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

⨍ Functions 4,043◇ Types & classes 931

↓ 2 callersFunctionchomp

chomp a string*/

auxprogs/compileSpliceCands/compileSpliceCands.c:31

↓ 2 callersFunctionchomp

auxprogs/aln2wig/aln2wig.c:27

↓ 2 callersFunctionclean

Remove empty directories or if forced

tests/short/auxprogs/filterbam/test_filterbam.py:22

↓ 2 callersFunctionclean

Remove empty directories or if forced

tests/short/auxprogs/bam2hints/test_bam2hints.py:25

↓ 2 callersFunctionclean

Remove empty directories or if forced

tests/short/auxprogs/homgenemapping/test_homgenemapping.py:30

↓ 2 callersFunctionclean

Remove empty directories or if forced

tests/short/auxprogs/bam2wig/test_bam2wig.py:23

↓ 2 callersFunctioncleanup_db

(paths, chunk, removeFASTA = True)

scripts/executeTestCGP.py:107

↓ 2 callersMethodcleanup_mysqldb

tests/short/examples/test_examples.py:188

↓ 2 callersMethodcloneMap

include/vitmatrix.hh:436

↓ 2 callersFunctioncompactifyBed

If several steps coincide then summarize them equivalently by one step in order to 1) Save memory or 2) output a bed file

auxprogs/filterBam/src/filterBam.cc:758

↓ 2 callersFunctioncompareAndSplit

auxprogs/joingenes/jg_transcript.cpp:91

↓ 2 callersFunctioncompare_files

(reffile, currentfile, html=False, outputfolder='output_html/')

tests/short/utils/aug_comparator.py:28

↓ 2 callersMethodcomputeLen

* Ensure all rows have the same length and compute and set this length. */

include/alignment.hh:391

↓ 2 callersMethodcomputeStairs

src/motif.cc:543

↓ 2 callersFunctioncompute_boundaries

include/json.hpp:14521

↓ 2 callersFunctioncontainsJustNonNucs

src/types.cc:468

↓ 2 callersMethodcountEqualSignsInQuerySequence

returns the number of equal signs in the query sequence - occur after "samtools calmd -e" was run */

auxprogs/filterBam/src/BamToolsAccess.cc:92

↓ 2 callersFunctioncreate

src/exoncand.cc:541

↓ 2 callersFunctioncutRelevantPiece

* cutRelevantPiece * If predictionStart and predictionEnd are set this function cuts * out the piece from predictionStart to predictionEnd, and stor

src/augustus.cc:560

↓ 2 callersMethoddecode

! @brief check whether a string is UTF-8 encoded The function checks each byte of a string whether it is UTF-8 encoded. The result of the

include/json.hpp:16298

↓ 2 callersMethoddecrement

src/statemodel.cc:473

↓ 2 callersFunctiondeleteGene

auxprogs/joingenes/jg_transcript.cpp:347

↓ 2 callersFunctiondisplayUsage

Display usage when --help

auxprogs/filterBam/src/functions/initOptions.cc:91

↓ 2 callersFunctiondisplay_help

auxprogs/joingenes/joingenes.cpp:32

↓ 2 callersMethoddrop

src/phylotree.cc:343

↓ 2 callersFunctioneigendecompose

* perform a decompososition of the rate matrix as Q = U * diag(lambda) * U^{-1} */

src/contTimeMC.cc:116

↓ 2 callersFunctionemplace

include/json.hpp:21954

↓ 2 callersMethodendTransaction

src/sqliteDB.cc:43

↓ 2 callersMethoderase

include/pp_hitseq.hh:122

↓ 2 callersMethoderaseUnneededSubstates

include/vitmatrix.hh:650

↓ 2 callersMethoderror

src/parser/parser.h:38

↓ 2 callersFunctionextractTransId

scripts/extractAnno.py:20

↓ 2 callersMethodfindGeneRanges

src/genomicMSA.cc:347

↓ 2 callersFunctionfindPossibleSpliceSites

searches on a genome in two ranges for splice sites and prints the resulting introns in gff format * if there are unknown strands, it searches in bot

