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Functions3,919 in github.com/bbuchfink/diamond

⨍ Functions 3,919◇ Types & classes 804

↓ 2 callersMethodgetA

src/lib/alp/njn_localmaxstat.hpp:139

↓ 2 callersMethodgetAlpha

src/lib/alp/njn_localmaxstat.hpp:141

↓ 2 callersMethodgetC

k for random walk : exponential prefactor

src/lib/alp/njn_localmaxstat.hpp:148

↓ 2 callersMethodgetK

lambda for associated random walk

src/lib/alp/njn_localmaxstat.hpp:147

↓ 2 callersMethodgetLambda

src/lib/alp/njn_localmaxstat.hpp:146

↓ 2 callersMethodgetRoot

src/contrib/mcl/lazy_disjoint_set.h:89

↓ 2 callersMethodgetSortedSplitters

* The sorted array of splitters, to be filled externally. */

src/lib/ips4o/classifier.hpp:76

↓ 2 callersMethodgetValue

src/lib/alp/njn_matrix.hpp:92

↓ 2 callersMethodgetValueUpper

present lower long int value in the array

src/lib/alp/njn_dynprogprob.hpp:173

↓ 2 callersMethodgetWrite

* Gets the write pointer. */

src/lib/ips4o/bucket_pointers.hpp:80

↓ 2 callersMethodget_appr_tail_prob_with_cov_without_errors

src/lib/alp/sls_pvalues.cpp:368

↓ 2 callersFunctionget_hgap_link

src/chaining/greedy_align.cpp:150

↓ 2 callersMethodget_n_partition_chunks

src/legacy/dmnd/dmnd.cpp:466

↓ 2 callersFunctionget_output_format

src/output/output_format.cpp:178

↓ 2 callersFunctionget_rev_flag

src/output/output.h:42

↓ 2 callersFunctionget_segment_flag

src/output/output.h:47

↓ 2 callersFunctiongetblock64

src/lib/murmurhash/MurmurHash3.cpp:64

↓ 2 callersMethodgood

src/util/string/tokenizer.h:209

↓ 2 callersFunctiongsl_sf_log_erfc

src/lib/gsl/gsl.h:405

↓ 2 callersFunctionhex_print

src/util/util.cpp:124

↓ 2 callersMethodhit

src/util/algo/pattern_matcher.h:46

↓ 2 callersFunctionhit_fp

src/test/hit_buffer_stress.cpp:31

↓ 2 callersFunctionhmax128

src/stats/matrix_adjust/kernel_sse41.h:132

↓ 2 callersFunctionhmax256

src/stats/matrix_adjust/kernel_avx2.h:108

↓ 2 callersFunctionhmax4

src/stats/matrix_adjust/kernel_arm64.h:118

↓ 2 callersFunctionhsum128

---- horizontal reductions --------------------------------------------------

src/stats/matrix_adjust/kernel_sse41.h:124

↓ 2 callersFunctionhsum256

src/stats/matrix_adjust/kernel_avx2.h:97

↓ 2 callersFunctionhsum4

---- horizontal reductions: single instruction on AArch64 -------------------

src/stats/matrix_adjust/kernel_arm64.h:117

↓ 2 callersMethodin_bounds

src/basic/sequence.h:282

↓ 2 callersMethodinit

src/chaining/diag_graph.h:115

↓ 2 callersFunctioninit_arch

src/util/simd.cpp:52

↓ 2 callersMethodinit_dict

src/data/sequence_file.cpp:589

↓ 2 callersMethodinit_dict_block

src/data/sequence_file.cpp:599

↓ 2 callersMethodinsert_overlap

* Inserts an interval into the tree if no other interval overlaps it. * Otherwise merge the interval with the being overlapped. *

src/lib/interval_tree/interval_tree.hpp:735

↓ 2 callersMethodisGood

returns "true" if the set of parameters "d_params" is fully defined for P-value calculation

