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Functions22,481 in github.com/EarlhamInst/KAT

↓ 9 callersFunction_reinitScoutState
deps/seqan-library-2.0.0/include/seqan/seeds/banded_chain_alignment_scout.h:173
↓ 9 callersFunction_setHost
deps/seqan-library-2.0.0/include/seqan/index/index_qgram_bucketrefinement.h:367
↓ 9 callersFunction_usesAffineGaps
deps/seqan-library-2.0.0/include/seqan/align/dp_setup.h:245
↓ 9 callersMethodas_short_string
Returns 3 char english string for the month ex: Jan, Feb, Mar, Apr
deps/boost/libs/date_time/src/gregorian/greg_month.cpp:56
↓ 9 callersMethodassign
deps/seqan-library-2.0.0/include/seqan/sequence/container_view.h:592
↓ 9 callersFunctionassignValue
deps/seqan-library-2.0.0/include/seqan/index/index_fm_sparse_string.h:291
↓ 9 callersMethodback
<b>Effects</b>: Returns a reference to the last element of the list. <b>Throws</b>: Nothing. <b>Complexity</b>: Constant. <b>Note</b>: Does not aff
deps/boost/boost/intrusive/slist.hpp:529
↓ 9 callersFunctionbegin
deps/seqan-library-2.0.0/include/seqan/sequence/string_set_base.h:1387
↓ 9 callersFunctionboyer_moore_search
deps/boost/boost/algorithm/searching/boyer_moore.hpp:217
↓ 9 callersMethodcend
deps/boost/boost/array.hpp:82
↓ 9 callersFunctioncheck_and_throw_dt
deps/boost/libs/locale/src/icu/date_time.cpp:33
↓ 9 callersFunctionclamp_range
deps/boost/boost/algorithm/clamp.hpp:90
↓ 9 callersFunctionclear
deps/seqan-library-2.0.0/include/seqan/ucsc_io/ucsc_record.h:147
↓ 9 callersFunctionclear
deps/seqan-library-2.0.0/include/seqan/align/gaps_base.h:1030
↓ 9 callersFunctionclear
deps/seqan-library-2.0.0/include/seqan/graph_align/graph_impl_align.h:444
↓ 9 callersMethodcompare
deps/boost/libs/locale/src/shared/message.cpp:410
↓ 9 callersMethodconcat
deps/boost/boost/fusion/view/joint_view/joint_view.hpp:68
↓ 9 callersMethodcontains
deps/boost/boost/date_time/period.hpp:209
↓ 9 callersMethodconvert
deps/boost/libs/locale/src/shared/message.cpp:274
↓ 9 callersMethoddeleter
deps/boost/boost/move/unique_ptr.hpp:109
↓ 9 callersFunctiondomain
deps/boost/boost/locale/message.hpp:796
↓ 9 callersMethoddone
Signify that thread is done and wait for all threads to be done.
deps/jellyfish-2.2.0/include/jellyfish/hash_counter.hpp:173
↓ 9 callersMethoddump
src/filter_kmer.cc:205
↓ 9 callersMethodelapsed_time
Gets the elapsed time, in milliseconds.
tests/gtest/src/gtest-all.cc:5203
↓ 9 callersMethodelapsed_time
Gets the elapsed time, in milliseconds.
deps/jellyfish-2.2.0/unit_tests/gtest/src/gtest-all.cc:5203
↓ 9 callersFunctionenclosingBlocks
deps/seqan-library-2.0.0/include/seqan/file/file_base.h:627
↓ 9 callersMethodend
<b>Effects</b>: Returns an iterator to the end of the list. <b>Throws</b>: Nothing. <b>Complexity</b>: Constant.
