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Functions4,043 in github.com/Gaius-Augustus/Augustus

⨍ Functions 4,043◇ Types & classes 931

↓ 6 callersFunctioncount

include/json.hpp:20863

↓ 6 callersMethodcountCigarOperations

* Count all CIGAR operation of the specified type. * * @param type [MIDNSHPX=] * @return summ of all operations */

auxprogs/filterBam/src/BamToolsAccess.cc:103

↓ 6 callersMethodexec

src/sqliteDB.cc:32

↓ 6 callersFunctionexecute

(cmd, print_err=True, output=None, error_out=None, mode='w')

tests/longrunning/single_genome/test_single.py:149

↓ 6 callersFunctionfind_block

(input, start, stop)

scripts/executeTestCGP.py:397

↓ 6 callersFunctionfind_block

(input, start, stop)

tests/longrunning/extract_accuracy_values.py:90

↓ 6 callersFunctionfind_tool

Function that tries to locate a tool with which

scripts/fix_in_frame_stop_codon_genes.py:207

↓ 6 callersMethodgetDiversity

* calculate diversity (sum of branch lengths) */

src/phylotree.cc:488

↓ 6 callersMethodgetDownScore

include/exoncand.hh:76

↓ 6 callersMethodgetEndPosition

returns alignment end position */

auxprogs/filterBam/src/BamToolsAccess.cc:38

↓ 6 callersMethodgetFeatureList

include/extrinsicinfo.hh:136

↓ 6 callersMethodgetFeatureType

auxprogs/homGeneMapping/include/gene.hh:73

↓ 6 callersMethodgetFirstCodingBase

src/exoncand.cc:76

↓ 6 callersMethodgetPostProb

include/graph.hh:98

↓ 6 callersMethodgetPrefixThresh

include/pp_profile.hh:945

↓ 6 callersMethodgetUpScore

include/exoncand.hh:75

↓ 6 callersMethodgetWeights

include/merkmal.hh:177

↓ 6 callersMethodhas_subtype

! @brief return whether the value has a subtype @return whether the value has a subtype @complexity Constant. @exceptionsafety No-t

include/json.hpp:4540

↓ 6 callersFunctionhowOftenOccursIt

src/types.cc:452

↓ 6 callersMethodisRoot

include/phylotree.hh:90

↓ 6 callersFunctionis_string

! @brief return whether value is a string This function returns true if and only if the JSON value is a string. @return `true` if type i

include/json.hpp:19095

↓ 6 callersMethodkey

Gets the user supplied key.

src/googletest/include/gtest/gtest.h:544

↓ 6 callersMethodload

functions used for debugging only

include/vitmatrix.hh:713

↓ 6 callersFunctionmodm

include/types.hh:531

↓ 6 callersFunctionname

Returns the test name.

src/googletest/include/gtest/gtest.h:710

↓ 6 callersMethodnull

include/json.hpp:5807

↓ 6 callersFunctionpred

(sourcepath, targetpath)

tests/short/utils/aug_out_filter.py:7

↓ 6 callersMethodprepareSampling

include/vitmatrix.hh:794

↓ 6 callersFunctionprintGeneList

src/gene.cc:3055

↓ 6 callersFunctionprintQali

auxprogs/filterBam/src/filterBam.cc:559

↓ 6 callersFunctionquantile

src/types.cc:505

↓ 6 callersMethodreportable_test_count

Gets the number of tests to be printed in the XML report.

src/googletest/src/gtest.cc:801

↓ 6 callersMethodsample

src/vitmatrix.cc:295

↓ 6 callersMethodseqProbUnderModel

* Double seqProbUnderModel(char *s, int len, int frame); * return the probability of sequence s of lenth len under this model * assume seq starts wi

src/contentmodel.cc:20

↓ 6 callersMethodstep

src/sqliteDB.cc:196

↓ 6 callersFunctionstrtoken

returns the tokens of a string split by the separator in an array of char **/

auxprogs/aln2wig/aln2wig.c:38

↓ 6 callersMethodsubtype

! @brief return the binary subtype Returns the numerical subtype of the value if it has a subtype. If it does not have a subtype, this fu

include/json.hpp:4519

↓ 6 callersFunctionsyncThreads

synchronize threads

auxprogs/homGeneMapping/src/main.cc:360

↓ 6 callersFunctiontokenize

auxprogs/utrrnaseq/src/Supporting_Methods.cpp:25

↓ 6 callersMethodtotal_test_count

Gets the number of all tests.

src/googletest/src/gtest.cc:806

↓ 5 callersFunctionAdvance

auxprogs/compileSpliceCands/list.c:122

↓ 5 callersFunctionEqFailure

Constructs and returns the message for an equality assertion (e.g. ASSERT_EQ, EXPECT_STREQ, etc) failure. The first four parameters are the expressio

src/googletest/src/gtest.cc:1333

↓ 5 callersFunctionFOpen

src/googletest/include/gtest/internal/gtest-port.h:2125

↓ 5 callersMethodFailed

Returns true iff the test failed.

src/googletest/src/gtest.cc:2192

↓ 5 callersFunctionFormatDeathTestOutput

Returns an indented copy of stderr output for a death test. This makes distinguishing death test output lines from regular log lines much easier.

src/googletest/src/gtest-death-test.cc:532

↓ 5 callersFunctionFormatTestCount

Formats the count of tests.

