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Functions3,919 in github.com/bbuchfink/diamond

⨍ Functions 3,919◇ Types & classes 804

↓ 7 callersMethodin_strand

src/basic/translated_position.h:154

↓ 7 callersMethodinit_random_access

src/data/sequence_file.cpp:807

↓ 7 callersMethodletters

src/data/blastdb/blastdb.cpp:300

↓ 7 callersFunctionload

src/util/simd/vector8_sse.h:108

↓ 7 callersFunctionmask_seqs

src/masking/masking.cpp:226

↓ 7 callersFunctionmemZero

src/lib/alp/njn_memutil.hpp:88

↓ 7 callersMethodopen_stats

src/data/sequence_file.h:239

↓ 7 callersFunctionratio_percentage

src/util/string/string.cpp:73

↓ 7 callersMethodrend

src/lib/mio/mmap.hpp:247

↓ 7 callersMethodreset

* Resets a partial block. */

src/lib/ips4o/buffers.hpp:106

↓ 7 callersFunctionscore_range

src/dp/ungapped_align.cpp:283

↓ 7 callersMethodseq_info

src/data/block/block.cpp:220

↓ 7 callersMethodstore

src/util/command_line_parser.cpp:83

↓ 7 callersMethodtell

src/util/io/file.cpp:286

↓ 7 callersMethodupdate

src/contrib/dna/timer.h:58

↓ 6 callersFunctionBlast_KarlinBlkFree

src/lib/blast/blastn_score.cpp:1137

↓ 6 callersMethodTmin

src/lib/alp/sls_basic.hpp:139

↓ 6 callersMethodappend

src/util/data_structures/double_array.h:117

↓ 6 callersFunctionappend_label

src/util/parallel/multiprocessing.h:86

↓ 6 callersMethodbackground_freqs

src/stats/score_matrix.h:201

↓ 6 callersMethodbegin

src/dp/dp.h:197

↓ 6 callersMethodbegin

src/util/data_structures/flat_array.h:88

↓ 6 callersMethodbit_size

src/basic/reduction.h:38

↓ 6 callersMethodblast_query_frame

src/basic/match.h:194

↓ 6 callersMethodcount

src/util/algo/external_sort.h:85

↓ 6 callersMethodcovered

src/util/geo/interval_partition.h:106

↓ 6 callersMethoddb_letters

src/legacy/daa/daa_file.h:140

↓ 6 callersMethoddelete_stack

src/util/parallel/parallelizer.cpp:226

↓ 6 callersFunctiondeletematrix

src/lib/tantan/LambdaCalculator.cc:37

↓ 6 callersFunctionempty

src/lib/mio/detail/string_util.hpp:146

↓ 6 callersMethodfile

src/util/io/file.cpp:311

↓ 6 callersFunctionfinalize_block

---- column-scaling update for 4 columns ------------------------------------

src/stats/matrix_adjust/kernel_arm64.h:157

↓ 6 callersFunctionfinalize_block

---- RAS (iterative proportional fitting) -----------------------------------

src/stats/matrix_adjust/kernel_sse41.h:180

↓ 6 callersFunctionfind_first_of

src/util/text_buffer.h:28

↓ 6 callersMethodformat_flags

src/data/sequence_file.h:216

↓ 6 callersMethodfree2

src/lib/alp/njn_matrix.hpp:594

↓ 6 callersMethodgaps

src/basic/match.h:408

↓ 6 callersMethodgetValue

src/contrib/mcl/lazy_disjoint_set.h:75

↓ 6 callersFunctionget_length_flag

src/output/output.h:33

↓ 6 callersMethodhgap

src/dp/swipe/full_matrix.h:39

↓ 6 callersMethodinit

src/lib/alp/njn_matrix.hpp:580

↓ 6 callersFunctioninterpret_number

src/util/string/string.cpp:83

↓ 6 callersFunctionis_amino_acid

src/basic/value.h:67

↓ 6 callersMethodis_left

src/lib/interval_tree/interval_tree.hpp:230

↓ 6 callersMethodlocal_position

src/data/string_set.h:161

↓ 6 callersFunctionmakematrix

src/lib/tantan/LambdaCalculator.cc:25

↓ 6 callersMethodmatrix8

src/stats/score_matrix.h:70

↓ 6 callersFunctionmerge_keys

src/util/algo/sort_helper.h:136

↓ 6 callersMethodmode

src/legacy/daa/daa_file.h:161

↓ 6 callersFunctionmul

src/util/simd/vector8_sse.h:120

↓ 6 callersMethodnext

src/output/join_blocks.cpp:70

