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Functions451 in github.com/ParBLiSS/FastANI

⨍ Functions 451◇ Types & classes 131

↓ 116 callersMethodempty

--------------------------------------------------------------- @brief returns true, if group has no children, false otherwise */

src/common/clipp.h:3377

↓ 102 callersMethodsize

@brief returns number of children */

src/common/clipp.h:3380

↓ 80 callersMethodend

@brief returns mutating iterator to position one past the last element */

src/common/clipp.h:3402

↓ 70 callersMethodbegin

--------------------------------------------------------------- @brief returns mutating iterator to position of first element */

src/common/clipp.h:3395

↓ 62 callersMethodblocking

--------------------------------------------------------------- @brief returns if a group/parameter is blocking/positional */

src/common/clipp.h:1494

↓ 55 callersMethodrepeatable

--------------------------------------------------------------- @brief returns if a group/parameter is repeatable */

src/common/clipp.h:1481

↓ 36 callersMethodrequired

--------------------------------------------------------------- @brief returns if a parameter is required */

src/common/clipp.h:1954

↓ 32 callersMethodexclusive

@brief returns if children are mutually exclusive alternatives */

src/common/clipp.h:3181

↓ 29 callersFunctionget_file_contents

tests/fastani_tests.cpp:21

↓ 28 callersMethodlevel

src/common/clipp.h:2828

↓ 21 callersMethodis_group

src/common/clipp.h:2738

↓ 20 callersMethodjoinable

@brief returns if a command line argument can be matched by a * combination of (partial) matches through any number of children */

src/common/clipp.h:3150

↓ 19 callersMethodscoped

@brief returns true if operators , & | and other combinating functions * will merge groups and false otherwise */

src/common/clipp.h:3168

↓ 17 callersMethodstr

src/common/clipp.h:6070

↓ 17 callersMethodwrite

src/common/clipp.h:6109

↓ 16 callersFunctioncore_genome_identity

src/cgi/core_genome_identity.cpp:27

↓ 15 callersFunctionoption

src/common/clipp.h:2190

↓ 15 callersFunctionread_fastani_output

tests/fastani_tests.cpp:32

↓ 13 callersMethodfirst_column

src/common/clipp.h:5743

↓ 13 callersMethodis_param

src/common/clipp.h:2737

↓ 12 callersMethodlength

src/common/clipp.h:1828

↓ 10 callersFunctionvalue

src/common/clipp.h:2206

↓ 9 callersMethodparam

src/common/clipp.h:4528

↓ 9 callersFunctionrepeat_input

(input_file, header, nas, nts, nlength)

tests/gen_tests_data.py:33

↓ 7 callersFunctionfirst_column

src/common/clipp.h:5432

↓ 7 callersMethodinnermost_repeat_group

src/common/clipp.h:4083

↓ 6 callersMethodparagraph_spacing

src/common/clipp.h:5772

↓ 5 callersMethodall_blocking

--------------------------------------------------------------- @brief returns true if all children is blocking */

src/common/clipp.h:3232

↓ 5 callersFunctionfwd_to_unsigned_int

/ * @brief forwards string to first non-whitespace char; * std string -> unsigned conv yields max value, but we want 0; * also checks

src/common/clipp.h:297

↓ 5 callersMethodlast_column

src/common/clipp.h:5751

↓ 5 callersMethodmatch

--------------------------------------------------------------- @brief returns either longest matching prefix of 'arg' in any * of the fl

src/common/clipp.h:2014

↓ 5 callersMethodundo

src/common/clipp.h:3083

↓ 4 callersMethodblank_lines_before_paragraph

src/common/clipp.h:5861

↓ 4 callersMethodblocked

src/common/clipp.h:4535

↓ 4 callersMethodcommon_flag_prefix

--------------------------------------------------------------- @brief returns longest common prefix of all flags */

src/common/clipp.h:3463

↓ 4 callersFunctiondoc_column

src/common/clipp.h:5446

↓ 4 callersMethodignore_newline_chars

src/common/clipp.h:5792

↓ 4 callersMethodindex

src/common/clipp.h:4525

↓ 4 callersMethodinvalidate

src/common/clipp.h:4108

↓ 4 callersMethodis_alternative

src/common/clipp.h:6097

↓ 4 callersFunctionlast_column

src/common/clipp.h:5462

↓ 4 callersFunctionmd2j

* @brief mash distance to jaccard estimate * @param[in] d mash distance [0.0 - 1.0] * @param[in] k kmer size * @return

src/map/include/map_stats.hpp:62

↓ 4 callersMethodrepeat

src/common/clipp.h:4533

↓ 4 callersFunctionwith_prefix

src/common/clipp.h:3878

↓ 4 callersFunctionwith_prefixes_short_long

src/common/clipp.h:3931

↓ 4 callersFunctionwith_suffix

src/common/clipp.h:3977

↓ 4 callersFunctionwith_suffixes_short_long

src/common/clipp.h:4030

↓ 4 callersMethodwrap_hard

@brief go to new line, and start a new paragraph */

src/common/clipp.h:5818

↓ 3 callersMethodall_optional

@brief returns true if all children are optional (=non-required) */

src/common/clipp.h:3207

↓ 3 callersMethodat

@brief position of the match within the subject string */

src/common/clipp.h:111

↓ 3 callersMethodconflict

src/common/clipp.h:4536

↓ 3 callersFunctiondoc_label

/ * * @brief prints first flag or value label of a parameter * *****************************************************************************/

