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Functions3,919 in github.com/bbuchfink/diamond

⨍ Functions 3,919◇ Types & classes 804

↓ 1 callersFunctionhave_hgap

src/dp/scalar/traceback.h:44

↓ 1 callersFunctionhave_vgap

src/dp/scalar/traceback.h:24

↓ 1 callersFunctionhex_dump

src/data/blastdb/asn1.cpp:204

↓ 1 callersMethodhighest_ranking

src/search/kmer_ranking.h:35

↓ 1 callersMethodhsp

src/basic/match.h:450

↓ 1 callersFunctionhsp_band

src/align/gapped_score.cpp:74

↓ 1 callersFunctionhst_size

src/search/seed_array/seed_histogram.h:65

↓ 1 callersMethodhstat

src/dp/swipe/banded_matrix.h:63

↓ 1 callersMethodid_len

src/data/blastdb/phr.cpp:240

↓ 1 callersFunctionideal_lambda

src/stats/comp_based_stats.cpp:501

↓ 1 callersMethodincrementCount

src/contrib/mcl/lazy_disjoint_set.h:48

↓ 1 callersFunctioninfo

src/run/tools.cpp:142

↓ 1 callersMethodinit

src/legacy/dmnd/dmnd.cpp:123

↓ 1 callersMethodinit

src/legacy/daa/daa_record.cpp:30

↓ 1 callersMethodinit

src/align/legacy/query_mapper.cpp:100

↓ 1 callersMethodinit

src/basic/basic.cpp:117

↓ 1 callersMethodinit

src/dp/scalar/smith_waterman.cpp:57

↓ 1 callersMethodinitGapped

Computes gapped Gumbel parameters: The NCBI convention is used for penalizing a gap: For example, a gap of length k is penalized as gapOpen1_+k*gapEpe

src/lib/alp/sls_alignment_evaluer.cpp:354

↓ 1 callersMethodinitParameters

Initializes Gumbel parameters using precalculated values:

src/lib/alp/sls_alignment_evaluer.cpp:656

↓ 1 callersMethodinit_channel_diag

src/dp/swipe/banded_matrix.h:82

↓ 1 callersMethodinit_channel_nw

src/dp/swipe/banded_matrix.h:86

↓ 1 callersMethodinit_float_views

src/stats/stats.cpp:60

↓ 1 callersFunctioninit_motif_table

src/masking/motifs.cpp:8027

↓ 1 callersFunctioninit_output

src/output/output_format.cpp:217

↓ 1 callersMethodinit_seq_access

src/legacy/dmnd/dmnd.cpp:380

↓ 1 callersMethodinit_target

src/dp/swipe/anchored.h:72

↓ 1 callersFunctioninsertionSort

src/lib/ips4o/base_case.hpp:52

↓ 1 callersFunctioninsertion_sort

src/util/algo/sort.h:30

↓ 1 callersFunctionintegerPower

src/lib/alp/njn_integer.hpp:130

↓ 1 callersMethodintersect

src/util/geo/diagonal_segment.h:89

↓ 1 callersFunctionintersection

src/contrib/dna/extension.cpp:56

↓ 1 callersMethodisFull

* Checks if buffer is full. */

src/lib/ips4o/buffers.hpp:170

↓ 1 callersMethodisReading

* Returns true if any thread is currently reading from here. */

src/lib/ips4o/bucket_pointers.hpp:129

↓ 1 callersFunctionis_blast_db

src/data/sequence_file.cpp:465

↓ 1 callersMethodis_enveloped_by

src/basic/hssp.cpp:233

↓ 1 callersFunctionis_eoc

src/data/blastdb/asn1.cpp:97

↓ 1 callersMethodis_fasta

src/data/fasta/fasta_file.h:65

↓ 1 callersFunctionis_fully_masked

src/util/sequence/sequence.cpp:164

↓ 1 callersFunctionis_linclust

src/cluster/helpers.cpp:269

↓ 1 callersFunctionis_printable_ascii

src/data/blastdb/asn1.cpp:217

↓ 1 callersMethodis_root

src/lib/interval_tree/interval_tree.hpp:240

↓ 1 callersFunctionj

src/util/geo/geo.h:29

↓ 1 callersFunctionjoin

* Creates a new interval from this and other, that contains both intervals and whatever * is between. */

