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

⨍ Functions 4,043◇ Types & classes 931

↓ 2 callersFunctionisFasta

src/fasta.cc:182

↓ 2 callersFunctionisFirstUTRExon

include/types.hh:600

↓ 2 callersFunctionisGFF

src/hints.cc:26

↓ 2 callersFunctionisGap

include/alignment.hh:266

↓ 2 callersMethodisHintedASS

include/extrinsicinfo.hh:194

↓ 2 callersMethodisHintedDSS

include/extrinsicinfo.hh:190

↓ 2 callersMethodisIntron

include/graph.hh:94

↓ 2 callersFunctionisLastUTRExon

include/types.hh:604

↓ 2 callersMethodisMapped

returns true if alignment is mapped */

auxprogs/filterBam/src/BamToolsAccess.cc:56

↓ 2 callersMethodisMapped

auxprogs/homGeneMapping/include/gene.hh:81

↓ 2 callersMethodisMateMapped

returns true if alignment's mate is mapped */

auxprogs/filterBam/src/BamToolsAccess.cc:62

↓ 2 callersFunctionisNc

include/types.hh:625

↓ 2 callersMethodisPaired

returns true if alignment part of paired-end read */

auxprogs/filterBam/src/BamToolsAccess.cc:50

↓ 2 callersMethodisPartofGene

auxprogs/homGeneMapping/include/gene.hh:83

↓ 2 callersMethodisUTR

auxprogs/homGeneMapping/include/gene.hh:80

↓ 2 callersMethodisUTR

include/graph.hh:97

↓ 2 callersMethodis_end

return whether the iterator is at end

include/json.hpp:10671

↓ 2 callersMethodis_errored

include/json.hpp:5453

↓ 2 callersMethodis_linked

include/vitmatrix.hh:279

↓ 2 callersFunctionis_number_unsigned

! @brief return whether value is an unsigned integer number This function returns true if and only if the JSON value is an unsigned integ

include/json.hpp:19001

↓ 2 callersFunctionjoin

auxprogs/joingenes/jg_transcript.cpp:615

↓ 2 callersFunctionjoining

auxprogs/joingenes/jg_transcript.cpp:769

↓ 2 callersMethodkey

create a key for a map function to find ortholog exons quickly

src/exoncand.cc:115

↓ 2 callersMethodlastCodon

include/pp_scoring.hh:119

↓ 2 callersMethodlenMod3

auxprogs/homGeneMapping/include/gene.hh:74

↓ 2 callersMethodlinkcount

include/vitmatrix.hh:276

↓ 2 callersFunctionlittle_endianess

! @brief determine system byte order @return true if and only if system's byte order is little endian @note from https://stackoverflow.com/a/1001328

include/json.hpp:7681

↓ 2 callersMethodloglikForCodonTuple

src/codonevo.cc:577

↓ 2 callersMethodmakeTolerant

include/pp_profile.hh:261

↓ 2 callersFunctionmake_genometbl_chunk

scripts/executeTestCGP.py:90

↓ 2 callersFunctionmapentrysize

src/vitmatrix.cc:435

↓ 2 callersFunctionmedianChrStartEndDiff

src/alignment.cc:833

↓ 2 callersMethodnextResult

auxprogs/homGeneMapping/src/sqliteDB.cc:110

↓ 2 callersMethodnumFitting

src/alignment.cc:863

↓ 2 callersFunctiononGenDSS

include/geneticcode.hh:47

↓ 2 callersMethodopen

src/randseqaccess.cc:393

↓ 2 callersFunctionoperator[]

! @brief access specified array element Returns a reference to the element at specified location @a idx. @note If @a idx is beyond the r

include/json.hpp:19988

↓ 2 callersMethodoutputGenes

include/orthograph.hh:84

↓ 2 callersFunctionoverlapping

auxprogs/joingenes/jg_transcript.cpp:1618

↓ 2 callersMethodoverlaps

* A coding gene overlaps a coding transcript if they have a common coding base. * A noncoding gene overlaps a noncoding transcript if they overlap on

src/gene.cc:2711

↓ 2 callersFunctionport_test

(paths_shared, paths, chunks)

scripts/executeTestCGP.py:181

↓ 2 callersMethodprintAccuracyForSequenceSet

src/extrinsicinfo.cc:2405

↓ 2 callersMethodprintAlignment

computes an readable alignment representation to stdout

src/pp_simscore.cc:682

↓ 2 callersMethodprintCodingSeq

src/gene.cc:2315

↓ 2 callersFunctionprintExonList

output all exon hints, for test issues

auxprogs/bam2hints/bam2hints.cc:209

↓ 2 callersFunctionprintExonpartList

output all exonpart hints, for test issues

auxprogs/bam2hints/bam2hints.cc:189

↓ 2 callersFunctionprintHelp

src/pp_simscore.cc:807

↓ 2 callersFunctionprintHints

print all hints (default) or the inalterable ones ("filter") to the outfile given with OUT

