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Functions3,919 in github.com/bbuchfink/diamond

⨍ Functions 3,919◇ Types & classes 804

↓ 4 callersMethodrawscore

src/stats/score_matrix.h:131

↓ 4 callersMethodref_len

src/legacy/daa/daa_file.h:167

↓ 4 callersMethodrel_score

src/chaining/diag_graph.h:66

↓ 4 callersMethodrelease

src/util/parallel/semaphore.h:160

↓ 4 callersMethodremove

src/masking/masking.cpp:95

↓ 4 callersMethodreport_cutoff

src/stats/score_matrix.cpp:238

↓ 4 callersMethodreserve

src/util/data_structures/flat_array.h:171

↓ 4 callersMethodreset

src/data/fasta/parser.h:53

↓ 4 callersFunctionreset_color

src/util/system/system.cpp:218

↓ 4 callersFunctionrev_diag

src/util/geo/geo.h:37

↓ 4 callersMethodreverse

src/basic/basic.cpp:174

↓ 4 callersFunctions_OpenWin

Initializes an SSequence structure for part of sequence contained in a * window. * @param parent Parent (whole) sequence [in] * @param start Window

src/lib/blast/blast_seg.cpp:1546

↓ 4 callersFunctions_ShiftWin1

src/lib/blast/blast_seg.cpp:1657

↓ 4 callersMethodscore

src/dp/swipe/banded_matrix.h:202

↓ 4 callersMethodscore_matrix

src/legacy/daa/daa_file.h:143

↓ 4 callersFunctionscore_range_s

src/dp/ungapped_align.cpp:295

↓ 4 callersMethodscovhsp

src/basic/hssp.cpp:398

↓ 4 callersMethodsd

src/util/util.h:62

↓ 4 callersFunctionseedp_mask

src/basic/seed.h:35

↓ 4 callersMethodseqid

src/data/sequence_file.cpp:813

↓ 4 callersMethodsetParent

src/contrib/mcl/lazy_disjoint_set.h:39

↓ 4 callersFunctionset_color

src/util/system/system.cpp:180

↓ 4 callersMethodset_end

src/util/data_structures/double_array.h:113

↓ 4 callersMethodset_score

src/dp/swipe/full_matrix.h:51

↓ 4 callersMethodsize

* Number of elements in buffer. */

src/lib/ips4o/buffers.hpp:184

↓ 4 callersMethodsource_length

src/data/sequence_set.cpp:120

↓ 4 callersMethodsource_seq_count

src/data/block/block.cpp:261

↓ 4 callersMethodstore

src/dp/score_vector_int8.h:150

↓ 4 callersFunctionstore_sv

src/dp/score_vector.h:81

↓ 4 callersMethodsubject

src/basic/match.h:325

↓ 4 callersFunctiontrim_cr

src/data/fasta/parser.h:27

↓ 4 callersFunctionunaligned_load

src/util/simd/vector8_sse.h:104

↓ 4 callersFunctionungapped_window

src/search/stage2.h:58

↓ 4 callersFunctionvmaskq_s8

src/util/simd.h:135

↓ 4 callersMethodwriteTo

* Writes a full block to other block. */

src/lib/ips4o/buffers.hpp:115

↓ 4 callersFunctionwrite_daa_record

src/legacy/daa/daa_write.cpp:56

↓ 4 callersFunctionxdrop_ungapped

src/dp/ungapped_align.cpp:32

↓ 3 callersFunctionBLAST_Gcd

src/lib/blast/blastn_score.cpp:274

↓ 3 callersFunctionBLAST_ScoreSetAmbigRes

src/lib/blast/blastn_score.cpp:2076

↓ 3 callersFunctionBlastScoreChk

src/lib/blast/blastn_score.cpp:1536

↓ 3 callersFunctionBlastSeqLocFree

src/lib/blast/blast_filter.cpp:179

↓ 3 callersFunctionBlast_GetRelativeEntropy

Documented in composition_adjustment.h. */

src/stats/matrix_adjust/matrix_adjust_wrapper.cpp:355

↓ 3 callersFunctionBlast_ScoreFreqFree

src/lib/blast/blastn_score.cpp:1166

↓ 3 callersFunctionCompositionMatrixAdjust

src/stats/matrix_adjust/matrix_adjust_wrapper.cpp:457

↓ 3 callersFunctionMultiplyByA

* Compute the product y = beta * y + alpha * A * x, where A is the * constraint matrix for the problem of generating optimal target * frequencies.