src/lib/interval_tree/interval_tree.hpp:168

↓ 1 callersFunctionjoin_query

src/output/join_blocks.cpp:207

↓ 1 callersFunctionjoin_sorted_lists

src/util/algo/sort_helper.h:86

↓ 1 callersMethodkappa

src/legacy/daa/daa_file.h:175

↓ 1 callersMethodlambda

src/stats/score_matrix.h:154

↓ 1 callersMethodlast

src/dp/scalar/smith_waterman.cpp:80

↓ 1 callersFunctionlast_component

src/util/system/system.cpp:323

↓ 1 callersMethodleft_i1

↓ 1 callersFunctionleft_most_filter

src/search/left_most.h:62

↓ 1 callersFunctionlegacy_pipeline

src/align/align.cpp:120

↓ 1 callersFunctionlen_sort

src/cluster/len_sort.cpp:211

↓ 1 callersMethodlength

src/lib/mio/shared_mmap.hpp:159

↓ 1 callersMethodlengths

src/data/sequence_set.cpp:112

↓ 1 callersMethodletters

src/data/fasta/fasta_file.cpp:331

↓ 1 callersFunctionlex_normalize_posix

src/util/system/system.cpp:346

↓ 1 callersFunctionlimits

src/dp/swipe/config.h:97

↓ 1 callersMethodlimits_begin

src/data/string_set.h:181

↓ 1 callersFunctionlineage

src/output/blast_tab_format.cpp:132

↓ 1 callersMethodlineage

src/data/sequence_file.cpp:936

↓ 1 callersFunctionlist_seeds

src/tools/tools.cpp:107

↓ 1 callersMethodlive

src/dp/swipe/target_iterator.h:94

↓ 1 callersFunctionload_mapping_file

src/data/taxon_list.cpp:56

↓ 1 callersFunctionload_seqs

src/cluster/volume.h:165

↓ 1 callersMethodlocal_position_batch

src/data/string_set.h:168

↓ 1 callersMethodlock

src/util/parallel/mutex.h:31

↓ 1 callersFunctionlog2_approximate

* Fast approximation of log2 (doesn't work when x<2) * @param x * @return log2 of x */

src/util/math/log2_fast.h:28

↓ 1 callersMethodlog_area

src/lib/alp/sls_pvalues.cpp:561

↓ 1 callersFunctionlog_erfc8

src/lib/gsl/gsl.h:297

↓ 1 callersMethodlong_mask

src/basic/shape.h:211

↓ 1 callersMethodlong_offsets

src/data/block/block.cpp:67

↓ 1 callersMethodlower

src/search/seed_array/seed_histogram.h:43

↓ 1 callersMethodlower_or_equal

src/search/seed_array/seed_histogram.h:45

↓ 1 callersFunctionlu_pivoting

src/lib/tantan/LambdaCalculator.cc:83

↓ 1 callersFunctionmake_gap_mask

src/dp/swipe/cell_update.h:76

↓ 1 callersFunctionmake_invalid_intro_handler

src/output/blast_tab_format.cpp:120

↓ 1 callersFunctionmake_invalid_match_handler

src/output/blast_tab_format.cpp:113

↓ 1 callersFunctionmake_open_mask

src/dp/swipe/cell_update.h:85

↓ 1 callersFunctionmake_partition

src/align/align.cpp:52

↓ 1 callersFunctionmakeindex

src/data/index.cpp:28

↓ 1 callersMethodmap

src/lib/mio/shared_mmap.hpp:246

↓ 1 callersMethodmap

src/lib/mio/mmap.hpp:298

↓ 1 callersFunctionmapping_file_format

src/data/taxon_list.cpp:42

↓ 1 callersMethodmask_bit

src/masking/masking.cpp:205

↓ 1 callersFunctionmask_motifs

src/masking/masking.cpp:114

↓ 1 callersMethodmasked

src/align/alt_hsp.cpp:65

↓ 1 callersMethodmasked_letters

src/masking/masking.cpp:80

↓ 1 callersFunctionmaster_thread

src/run/double_indexed.cpp:580

↓ 1 callersMethodmatch_reward

src/legacy/daa/daa_file.h:152

↓ 1 callersMethodmatrix32_scaled_pointers

src/stats/score_matrix.h:104

↓ 1 callersMethodmatrix8u

src/stats/score_matrix.h:93

↓ 1 callersMethodmatrix8u_high

src/stats/score_matrix.h:88

↓ 1 callersMethodmatrix8u_low

src/stats/score_matrix.h:83

↓ 1 callersMethodmatrix_scale

src/dp/dp.h:118

↓ 1 callersMethodmax

src/basic/statistics.h:62

↓ 1 callersMethodmax_chunk_size

src/search/seed_array/seed_histogram.cpp:35

↓ 1 callersFunctionmax_index

src/lib/tantan/LambdaCalculator.cc:53

↓ 1 callersMethodmax_len

src/dp/dp.h:245

↓ 1 callersFunctionmax_open_files_per_process

src/util/system/system.cpp:68

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