auxprogs/bam2hints/bam2hints.cc:264

↓ 2 callersFunctionprintIntronList

output all intron hints, for test issues

auxprogs/bam2hints/bam2hints.cc:199

↓ 2 callersFunctionprintList

auxprogs/compileSpliceCands/compileSpliceCands.c:362

↓ 2 callersFunctionprintMatePairs

auxprogs/filterBam/src/functions/MatePairs.cc:76

↓ 2 callersFunctionprintOomError

prints out an error message when allocating memory fails and exits*/

auxprogs/compileSpliceCands/compileSpliceCands.c:38

↓ 2 callersMethodprintProteinSeq

src/gene.cc:2356

↓ 2 callersMethodprintSimilarityMatrix

prints the similarity matrix

src/pp_simscore.cc:653

↓ 2 callersFunctionprintSizeOfCoverInfo

auxprogs/filterBam/src/filterBam.cc:735

↓ 2 callersFunctionprint_tc_header

tests/short/examples/test_examples.py:739

↓ 2 callersFunctionprocessQuery

auxprogs/filterBam/src/filterBam.cc:840

↓ 2 callersMethodprojectToAli

include/liftover.hh:78

↓ 2 callersMethodprojectToGenome

include/liftover.hh:147

↓ 2 callersMethodprune

* prune all leaf nodes of species that are not present as indicated by a bit vector * (i-th bit in the vector is 1 if species i is present and 0 if s

src/phylotree.cc:514

↓ 2 callersMethodpushIntron

src/gene.cc:934

↓ 2 callersMethodpushOn

include/pp_fastBlockSearcher.hh:219

↓ 2 callersMethodreadAlignment

src/codonMSA.cc:96

↓ 2 callersFunctionreadDblEnv

map<const char*, string> seqnames;

src/pp_prepare_align.cc:51

↓ 2 callersMethodreadExtrinsicCFGFile

src/randseqaccess.cc:52

↓ 2 callersFunctionreadFastaHeader

src/fasta.cc:157

↓ 2 callersFunctionreadIntEnv

src/pp_prepare_align.cc:62

↓ 2 callersFunctionread_sequences_from_stream

src/pp_prepare_align.cc:654

↓ 2 callersFunctionreference_from_file

src/train_logReg_param.cc:681

↓ 2 callersMethodremoveChild

include/phylotree.hh:87

↓ 2 callersMethodremoveGapOnlyCols

src/alignment.cc:954

↓ 2 callersFunctionrenameTaxa

auxprogs/joingenes/jg_ios.cpp:356

↓ 2 callersMethodreset

include/sqliteDB.hh:97

↓ 2 callersMethodresetPredEnd

include/vitmatrix.hh:763

↓ 2 callersMethodrev

include/geneticcode.hh:180

↓ 2 callersFunctionreverseComplementString

include/geneticcode.hh:132

↓ 2 callersFunctionreverseGeneList

src/gene.cc:3153

↓ 2 callersFunctionreverseGeneSequence

* reverseGeneSequence * Reverses the order of the genes and changes the positions of the exons and introns * relative to the sequence length 'endpos

src/gene.cc:3230

↓ 2 callersMethodsameFrame

auxprogs/homGeneMapping/src/gene.cc:61

↓ 2 callersMethodseqProb

src/exonmodel.cc:1925

↓ 2 callersMethodseqProb

* evaluate a sequence * seq is the beginning of the motif, but * for restrictions see addSequence */

src/motif.cc:308

↓ 2 callersMethodseqProb

src/intronmodel.cc:1046

↓ 2 callersMethodsetAAPostProbs

src/codonevo.cc:91

↓ 2 callersMethodsetActiveFlag

* HintGroup::setActiveFlag */

src/hints.cc:809

↓ 2 callersMethodsetContainment

include/orthoexon.hh:83

↓ 2 callersMethodsetDiscardFlag

* HintGroup::setDiscardFlag */

src/hints.cc:819

↓ 2 callersMethodsetEvidence

auxprogs/homGeneMapping/src/gene.cc:69

↓ 2 callersMethodsetFrame

src/hints.cc:505

↓ 2 callersMethodsetMult

auxprogs/homGeneMapping/include/gene.hh:69

↓ 2 callersMethodsetPatProb

src/contentmodel.cc:170

↓ 2 callersMethodsetPathAndProb

src/namgene.cc:1593

↓ 2 callersMethodsetPrior

* use a normal distribution with mean 1 and standard deviation sigma as prior for omega */

src/codonevo.cc:63

↓ 2 callersMethodsetSampleCount

* Gene::addSampleCount * add p to the apostprob of the transcript as well to the apostprob of all states */

src/gene.cc:1114

↓ 2 callersMethodsetScore

src/graph.cc:780

↓ 2 callersMethodsetStatePostProbs

src/gene.cc:1081

↓ 2 callersMethodsetStrand

src/hints.cc:516

↓ 2 callersMethodsetTruncFlag

* setTruncFlag * set the left and right truncated flag if appropriate * This is for truncated 'interval' states. */

src/gene.cc:309

↓ 2 callersMethodsetWeight

include/gene.hh:575

↓ 2 callersMethodset_begin

! @brief set the iterator to the first value @pre The iterator is initialized; i.e. `m_object != nullptr`. */

include/json.hpp:10940

↓ 2 callersMethodset_mean_std

* get mean and std of sample features for standardization */

src/train_logReg_param.cc:126

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