src/lib/alp/sls_alignment_evaluer.hpp:170

↓ 2 callersFunctionis_abs_posix

src/util/system/system.cpp:334

↓ 2 callersMethodis_outranked

src/align/legacy/banded_swipe_pipeline.cpp:122

↓ 2 callersFunctionjoin

src/util/parallel/multiprocessing.cpp:46

↓ 2 callersMethodjoin

src/util/parallel/simple_thread_pool.h:148

↓ 2 callersFunctionjoin_blocks

src/output/join_blocks.cpp:337

↓ 2 callersMethodjoint_probs_f

src/stats/score_matrix.h:205

↓ 2 callersMethodkey_begin

src/cluster/radixed_table.h:31

↓ 2 callersFunctionlazy_masking

src/align/extend.cpp:168

↓ 2 callersMethodlength

src/basic/sequence.h:64

↓ 2 callersMethodlength_sorted

src/data/block/block.cpp:229

↓ 2 callersMethodletter

src/basic/packed_transcript.h:73

↓ 2 callersMethodletter_count

src/cluster/volume.h:151

↓ 2 callersMethodlib

src/util/io/decompressor.h:97

↓ 2 callersFunctionload_hits

src/align/load_hits.h:44

↓ 2 callersFunctionlog2_const

src/lib/ips4o/utils.hpp:59

↓ 2 callersFunctionlog_diff

src/lib/alp/sls_pvalues.cpp:555

↓ 2 callersFunctionlooks_like_dna

src/util/sequence/sequence.cpp:199

↓ 2 callersFunctionmake_multiple

src/util/util.h:211

↓ 2 callersFunctionmake_profile16

src/dp/score_profile.cpp:103

↓ 2 callersMethodmap8

src/basic/reduction.h:57

↓ 2 callersMethodmap8b

src/basic/reduction.h:62

↓ 2 callersMethodmapping_quality

src/basic/match.h:414

↓ 2 callersFunctionmask

src/masking/tantan.cpp:102

↓ 2 callersMethodmatrix8_high

src/stats/score_matrix.h:78

↓ 2 callersMethodmatrix8_low

src/stats/score_matrix.h:73

↓ 2 callersFunctionmatrix_adjust

src/stats/matrix_adjust/kernel_avx2.h:207

↓ 2 callersFunctionmax_diag

src/util/geo/geo.h:45

↓ 2 callersFunctionmax_hsp_culling

src/align/culling.cpp:34

↓ 2 callersFunctionmegabytes

src/util/util.h:205

↓ 2 callersMethodmem_size

src/data/block/block.cpp:265

↓ 2 callersFunctionmerge_and_extend_seeds

src/contrib/dna/extension_seed_matches.cpp:80

↓ 2 callersMethodmidline_char

src/basic/match.h:359

↓ 2 callersFunctionmin_diag

src/util/geo/geo.h:41

↓ 2 callersFunctionmultinode

src/cluster/multinode.cpp:189

↓ 2 callersMethodn_anchors

src/basic/match.h:416

↓ 2 callersFunctionn_bracket

src/lib/alp/njn_localmaxstatutil.cpp:208

↓ 2 callersFunctionn_meanPowerAssoc

src/lib/alp/njn_localmaxstatutil.cpp:193

↓ 2 callersFunctionn_totalProbAssoc

src/lib/alp/njn_localmaxstatutil.cpp:184

↓ 2 callersMethodnew_query

src/search/hit_buffer.h:88

↓ 2 callersMethodnext_bin_size

src/search/hit_buffer.h:238

↓ 2 callersFunctionnode_degree

src/tools/greedy_vertex_cover.cpp:221

↓ 2 callersMethodoid2block_id

src/data/block/block.cpp:209

↓ 2 callersMethodoid_begin

src/data/block/block.h:77

↓ 2 callersMethodoid_count

src/data/block/block.h:112

↓ 2 callersMethodpart

src/util/algo/radix_cluster.h:42

↓ 2 callersMethodpartially_release_memory

src/lib/alp/sls_alp.cpp:328

↓ 2 callersFunctionpartition_size

src/search/seed_array/seed_histogram.h:57

↓ 2 callersMethodpeek

src/util/io/file.cpp:393

↓ 2 callersMethodpointers

src/dp/score_profile.h:42

↓ 2 callersMethodpoll_query

src/util/parallel/filestack.cpp:422

↓ 2 callersMethodpop_exclusive

src/util/parallel/filestack.cpp:251

↓ 2 callersMethodpos

src/search/seed_array/seed_iterator.h:141

↓ 2 callersMethodprefix_score

src/chaining/diag_graph.h:173

↓ 2 callersMethodprint

src/basic/sequence.h:93

↓ 2 callersMethodprint

src/chaining/greedy_align.cpp:73

↓ 2 callersFunctionprint_cigar

src/output/sam_format.cpp:67

↓ 2 callersFunctionprint_diag

src/chaining/smith_waterman.cpp:31

↓ 2 callersMethodprint_footer

src/output/xml_format.cpp:171

↓ 2 callersFunctionprint_hsp

src/output/output_format.cpp:170

↓ 2 callersMethodproducer_count

src/util/data_structures/queue.h:135

↓ 2 callersFunctionpsqrt

src/lib/alp/njn_function.hpp:100

↓ 2 callersMethodpush

src/legacy/util/task_queue.h:79

↓ 2 callersMethodpush

src/util/algo/external_sort.h:52

↓ 2 callersMethodpush_back

src/masking/def.h:71

↓ 2 callersMethodpush_back

src/basic/packed_transcript.h:160

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