src/common/clipp.h:6904

↓ 3 callersFunctionfirst_integer_match

src/common/clipp.h:993

↓ 3 callersMethodgreedy

--------------------------------------------------------------- @brief returns if a parameter should match greedily */

src/common/clipp.h:1969

↓ 3 callersFunctionignore_newline_chars

src/common/clipp.h:5662

↓ 3 callersMethodis_last_in_path

src/common/clipp.h:2842

↓ 3 callersMethodis_singleton

src/common/clipp.h:6094

↓ 3 callersFunctionj2md

* @brief jaccard estimate to mash distance * @param[in] j jaccard estimate * @param[in] k kmer size * @return mash

src/map/include/map_stats.hpp:44

↓ 3 callersFunctionlongest_prefix_match

src/common/clipp.h:878

↓ 3 callersMethodparam_count

--------------------------------------------------------------- @brief returns recursive parameter count */

src/common/clipp.h:3421

↓ 3 callersMethodsearchIndex

* @brief search hash associated with given position inside the index * @details if MIIter_t iter is returned, than *i

src/map/include/winSketch.hpp:259

↓ 3 callersFunctionset

src/common/clipp.h:1071

↓ 3 callersMethodstart_of_repeat_group

src/common/clipp.h:4116

↓ 3 callersFunctiontrim

src/common/clipp.h:727

↓ 2 callersFunctionaddMinimizers

src/map/include/commonFunc.hpp:92

↓ 2 callersMethodafter_index

src/common/clipp.h:4570

↓ 2 callersMethodall_flagless

@brief returns if all children are value parameters (recursive) */

src/common/clipp.h:3249

↓ 2 callersMethodany_error

@brief returns true if any parsing error / violation of the * command line interface definition occurred */

src/common/clipp.h:5134

↓ 2 callersMethodbad_repeat

src/common/clipp.h:4538

↓ 2 callersMethoddata

src/common/clipp.h:2756

↓ 2 callersFunctionestimateMinimumHitsRelaxed

* @brief Estimate minimum number of shared sketches * s.t. upper bound identity is >= desired identity

src/map/include/map_stats.hpp:142

↓ 2 callersFunctionfirst_number_match

src/common/clipp.h:933

↓ 2 callersFunctiongetHash

* @brief hashing kmer string (borrowed from mash) */

src/map/include/commonFunc.hpp:71

↓ 2 callersMethodgood

src/common/clipp.h:5734

↓ 2 callersMethodhanging_indent

src/common/clipp.h:5763

↓ 2 callersMethodignore_blocking

src/common/clipp.h:4106

↓ 2 callersMethodinsert_ref

* @brief insert a minimizer from the reference sequence into the map * @param[in] m reference minimizer to insert

src/map/include/slidingMap.hpp:137

↓ 2 callersMethodis_first_in_parent

src/common/clipp.h:2832

↓ 2 callersFunctionks_getuntil

src/common/kseq.h:145

↓ 2 callersFunctionlongest_common_prefix

src/common/clipp.h:795

↓ 2 callersFunctionmake_man_page

/ * * @brief generates man sections from command line parameters * with sections "synopsis" and "options" * *******************************

src/common/clipp.h:6852

↓ 2 callersFunctionmd_lower_bound

* @brief Given a distance d, compute the lower bound on d within required confidence interval * @details If a given ma

src/map/include/map_stats.hpp:79

↓ 2 callersFunctionoperator<<

src/common/prettyprint.hpp:435

↓ 2 callersFunctionparagraph_spacing

src/common/clipp.h:5615

↓ 2 callersFunctionparse

/ * * @brief parses vector of arg strings and executes actions * *****************************************************************************/

src/common/clipp.h:5280

↓ 2 callersFunctionparseFileList

src/map/include/parseCmdArgs.hpp:32

↓ 2 callersFunctionparse_and_execute

/ * * @brief parses input args & executes actions * *****************************************************************************/

src/common/clipp.h:5258

↓ 2 callersMethodprefix

src/common/clipp.h:1782

↓ 2 callersMethodroot

src/common/clipp.h:2939

↓ 2 callersFunctionsanitize_args

/ * * @brief correct some common problems * does not - and MUST NOT - change the number of arguments * (no insertions or deletions al

src/common/clipp.h:5172

↓ 1 callersFunctionMurmurHash3_x64_128

src/common/murmur3.h:226

↓ 1 callersMethodadd_match

---------------------------------------------------------------

src/common/clipp.h:4894

↓ 1 callersMethodall_required

@brief returns true, if all children are required to match */

src/common/clipp.h:3194

↓ 1 callersMethodany_optional

--------------------------------------------------------------- @brief returns true if any child is optional (=non-required) */

src/common/clipp.h:3203

↓ 1 callersMethodany_required

--------------------------------------------------------------- @brief returns true, if any child is required to match */

src/common/clipp.h:3188

↓ 1 callersMethodbegin_dfs

--------------------------------------------------------------- @brief returns augmented iterator for depth first searches * @details traverser

src/common/clipp.h:3413

↓ 1 callersMethodbuild

* @brief build the sketch table * @details compute and save minimizers from the reference sequence(s) * assuming a fixe

src/map/include/winSketch.hpp:124

↓ 1 callersMethodcbegin

@brief returns non-mutating iterator to position of first element */

src/common/clipp.h:3399

↓ 1 callersMethodcend

@brief returns non-mutating iterator to position one past the last element */

src/common/clipp.h:3406

↓ 1 callersFunctioncomputeCGI

* @brief compute and report AAI/ANI * @param[in] parameters algorithm parameters * @param[in] result

src/cgi/include/computeCoreIdentity.hpp:166

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