↓ 6 callersMethodoriented_query_range

src/basic/match.h:430

↓ 6 callersMethodposition

src/data/string_set.h:155

↓ 6 callersMethodptr

src/data/string_set.h:110

↓ 6 callersMethodquery_char

src/basic/match.h:335

↓ 6 callersMethodrank_taxid

src/data/sequence_file.cpp:906

↓ 6 callersMethodraw_len

src/data/string_set.h:139

↓ 6 callersMethodread

src/output/output_format.cpp:40

↓ 6 callersFunctionreduce_seq

src/search/sse_dist.h:56

↓ 6 callersFunctionseed_partition

src/basic/seed.h:43

↓ 6 callersMethodself_aln_score

src/data/block/block.cpp:205

↓ 6 callersFunctionserialize

src/legacy/dmnd/dmnd.cpp:50

↓ 6 callersMethodset_if_blank

src/util/options/option.h:100

↓ 6 callersMethodsingle_query_file

src/basic/config.cpp:145

↓ 5 callersMethodaccession_to_oid

src/data/sequence_file.cpp:798

↓ 5 callersFunctionaligned_free

src/util/memory/alignment.h:39

↓ 5 callersFunctionapprox_id

src/stats/stats.cpp:136

↓ 5 callersMethodassign

src/util/data_structures/array.h:66

↓ 5 callersFunctionauto_append_extension

src/util/system/system.cpp:164

↓ 5 callersMethodband

src/dp/swipe/config.h:71

↓ 5 callersMethodbarrier

src/lib/ips4o/thread_pool.hpp:64

↓ 5 callersMethodbegin

src/util/data_structures/deque.h:201

↓ 5 callersMethodblank

src/util/data_structures/hash_table.h:43

↓ 5 callersMethodblast_bit_Score

src/contrib/dna/build_score.cpp:85

↓ 5 callersMethodcend

src/data/string_set.h:252

↓ 5 callersMethodcend

src/util/data_structures/sparse_flat_array.h:164

↓ 5 callersFunctionchunk

---- KL contribution of 4 columns ------------------------------------------- N (=20) is a multiple of the 4-lane vector width, so no tail/column mask

src/stats/matrix_adjust/kernel_arm64.h:123

↓ 5 callersFunctionchunk

---- relative entropy sum(x * (log x - lnPQ)) over x > 0 -------------------- With 4-wide vectors, N = 20 columns split into exactly 5 full chunks, so

src/stats/matrix_adjust/kernel_sse41.h:143

↓ 5 callersFunctioncount_true_aa

src/stats/cbs.cpp:72

↓ 5 callersFunctionculling

src/align/culling.cpp:187

↓ 5 callersMethoddata

* Pointer to data. */

src/lib/ips4o/buffers.hpp:70

↓ 5 callersMethoddata_size

src/util/data_structures/flat_array.h:84

↓ 5 callersMethoddb_seqs_used

src/legacy/daa/daa_file.h:137

↓ 5 callersFunctiondeserialize

src/basic/match.h:496

↓ 5 callersMethoddict_id

src/data/block/block.cpp:138

↓ 5 callersMethodend

src/util/algo/radix_cluster.h:38

↓ 5 callersFunctionextract_channel

src/dp/score_vector.h:194

↓ 5 callersFunctionfile_exists

src/util/parallel/multiprocessing.cpp:84

↓ 5 callersFunctionfinish_daa_query_record

src/legacy/daa/daa_write.cpp:51

↓ 5 callersMethodget

src/basic/statistics.h:67

↓ 5 callersMethodgetComparator

* The comparison operator. */

src/lib/ips4o/classifier.hpp:83

↓ 5 callersMethodget_edge

src/chaining/diag_graph.h:150

↓ 5 callersFunctiongetblock32

src/lib/murmurhash/MurmurHash3.cpp:59

↓ 5 callersMethodgood

src/search/seed_array/seed_iterator.h:34

↓ 5 callersMethodgood

src/util/algo/external_sort.h:69

↓ 5 callersMethodgood

src/util/geo/interval_partition.h:60

↓ 5 callersMethodid_percent

src/basic/hssp.cpp:402

↓ 5 callersMethodideal_lambda

src/stats/score_matrix.h:217

↓ 5 callersMethodincrease_elem_by_x

src/lib/alp/sls_alp_data.hpp:144

↓ 5 callersMethodis_open

Returns whether a valid memory mapping has been created. */

src/lib/mio/mmap.hpp:166

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