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Functions3,919 in github.com/bbuchfink/diamond

⨍ Functions 3,919◇ Types & classes 804

↓ 5 callersMethodjoint_probs

src/stats/score_matrix.h:197

↓ 5 callersFunctionkeep_target_id

src/search/search.h:117

↓ 5 callersMethodlast_round

src/cluster/multinode.h:113

↓ 5 callersMethodmax_oid

src/cluster/multinode.h:133

↓ 5 callersFunctionn_setParameters

src/lib/alp/njn_localmaxstatutil.cpp:171

↓ 5 callersMethodnotify_all

* Wakes up waiting threads. */

src/lib/ips4o/synchronization.hpp:131

↓ 5 callersMethodnumThreads

src/lib/ips4o/thread_pool.hpp:104

↓ 5 callersMethodoperator[]

src/dp/dp.h:261

↓ 5 callersMethodpointers

src/stats/score_matrix.cpp:209

↓ 5 callersFunctionpopcount64

src/util/intrin.h:35

↓ 5 callersFunctionprint_taxon_names

src/data/sequence_file.h:315

↓ 5 callersMethodptr

src/data/fasta/parser.h:60

↓ 5 callersMethodquery_range

src/util/geo/diagonal_segment.h:40

↓ 5 callersMethodread

src/util/parallel/filestack.cpp:169

↓ 5 callersFunctionread_varuint32

src/util/algo/varint.h:52

↓ 5 callersMethodround_count

src/cluster/multinode.h:109

↓ 5 callersMethodrow

src/dp/scalar/smith_waterman.cpp:133

↓ 5 callersFunctionrun

src/chaining/greedy_align.cpp:482

↓ 5 callersFunctions_CloseWin

Frees the SSequence structure corresponding to a sequence window * Does not free palpha like s_SSequenceFree (two functions needed?). * @param win

src/lib/blast/blast_seg.cpp:1698

↓ 5 callersFunctions_lnfact

calculate log(n!) using either tabulated data or Sterling's formula * @param n [in] * @return log(n!) */