deps/boost/boost/intrusive/slist.hpp:578
↓ 9 callersMethodend
deps/boost/boost/regex/v4/match_results.hpp:336
↓ 9 callersFunctionends_with
deps/boost/boost/algorithm/string/predicate.hpp:139
↓ 9 callersMethodenqueue_no_check
deps/jellyfish-2.2.0/include/jellyfish/circular_buffer.hpp:143
↓ 9 callersFunctionequal
deps/boost/boost/range/algorithm/equal.hpp:133
↓ 9 callersMethodexec_join
deps/jellyfish-2.2.0/include/jellyfish/thread_exec.hpp:46
↓ 9 callersFunctionextension
deps/boost/boost/filesystem/convenience.hpp:34
↓ 9 callersMethodfill
deps/jellyfish-2.2.0/include/jellyfish/mer_heap.hpp:77
↓ 9 callersFunctionfind_first_of
<b>Effects</b>: Determines the lowest position xpos, if possible, such that both of the following conditions obtain: a) pos <= xpos and xpos < size();
deps/boost/boost/container/string.hpp:2387
↓ 9 callersFunctionfunction_equal
deps/boost/boost/bind/bind.hpp:1517
↓ 9 callersMethodget
deps/jellyfish-2.2.0/include/jellyfish/atomic_bits_array.hpp:88
↓ 9 callersFunctiongetChunk
deps/seqan-library-2.0.0/include/seqan/basic/iterator_adaptor.h:795
↓ 9 callersFunctiongetEmissionProbability
deps/seqan-library-2.0.0/include/seqan/graph_types/graph_impl_hmm.h:878
↓ 9 callersFunctiongetStepSize
deps/seqan-library-2.0.0/include/seqan/index/index_qgram.h:589
↓ 9 callersFunctiongetValue
deps/seqan-library-2.0.0/include/seqan/graph_types/graph_iterator_edge.h:202
↓ 9 callersMethodget_permissions
Returns stored os-dependent permissions
deps/boost/boost/interprocess/permissions.hpp:122
↓ 9 callersMethodget_size
deps/boost/boost/intrusive/detail/size_holder.hpp:36
↓ 9 callersFunctiongettext
deps/boost/boost/locale/message.hpp:624
↓ 9 callersFunctiongettimeofday
deps/boost/boost/config/platform/vxworks.hpp:291
↓ 9 callersFunctiongoNext
deps/seqan-library-2.0.0/include/seqan/modifier/modifier_reverse.h:134
↓ 9 callersMethodhas
Returns true if there is an argument corresponding to the specified parameter name
deps/boost/boost/test/utils/runtime/argument.hpp:85
↓ 9 callersMethodhash_to_bucket
deps/boost/boost/unordered/detail/implementation.hpp:2983
↓ 9 callersFunctionid
deps/boost/boost/thread/detail/thread.hpp:661
↓ 9 callersFunctionimbue
deps/boost/boost/regex/icu.hpp:164
↓ 9 callersFunctioninspect_duration
deps/boost/libs/chrono/example/time2_demo.cpp:1180
↓ 9 callersFunctioninspect_duration
deps/boost/libs/chrono/example/miscellaneous.cpp:78
↓ 9 callersFunctioninvalid_file
deps/boost/boost/interprocess/detail/os_file_functions.hpp:214
↓ 9 callersFunctionisDoubleArgument
deps/seqan-library-2.0.0/include/seqan/arg_parse/arg_parse_argument.h:354
↓ 9 callersMethodis_first_in_group
deps/boost/boost/unordered/detail/implementation.hpp:4736
↓ 9 callersFunctionis_infinity
check to see if date is one of the infinity values
deps/boost/boost/date_time/date.hpp:121
↓ 9 callersMethodis_suspended
deps/boost/boost/chrono/stopwatches/suspendable_stopwatch.hpp:257
↓ 9 callersMethodkey
deps/boost/libs/locale/src/shared/message.cpp:177
↓ 9 callersFunctionlabel
deps/seqan-library-2.0.0/include/seqan/graph_align/graph_impl_align.h:1193
↓ 9 callersMethodlaunch_policy
deps/boost/boost/thread/future.hpp:1387
↓ 9 callersMethodlock
deps/boost/boost/thread/future.hpp:133
↓ 9 callersMethodlock_shared
deps/boost/boost/thread/pthread/shared_mutex.hpp:182
↓ 9 callersFunctionmake_move_iterator
deps/boost/boost/move/iterator.hpp:173
↓ 9 callersFunctionmake_permissions
deps/boost/libs/filesystem/src/operations.cpp:620
