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Functions3,919 in github.com/bbuchfink/diamond

⨍ Functions 3,919◇ Types & classes 804

↓ 1 callersFunctionbenchmark

src/tools/benchmark.cpp:571

↓ 1 callersFunctionbenchmark_transpose

src/tools/benchmark.cpp:219

↓ 1 callersFunctionbenchmark_ungapped

src/tools/benchmark.cpp:136

↓ 1 callersFunctionbenchmark_ungapped_sse

src/tools/benchmark.cpp:181

↓ 1 callersMethodbin

src/search/hit_buffer.h:59

↓ 1 callersMethodbit_mask

src/util/data_structures/range_partition.h:82

↓ 1 callersMethodbit_size_exact

src/basic/reduction.h:43

↓ 1 callersFunctionbitsToNats

src/lib/alp/njn_function.hpp:80

↓ 1 callersMethodbitscore_norm

src/stats/score_matrix.h:149

↓ 1 callersMethodblank

src/dp/dp.h:112

↓ 1 callersMethodbool

src/lib/alp/njn_dynprogprob.hpp:104

↓ 1 callersMethodbucket_index

src/util/algo/degree_partition.h:152

↓ 1 callersMethodbuild

* Builds the tree from the sorted splitters. */

src/lib/ips4o/classifier.hpp:88

↓ 1 callersMethodbuild

src/data/taxon_list.cpp:98

↓ 1 callersMethodbuild_graph

src/contrib/mcl/sparse_matrix_stream.h:159

↓ 1 callersFunctionbuild_iterators

src/search/seed_array/seed_array_impl.h:115

↓ 1 callersFunctionbuild_map_hsp

src/contrib/dna/extension_chain.cpp:42

↓ 1 callersFunctionbuild_mapping

src/legacy/daa/merge.cpp:32

↓ 1 callersFunctionbuild_merged

src/cluster/merge.cpp:48

↓ 1 callersMethodcalculate

src/lib/tantan/LambdaCalculator.cc:395

↓ 1 callersMethodcalculate_P_values

src/lib/alp/sls_pvalues.cpp:934

↓ 1 callersFunctioncan_add

src/cluster/len_sort.cpp:45

↓ 1 callersFunctionchain_backtrack

src/contrib/dna/chain.cpp:131

↓ 1 callersFunctionchain_round

src/cluster/merge.cpp:41

↓ 1 callersFunctionchaining_and_extension

src/contrib/dna/extension_chain.cpp:425

↓ 1 callersFunctionchaining_dynamic_program

src/contrib/dna/chain.cpp:222

↓ 1 callersMethodcheck_fully_masked

src/align/alt_hsp.cpp:68

↓ 1 callersMethodcheck_idx

src/data/string_set.h:120

↓ 1 callersFunctionclass_label

src/data/blastdb/asn1.cpp:152

↓ 1 callersMethodclear

* Removes all from this tree. */

src/lib/interval_tree/interval_tree.hpp:674

↓ 1 callersMethodclear

src/basic/packed_transcript.h:201

↓ 1 callersMethodclear_disjoint_set

src/contrib/mcl/sparse_matrix_stream.h:285

↓ 1 callersMethodcolor

* Returns the color of the node. */

src/lib/interval_tree/interval_tree.hpp:248

↓ 1 callersMethodcolumn

src/dp/scalar/smith_waterman.cpp:174

↓ 1 callersMethodcolumn_ptrs

src/dp/swipe/anchored.h:160

↓ 1 callersMethodcompute

Main entry: scores as N x N ints.