src/googletest/src/gtest.cc:2854

↓ 5 callersFunctionGetLastErrnoDescription

Returns the message describing the last system error in errno.

src/googletest/src/gtest-death-test.cc:337

↓ 5 callersMethodGetToken

include/tokenizer.hh:25

↓ 5 callersFunctionInt32FromEnvOrDie

Parses the environment variable var as an Int32. If it is unset, returns default_val. If it is not an Int32, prints an error and aborts.

src/googletest/src/gtest.cc:5368

↓ 5 callersMethodNextTokenBlank

src/tokenizer.cc:30

↓ 5 callersMethodactivate

include/vitmatrix.hh:272

↓ 5 callersFunctionactivation_f

src/train_logReg_param.cc:157

↓ 5 callersMethodaddDistance

include/phylotree.hh:84

↓ 5 callersMethodaddGene

src/gene.cc:2676

↓ 5 callersMethodaddToEvaluation

src/evaluation.cc:18

↓ 5 callersFunctionat

! @brief access specified array element with bounds checking Returns a reference to the element at specified location @a idx, with bounds

include/json.hpp:19793

↓ 5 callersMethodbegin

src/googletest/include/gtest/internal/gtest-param-util.h:193

↓ 5 callersMethodbound

include/vitmatrix.hh:305

↓ 5 callersFunctionclear

! @brief clears the contents Clears the content of a JSON value and resets it to the default value as if @ref basic_json(value_t) would h

include/json.hpp:21636

↓ 5 callersMethodclose

closes the current BAM file */

auxprogs/filterBam/src/BamToolsAccess.cc:206

↓ 5 callersFunctioncreateCopyOf

auxprogs/joingenes/jg_transcript.cpp:326

↓ 5 callersMethodend

src/googletest/include/gtest/internal/gtest-param-util.h:194

↓ 5 callersMethoderaseAndDecCounts

include/vitmatrix.hh:414

↓ 5 callersMethodfileType

include/genbank.hh:144

↓ 5 callersFunctionfilter

(sourcepath, targetpath, ignoredlines)

tests/short/utils/aug_out_filter.py:67

↓ 5 callersMethodgetAliLen

start position of HECT in alignment

include/orthoexon.hh:65

↓ 5 callersMethodgetAnnoSequenceList

* GBProcessor::getAnnoSequenceList() * * gets the list of all annotated sequences from * */

src/genbank.cc:292

↓ 5 callersMethodgetConsScore

include/orthoexon.hh:51

↓ 5 callersMethodgetContainment

include/orthoexon.hh:55

↓ 5 callersMethodgetEomega

include/orthoexon.hh:44

↓ 5 callersFunctiongetFullStateId

* getFullStateId: merge state/substate pairs into single integers (used in calls of viterbi) * precondition: state >= -1, substate

include/statemodel.hh:37

↓ 5 callersMethodgetIndex

src/merkmal.cc:155

↓ 5 callersMethodgetLeftExtOmega

include/orthoexon.hh:46

↓ 5 callersMethodgetLeftIntOmega

include/orthoexon.hh:48

↓ 5 callersMethodgetLen

include/graph.hh:99

↓ 5 callersMethodgetName

include/hints.hh:171

↓ 5 callersMethodgetNumSeqsWithInfo

reading in the bonus/malus table

include/extrinsicinfo.hh:388

↓ 5 callersMethodgetNumStates

include/contTimeMC.hh:35

↓ 5 callersMethodgetOffset

include/merkmal.hh:63

↓ 5 callersMethodgetRateMatrices

precomputes or reads the rate matrices which does not require t yet

src/codonevo.cc:160

↓ 5 callersMethodgetRightExtOmega

include/orthoexon.hh:47

↓ 5 callersMethodgetRightIntOmega

include/orthoexon.hh:49

↓ 5 callersMethodgetRoot

include/lldouble.hh:141

↓ 5 callersMethodgetStart

src/exoncand.cc:34

↓ 5 callersMethodgetSuffixThresh

include/pp_profile.hh:958

↓ 5 callersFunctiongetTranslation

TODO: move this to GeneticCode

src/gene.cc:2338

↓ 5 callersMethodgetVarOmega

include/orthoexon.hh:45

↓ 5 callersMethodget_character

include/json.hpp:4770

↓ 5 callersFunctionget_feature

src/train_logReg_param.cc:170

↓ 5 callersFunctiongroupTranscriptsToGenes

* groupTranscriptsToGenes * summarize overlapping transcripts to genes */

src/gene.cc:3175

↓ 5 callersMethodhas

include/pp_profile.hh:203

↓ 5 callersMethodhasMoreElements

include/gene.hh:622

↓ 5 callersMethodindex

src/googletest/include/gtest/internal/gtest-death-test-internal.h:288

↓ 5 callersFunctioninitialExon

include/types.hh:667

↓ 5 callersFunctioninternalExon

include/types.hh:678

↓ 5 callersMethodisExon

auxprogs/homGeneMapping/include/gene.hh:77

↓ 5 callersMethodisIntron

auxprogs/homGeneMapping/include/gene.hh:79

↓ 5 callersFunctionisNcIntron

include/types.hh:617

↓ 5 callersMethodisType

auxprogs/homGeneMapping/include/gene.hh:82

↓ 5 callersMethodis_begin

return whether the iterator can be dereferenced

include/json.hpp:10665

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