src/stats/matrix_adjust/ncbi.cpp:162

↓ 3 callersFunctionMurmurHash3_x64_128

src/lib/murmurhash/MurmurHash3.cpp:269

↓ 3 callersFunctionNlm_DenseMatrixNew

Documented in nlm_linear_algebra.h. */

src/stats/matrix_adjust/linear_algebra_ncbi.h:35

↓ 3 callersFunctionNlm_EuclideanNorm

Documented in nlm_linear_algebra.h. */

src/stats/matrix_adjust/linear_algebra_ncbi.h:189

↓ 3 callersFunctionReadPascalString

src/data/blastdb/ber.h:56

↓ 3 callersMethodadd

src/align/legacy/banded_swipe_pipeline.cpp:79

↓ 3 callersFunctionadd_cbs

src/dp/ungapped_align.cpp:124

↓ 3 callersFunctionadd_cbs_scalar

src/dp/swipe/cell_update.h:66

↓ 3 callersMethodappend

src/data/block/block.cpp:103

↓ 3 callersMethodapprox_id

src/basic/match.h:393

↓ 3 callersMethodassign_reversed

src/util/data_structures/array.h:78

↓ 3 callersFunctionband

src/align/gapped_score.cpp:41

↓ 3 callersFunctionbaseCaseSort

src/lib/ips4o/base_case.hpp:75

↓ 3 callersMethodbegin

src/util/data_structures/reorder_queue.h:47

↓ 3 callersMethodbias

src/stats/score_matrix.h:126

↓ 3 callersFunctionblock_id

src/search/seed_array/flags.h:59

↓ 3 callersFunctionblock_size

src/basic/config.cpp:97

↓ 3 callersMethodblock_size

src/basic/config.h:440

↓ 3 callersMethodbuckets

src/cluster/file_array.h:95

↓ 3 callersFunctionbuild_hsp_from_cigar

src/contrib/dna/alignment.cpp:204

↓ 3 callersFunctionbuild_title

src/data/blastdb/phr.cpp:259

↓ 3 callersFunctioncalculate_inv_sum

src/lib/tantan/LambdaCalculator.cc:170

↓ 3 callersMethodcells

src/dp/swipe/config.h:80

↓ 3 callersMethodcend

src/util/data_structures/flat_array.h:100

↓ 3 callersFunctioncheb_eval_e

src/lib/gsl/gsl.h:120

↓ 3 callersFunctionchunk

src/stats/matrix_adjust/kernel_avx2.h:119

↓ 3 callersFunctionclip

src/util/sequence/sequence.h:30

↓ 3 callersMethodclose_dict_block

src/data/sequence_file.cpp:607

↓ 3 callersFunctioncluster_steps

src/cluster/helpers.cpp:243

↓ 3 callersMethodcompressor

src/basic/config.cpp:149

↓ 3 callersMethodcontains

src/data/seed_set.h:37

↓ 3 callersMethodcopy

src/lib/alp/njn_matrix.hpp:518

↓ 3 callersFunctioncpuid

src/util/simd.cpp:35

↓ 3 callersFunctioncreate_temp_directory

src/util/system/system.cpp:561

↓ 3 callersMethodcull

src/output/target_culling.h:117

↓ 3 callersFunctiondecode_integer

src/data/blastdb/ber.h:45

↓ 3 callersFunctiondecode_string

src/data/blastdb/asn1.cpp:252

↓ 3 callersFunctiondeserialize

src/legacy/dmnd/dmnd.cpp:60

↓ 3 callersMethodempty

* Returns wether or not the tree is empty */

src/lib/interval_tree/interval_tree.hpp:1107

↓ 3 callersMethodescape

src/util/escape_sequences.h:42

↓ 3 callersMethodexpand_from_8bit

src/dp/score_vector_int8.h:164

↓ 3 callersFunctionextend

src/align/extend.cpp:226

↓ 3 callersMethodfgetc

src/util/io/zstd_bridge.cpp:74

↓ 3 callersFunctionfile_size

src/util/system/system.cpp:137

↓ 3 callersFunctionfinalize_block

src/stats/matrix_adjust/kernel_avx2.h:156

↓ 3 callersFunctionfinish_daa

src/legacy/daa/daa_write.cpp:75

↓ 3 callersMethodfinish_writing

src/search/hit_buffer.cpp:130

↓ 3 callersFunctionfnmadd128

src/stats/matrix_adjust/kernel_sse41.h:48

↓ 3 callersMethodframe_shift

src/stats/score_matrix.h:182

↓ 3 callersMethodgap_openings

src/basic/match.h:406

↓ 3 callersFunctiongenerate_output

src/align/output.cpp:32

↓ 3 callersMethodget

src/util/data_structures/bit_vector.h:56

↓ 3 callersMethodgetListOfSets

src/contrib/mcl/lazy_disjoint_set.h:124

↓ 3 callersMethodgetMatrix

src/lib/alp/njn_matrix.hpp:91

↓ 3 callersMethodgetParent

src/contrib/mcl/lazy_disjoint_set.h:36

↓ 3 callersMethodgetProbLost

src/lib/alp/njn_dynprogproblim.hpp:148

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