src/masking/lambda.cpp:38

↓ 1 callersMethodcomputeMappingQuality

src/contrib/dna/chain.h:97

↓ 1 callersFunctioncompute_residue_matches_of_chain

src/contrib/dna/extension_chain.cpp:30

↓ 1 callersFunctioncompute_wfa_extension

src/contrib/dna/alignment.cpp:92

↓ 1 callersFunctioncompute_wfa_global

src/contrib/dna/alignment.cpp:116

↓ 1 callersMethodcontains

src/contrib/dna/dna_index.cpp:64

↓ 1 callersMethodcontext

src/legacy/daa/daa_record.h:46

↓ 1 callersMethodcontiguous

src/basic/shape.h:206

↓ 1 callersFunctioncopy_match_record_raw

src/legacy/daa/daa_record.cpp:87

↓ 1 callersMethodcopy_seq

src/align/alt_hsp.cpp:55

↓ 1 callersMethodcount

src/util/data_structures/flat_array.h:112

↓ 1 callersMethodcrbegin

src/lib/mio/mmap.hpp:237

↓ 1 callersMethodcreate_partition_balanced

src/legacy/dmnd/dmnd.cpp:421

↓ 1 callersFunctioncustom_scores

src/stats/score_matrix.cpp:111

↓ 1 callersFunctiondb_filter

src/align/global_ranking/extend.cpp:165

↓ 1 callersFunctiondb_info

src/data/sequence_file.cpp:864

↓ 1 callersMethoddb_precedence

src/output/join_blocks.cpp:138

↓ 1 callersMethoddb_version

src/data/blastdb/blastdb.cpp:305

↓ 1 callersMethoddeactivate

src/chaining/diag_graph.h:51

↓ 1 callersFunctiondecode

src/data/blastdb/asn1.cpp:144

↓ 1 callersMethoddecode

src/data/blastdb/pin.cpp:140

↓ 1 callersFunctiondecode_defline

src/data/blastdb/phr.cpp:155

↓ 1 callersFunctiondecode_impl

src/data/blastdb/asn1.cpp:101

↓ 1 callersFunctiondecode_oid

src/data/blastdb/asn1.cpp:223

↓ 1 callersMethoddecode_seed

src/basic/basic.cpp:299

↓ 1 callersFunctiondecode_seqid

src/data/blastdb/phr.cpp:50

↓ 1 callersFunctiondefault_round_approx_id

src/cluster/helpers.cpp:277

↓ 1 callersFunctiondefault_round_cov

src/cluster/helpers.cpp:289

↓ 1 callersMethoddelete_memory_for_matrix

src/lib/alp/sls_alp_data.hpp:496

↓ 1 callersFunctiondescribe_value

src/data/blastdb/asn1.cpp:256

↓ 1 callersFunctiondetect_compressor

src/util/io/file.cpp:44

↓ 1 callersFunctiondetect_primary_chains

src/contrib/dna/chain.cpp:63

↓ 1 callersMethoddiag

src/dp/scalar/smith_waterman.cpp:148

↓ 1 callersFunctiondiag_alignment

src/dp/scan_diags.cpp:277

↓ 1 callersFunctiondiag_scores

src/tools/benchmark.cpp:461

↓ 1 callersMethoddiag_segment

src/align/target.h:62

↓ 1 callersMethoddiamond_build

src/legacy/daa/daa_file.h:131

↓ 1 callersMethoddict_self_aln_score

src/data/sequence_file.cpp:646

↓ 1 callersMethoddict_seq

src/data/sequence_file.cpp:756

↓ 1 callersMethoddict_size

src/data/sequence_file.h:210

↓ 1 callersMethoddisk_size

src/data/sequence_file.cpp:665

↓ 1 callersFunctiondynamic_programm

src/contrib/dna/smith_watermann.cpp:39

↓ 1 callersFunctionedge_pass_four

src/tools/greedy_vertex_cover.cpp:274

↓ 1 callersFunctionedge_pass_one

src/tools/greedy_vertex_cover.cpp:151

↓ 1 callersFunctionedge_pass_three

src/tools/greedy_vertex_cover.cpp:247

↓ 1 callersFunctionedge_pass_two

src/tools/greedy_vertex_cover.cpp:230

↓ 1 callersMethodend

src/lib/interval_tree/interval_tree.hpp:1074

↓ 1 callersFunctionends_with_sep

src/util/system/system.cpp:319

↓ 1 callersMethodenqueue

src/util/parallel/thread_pool.h:129

↓ 1 callersMethodensure_capacity

src/util/data_structures/growable_buffer.h:62

↓ 1 callersFunctioneq

src/lib/alp/njn_approx.hpp:77

↓ 1 callersMethoderase

src/util/data_structures/double_array.h:80

↓ 1 callersFunctionerfc8

src/lib/gsl/gsl.h:288

↓ 1 callersFunctioneuclidAlgorithm

src/lib/alp/njn_integer.hpp:85

↓ 1 callersFunctionevalue

src/tools/benchmark.cpp:475

↓ 1 callersMethodevalue

src/basic/match.h:383

↓ 1 callersFunctionexchange_if_larger

src/util/parallel/atomic.h:38

↓ 1 callersFunctionexchange_if_smaller

src/util/parallel/atomic.h:26

↓ 1 callersFunctionexp128_ps

---- vectorized exp / log (Cephes-style, same coefficients as the AVX2 code)

src/stats/matrix_adjust/kernel_sse41.h:53

↓ 1 callersFunctionexp256_ps

src/stats/matrix_adjust/kernel_avx2.h:27

↓ 1 callersFunctionexp_ps

---- cephes-style exp, 4 lanes ---------------------------------------------

src/stats/matrix_adjust/kernel_arm64.h:35

↓ 1 callersFunctionextend_chains

src/contrib/dna/extension_chain.cpp:267

↓ 1 callersFunctionextend_chunk

src/align/extend.cpp:183

↓ 1 callersFunctionextend_seeds_ungapped

src/contrib/dna/extension_seed_matches.cpp:27

↓ 1 callersFunctionextract_dir

src/util/util.cpp:60

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