↓ 9 callersFunctionminute
Get period_type for: minute [0..59]
deps/boost/boost/locale/date_time.hpp:137
↓ 9 callersMethodmove_assign
deps/boost/boost/unordered/detail/implementation.hpp:3373
↓ 9 callersMethodmultitoken
Specifies that the value can span multiple tokens. */
deps/boost/boost/program_options/value_semantic.hpp:274
↓ 9 callersMethodnb_files
deps/jellyfish-2.2.0/include/jellyfish/dumper.hpp:92
↓ 9 callersMethodnext
deps/boost/libs/locale/src/icu/time_zone.cpp:88
↓ 9 callersMethodnext
deps/boost/libs/regex/src/fileiter.cpp:568
↓ 9 callersFunctionordGreater
deps/seqan-library-2.0.0/include/seqan/basic/fundamental_comparison.h:142
↓ 9 callersMethodparse
deps/boost/libs/locale/src/util/locale_data.cpp:16
↓ 9 callersFunctionparse_config_file
deps/boost/libs/program_options/src/parsers.cpp:100
↓ 9 callersMethodpbase
deps/boost/boost/detail/basic_pointerbuf.hpp:50
↓ 9 callersFunctionposLocalToX
deps/seqan-library-2.0.0/include/seqan/sequence/string_set_base.h:555
↓ 9 callersMethodpriv_storage
deps/boost/boost/container/string.hpp:385
↓ 9 callersFunctionraise_runtime_error
deps/boost/libs/regex/src/regex.cpp:88
↓ 9 callersFunctionrebalance_after_insertion
deps/boost/boost/intrusive/rbtree_algorithms.hpp:548
↓ 9 callersFunctionrebalance_after_insertion
deps/boost/boost/intrusive/avltree_algorithms.hpp:563
↓ 9 callersFunctionregex_match
deps/boost/boost/regex/v4/regex_match.hpp:44
↓ 9 callersMethodrelease
Effects: Returns a pointer to the referenced mutex, or 0 if there is no mutex to reference. Postconditions: mutex() == 0 and owns() == false.
deps/boost/boost/interprocess/sync/scoped_lock.hpp:349
↓ 9 callersMethodreset
deps/jellyfish-2.2.0/include/jellyfish/token_ring.hpp:76
↓ 9 callersFunctionresize
deps/seqan-library-2.0.0/include/seqan/file/string_external.h:1954
↓ 9 callersFunctionrotate
rotate n with its parent | complexity : constant | exception : nothrow
deps/boost/boost/intrusive/splaytree_algorithms.hpp:687
↓ 9 callersFunctionscore
deps/seqan-library-2.0.0/include/seqan/graph_msa/graph_align_tcoffee_refinement.h:237
↓ 9 callersFunctionscoreGap
deps/seqan-library-2.0.0/include/seqan/score/score_simple.h:259
↓ 9 callersFunctionscoringScheme
deps/seqan-library-2.0.0/include/seqan/find/find_pattern_base.h:435
↓ 9 callersFunctionseek
deps/seqan-library-2.0.0/include/seqan/file/file_base.h:279
↓ 9 callersMethodset
deps/boost/libs/locale/src/shared/date_time.cpp:218
↓ 9 callersMethodsetHashSize
src/gcp.hpp:114
↓ 9 callersMethodsetMultipleInputs
lib/src/input_handler.cc:42
↓ 9 callersFunctionsetPosition
deps/seqan-library-2.0.0/include/seqan/basic/iterator_counting.h:134
↓ 9 callersFunctionsetValue
deps/seqan-library-2.0.0/include/seqan/basic/holder_tristate.h:760
↓ 9 callersMethodset_exception_at_thread_exit
deps/boost/boost/thread/future.hpp:434
↓ 9 callersMethodset_first
deps/boost/boost/regex/v4/match_results.hpp:523
↓ 9 callersMethodset_second
deps/boost/boost/regex/v4/match_results.hpp:466
↓ 9 callersMethodshift_right
Shift a base to the right and the rightmost base is return . "ACGT", shift_right('A') becomes "AACG" and 'T' is returned
deps/jellyfish-2.2.0/swig/python/jellyfish.py:129
↓ 9 callersFunctionswap
deps/boost/boost/unordered/unordered_map.hpp:2479
↓ 9 callersMethodswap
swap
deps/boost/boost/container/detail/pair.hpp:441
↓ 9 callersFunctiontest_cntranslate
deps/boost/libs/locale/test/test_message.cpp:250
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