.cc:70

↓ 1 callersFunctionReadIDToTaxonMap

src/build_db.cc:435

↓ 1 callersFunctionReportStats

src/classify.cc:431

↓ 1 callersFunctionResolveTree

src/classify.cc:694

↓ 1 callersFunctionSetMinimizerLCA

src/build_db.cc:296

↓ 1 callersFunctionTokenizeString

src/classify.cc:314

↓ 1 callersFunctionTranslateToAllFrames

src/aa_translate.cc:41

↓ 1 callersFunctionTrimPairInfo

src/classify.cc:748

↓ 1 callersMethodWriteTable

src/compact_hash.cc:99

↓ 1 callersFunctionaddHashToSparseList

src/hyperloglogplus.cc:192

↓ 1 callersMethodadd_kmer

src/readcounts.h:55

↓ 1 callersFunctionalpha

* Bias correction factors for specific m's * @param m * @return */

src/hyperloglogplus.cc:241

↓ 1 callersFunctionasn1_is_end_of_sequence

src/blast_defline.c:89

↓ 1 callersMethodcapacity

src/compact_hash.h:89

↓ 1 callersFunctiondaemonize

src/classify.cc:143

↓ 1 callersFunctiondb_tag_to_string

src/blast_to_fasta.c:316

↓ 1 callersFunctiondeflines_to_header

src/blast_to_fasta.c:382

↓ 1 callersFunctiondestroy_blast_defline

src/blast_defline.c:553

↓ 1 callersMethoddistinctKmerCount

src/readcounts.h:104

↓ 1 callersFunctionencodeHashIn32Bit

* Encode the 64-bit hash code x as an 32-bit integer, to be used in the sparse representation. * * Difference from the algorithm described in the pa

src/hyperloglogplus.cc:166

↓ 1 callersFunctionextractBits

src/hyperloglogplus.cc:71

↓ 1 callersMethodfile_format

src/seqreader.h:157

↓ 1 callersFunctionfindPerfect

src/k2mask.cc:166

↓ 1 callersFunctionfree_asn1

src/blast_defline.c:22

↓ 1 callersFunctionfree_hdr_data

src/blast_to_fasta.c:296

↓ 1 callersFunctionfree_idx_data

src/blast_to_fasta.c:253

↓ 1 callersFunctionfree_seq_data

src/blast_to_fasta.c:572

↓ 1 callersFunctionget_blast_defline

src/blast_defline.c:507

↓ 1 callersFunctionget_blast_deflines

src/blast_defline.c:561

↓ 1 callersFunctionget_date

src/blast_defline.c:178

↓ 1 callersFunctionget_db_tag

src/blast_defline.c:204

↓ 1 callersFunctionget_deflines

src/blast_to_fasta.c:391

↓ 1 callersFunctionget_gi_import_id

src/blast_defline.c:232

↓ 1 callersFunctionget_id_pat

src/blast_defline.c:285

↓ 1 callersFunctionget_links

src/blast_defline.c:482

↓ 1 callersFunctionget_memberships

src/blast_defline.c:470

↓ 1 callersFunctionget_other_info

src/blast_defline.c:495

↓ 1 callersFunctionget_patent_seq_id

src/blast_defline.c:257

↓ 1 callersFunctionget_pdb_seq_id

src/blast_defline.c:215

↓ 1 callersFunctionget_seq_id

src/blast_defline.c:305

↓ 1 callersFunctionhas_ambiguous_data

src/blast_to_fasta.c:431

↓ 1 callersFunctionhelp

src/blast_to_fasta.c:596

↓ 1 callersMethodincrementReadCount

src/readcounts.h:24

↓ 1 callersFunctioninit_asn1

src/blast_defline.c:8

↓ 1 callersFunctioninit_blast_defline

src/blast_defline.c:534

↓ 1 callersFunctioninit_hdr_data

src/blast_to_fasta.c:279

↓ 1 callersFunctioninit_idx_data

src/blast_to_fasta.c:226

↓ 1 callersFunctioninit_seq_data

src/blast_to_fasta.c:400

↓ 1 callersMethodkmerCount

src/readcounts.h:25

↓ 1 callersMethodlast_minimizer

Return last minimizer, only valid if NextMinimizer last returned non-NULL

src/mmscanner.h:43

↓ 1 callersFunctionmask

src/k2mask.cc:243

↓ 1 callersFunctionmax_block_size

src/blast_to_fasta.c:419

↓ 1 callersFunctionnext_sequence

src/blast_to_fasta.c:529

↓ 1 callersFunctionnlz

Taken from Hackers Delight

src/blast_utils.c:6

↓ 1 callersFunctionpdb_seq_id_to_string

src/blast_to_fasta.c:337

↓ 1 callersFunctionread_ambiguous_data

src/blast_to_fasta.c:449

↓ 1 callersFunctionread_idx_data

src/blast_to_fasta.c:235

↓ 1 callersFunctionread_long

src/blast_to_fasta.c:199

↓ 1 callersFunctionread_seq_block

src/blast_to_fasta.c:443

↓ 1 callersFunctionreconstruct_sequence

src/blast_to_fasta.c:480

↓ 1 callersFunctionregisterHistogram

* returns a 'register histogram' vector C, * where C[i] is the number of elements in M with value i * it's size is q+1 = 64-p+1 * used in Ertl's

src/hyperloglogplus.cc:323

↓ 1 callersFunctionreset_blast_defline

src/blast_defline.c:544

↓ 1 callersFunctionrunSymmetricDust

src/k2mask.cc:204

↓ 1 callersFunctionshiftWindow

src/k2mask.cc:121

↓ 1 callersFunctionsparseRegisterHistogram

src/hyperloglogplus.cc:342

↓ 1 callersFunctionstricasecmp

src/k2mask.cc:111

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