src/lib/blast/blast_seg.cpp:1834

↓ 5 callersFunctionserialize

src/basic/match.h:468

↓ 5 callersFunctionset

src/util/simd/vector8_sse.h:100

↓ 5 callersFunctionset_max

src/dp/swipe/cell_update.h:94

↓ 5 callersMethodsize

src/util/algo/partition.h:47

↓ 5 callersFunctionsort

src/dp/swipe/swipe_wrapper.cpp:62

↓ 5 callersMethodsubject_char

src/basic/match.h:348

↓ 5 callersMethodtype

src/data/sequence_file.h:186

↓ 5 callersMethodunset

src/util/options/option.h:75

↓ 5 callersFunctionvhsumq_u16

src/util/simd.h:117

↓ 5 callersFunctionwrite_daa_query_record

src/legacy/daa/daa_write.cpp:37

↓ 4 callersFunctionBlast_ApplyPseudocounts

Documented in composition_adjustment.h. */

src/stats/matrix_adjust/matrix_adjust_wrapper.cpp:62

↓ 4 callersFunctionNlm_DenseMatrixFree

Documented in nlm_linear_algebra.h. */

src/stats/matrix_adjust/linear_algebra_ncbi.h:87

↓ 4 callersFunctionSBlastScoreMatrixFree

src/lib/blast/blastn_score.cpp:239

↓ 4 callersFunction_PSIDeallocateMatrix

src/lib/blast/blastn_score.cpp:174

↓ 4 callersMethodabsolute_query_range

src/output/output_format.cpp:86

↓ 4 callersMethodadd_hit

src/align/extend.h:44

↓ 4 callersFunctionaligned_malloc

src/util/memory/alignment.h:25

↓ 4 callersFunctionassert_diag_bounds

src/util/geo/geo.h:53

↓ 4 callersMethodblank

src/dp/swipe/config.h:65

↓ 4 callersMethodblast_eValue

src/contrib/dna/build_score.cpp:91

↓ 4 callersMethodcbegin

src/util/data_structures/sparse_flat_array.h:160

↓ 4 callersFunctionchecked_double_array_count

src/util/algo/hash_join.h:30

↓ 4 callersMethodclear

src/dp/dp.h:241

↓ 4 callersMethodclear

src/util/data_structures/flat_array.h:69

↓ 4 callersMethodclone

src/output/output_format.h:309

↓ 4 callersFunctioncmp_mask

src/dp/swipe/stat_cell.h:24

↓ 4 callersFunctioncompute_ksw_cigar

src/contrib/dna/alignment.cpp:36

↓ 4 callersFunctioncompute_wfa_cigar

src/contrib/dna/alignment.cpp:141

↓ 4 callersMethodcontains

src/search/seed_array/flags.h:32

↓ 4 callersMethodcov_percent

src/util/geo/diagonal_segment.h:77

↓ 4 callersFunctionctz

src/util/intrin.h:44

↓ 4 callersMethoddata

src/util/text_buffer.h:70

↓ 4 callersMethoddb_seqs

src/legacy/daa/daa_file.h:134

↓ 4 callersMethoddiag

src/dp/swipe/full_matrix.h:43

↓ 4 callersMethodend

src/basic/sequence.h:72

↓ 4 callersMethodend

src/util/data_structures/flat_array.h:92

↓ 4 callersMethodend_random_access

src/legacy/dmnd/dmnd.cpp:599

↓ 4 callersMethodeof

src/legacy/dmnd/dmnd.cpp:376

↓ 4 callersMethodevaluate

src/contrib/mcl/recursive_parser.h:200

↓ 4 callersMethodevalue

src/legacy/daa/daa_file.h:180

↓ 4 callersMethodfinish

src/tools/tools.cpp:113

↓ 4 callersMethodfinish

src/data/seed_set.cpp:57

↓ 4 callersFunctionflag_only

src/util/enum.h:92

↓ 4 callersFunctionfrom_string

src/util/enum.h:50

↓ 4 callersMethodgap_extension_penalty

src/legacy/daa/daa_file.h:149

↓ 4 callersMethodgap_open_penalty

src/legacy/daa/daa_file.h:146

↓ 4 callersMethodget

src/legacy/dmnd/compact_array.h:69

↓ 4 callersMethodgetCount

src/contrib/mcl/lazy_disjoint_set.h:45

↓ 4 callersMethodgetM

src/lib/alp/njn_vector.hpp:73

↓ 4 callersMethodgetVector

src/lib/alp/njn_vector.hpp:74

↓ 4 callersMethodgetdelim

src/util/io/file.cpp:355

↓ 4 callersMethodgood

src/legacy/daa/daa_record.h:89

↓ 4 callersMethodhas_self_aln

src/data/block/block.h:95

↓ 4 callersFunctioninvert

src/lib/tantan/LambdaCalculator.cc:148

↓ 4 callersFunctionis_absolute_path

src/util/system/system.cpp:463

↓ 4 callersFunctionjoin

src/util/string/string.h:68

↓ 4 callersFunctionjoin_path

src/util/system/system.cpp:487

↓ 4 callersMethodkey

src/util/algo/sort_helper.h:121

↓ 4 callersMethodlambda

src/legacy/daa/daa_file.h:170

↓ 4 callersFunctionlog2

* Compute the logarithm to base 2, rounded down. */

src/lib/ips4o/utils.hpp:55

↓ 4 callersMethodmatrix32

src/stats/score_matrix.h:99

↓ 4 callersMethodmean

src/util/util.h:58

↓ 4 callersFunctionmerge

src/chaining/greedy_align.cpp:439

↓ 4 callersMethodmerge

src/contrib/mcl/lazy_disjoint_set.h:97

↓ 4 callersFunctionnext_pow2

src/util/math/integer.h:46

↓ 4 callersMethodoffset

src/util/data_structures/double_array.h:126

↓ 4 callersMethodoid_end

src/data/block/block.h:81

↓ 4 callersMethodop

src/basic/packed_transcript.h:46

↓ 4 callersMethodoriented_range

src/basic/match.h:168

↓ 4 callersFunctionpair_count

src/tools/composition_matrix.cpp:46

↓ 4 callersFunctionpopcount32

src/util/intrin.h:26

↓ 4 callersMethodprint_match

src/output/xml_format.cpp:31

↓ 4 callersFunctionpsnip_builtin_clz32

src/lib/psnip/builtin.h:517

↓ 4 callersFunctionpsnip_builtin_clz64

src/lib/psnip/builtin.h:535

↓ 4 callersFunctionpsnip_builtin_ctz32

src/lib/psnip/builtin.h:668

↓ 4 callersFunctionpsnip_builtin_ctz64

src/lib/psnip/builtin.h:679

↓ 4 callersMethodpush_back

src/data/string_set.h:72

↓ 4 callersMethodquery

src/basic/match.h:321

↓ 4 callersMethodquery_last

src/util/geo/diagonal_segment.h:55

↓ 4 callersMethodraw_bytes

src/data/block/block.h:105

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