auxprogs/compileSpliceCands/compileSpliceCands.c:144

↓ 2 callersFunctionfind_values

tests/longrunning/extract_accuracy_values.py:19

↓ 2 callersMethodfirstCodon

include/pp_scoring.hh:116

↓ 2 callersMethodfitch

src/phylotree.cc:533

↓ 2 callersFunctionfrom_json_array_impl

include/json.hpp:3574

↓ 2 callersMethodgenerateRandSeq

src/contentmodel.cc:65

↓ 2 callersMethodget

include/pp_profile.hh:101

↓ 2 callersMethodgetAddInfo

0x7FFF bit mask for retrieving bits 1-15

include/liftover.hh:38

↓ 2 callersMethodgetAliPos

include/alignment.hh:93

↓ 2 callersMethodgetAlpha

include/merkmal.hh:168

↓ 2 callersMethodgetAnnoSeq

include/speciesgraph.hh:88

↓ 2 callersMethodgetChrPos

include/alignment.hh:97

↓ 2 callersFunctiongetChromosome

searches a needed genome given by chromosomename and returns is as string*/

auxprogs/compileSpliceCands/compileSpliceCands.c:187

↓ 2 callersFunctiongetCodonRateMatrix

src/codonevo.cc:330

↓ 2 callersMethodgetColumn

include/matrix.hh:77

↓ 2 callersMethodgetEndInWindow

include/orthoexon.hh:68

↓ 2 callersMethodgetEvidence

auxprogs/homGeneMapping/src/gene.cc:73

↓ 2 callersMethodgetExInHeads

include/gene.hh:379

↓ 2 callersMethodgetExonListInRange

src/extrinsicinfo.cc:855

↓ 2 callersMethodgetFactor

src/pp_scoring.cc:893

↓ 2 callersFunctiongetFrame

auxprogs/homGeneMapping/src/gene.cc:96

↓ 2 callersMethodgetIntraFreq

* @param[in] c A block column * @param[in] f A frame in {0,1,2} * @return The frequency of introns after block column c and f

include/pp_profile.hh:162

↓ 2 callersMethodgetIntronInterFreq

* @param[in] b A block number * @param[in] n Number of introns * @return The frequency of n introns in the inter-block section before

include/pp_profile.hh:708

↓ 2 callersFunctiongetIntronStateType

↓ 2 callersMethodgetLambda

include/contTimeMC.hh:146

↓ 2 callersMethodgetLen

include/liftover.hh:37

↓ 2 callersMethodgetLogRegScore

src/orthoexon.cc:256

↓ 2 callersMethodgetMu

include/contTimeMC.hh:147

↓ 2 callersMethodgetMult

auxprogs/homGeneMapping/include/gene.hh:72

↓ 2 callersMethodgetNearestBaseCountIndex

src/motif.cc:493

↓ 2 callersMethodgetNextGene

pops the first alignment from list

src/genomicMSA.cc:1177

↓ 2 callersMethodgetNumCommonSeqs

* determine the number of sequences in the set of sequences annoseq, * for which we have extrinsic information */

src/extrinsicinfo.cc:2388

↓ 2 callersMethodgetNumPatterns

include/contentmodel.hh:59

↓ 2 callersMethodgetParent

include/phylotree.hh:100

↓ 2 callersMethodgetPartialThresh

include/pp_profile.hh:473

↓ 2 callersMethodgetPatProb

include/contentmodel.hh:52

↓ 2 callersMethodgetPhyleticPattern

* phyletic patterns *----------------------- * label of Species i in {0,1,2,3,4,5} equiv. {"0","1","-","_","g","l"} * * 0 - EC present in i, but

src/orthoexon.cc:79

↓ 2 callersMethodgetPi

include/contTimeMC.hh:49

↓ 2 callersMethodgetPredSubstateMap

returns the predecessor substate map, creates one if none exists

include/vitmatrix.hh:391

↓ 2 callersMethodgetPrior

include/codonevo.hh:57

↓ 2 callersFunctiongetPtr

* make a list of genes (with alternative transcrips) to * a pure pointer list of transcripts */

src/gene.cc:3028

↓ 2 callersMethodgetSeq

src/randseqaccess.cc:321

↓ 2 callersMethodgetSequenceList

src/genbank.cc:321

↓ 2 callersMethodgetSource

auxprogs/homGeneMapping/src/gene.cc:35

↓ 2 callersFunctiongetSpeciesID

* returns the speciesid for a given species name * if the species name is not in the database it is inserted */

src/load2db.cc:433

↓ 2 callersMethodgetSpeciesID

src/sqliteDB.cc:149

↓ 2 callersMethodgetStartInWindow

include/orthoexon.hh:67

↓ 2 callersMethodgetSubMatrixQ

include/contTimeMC.hh:52

↓ 2 callersFunctionget_idx_curr_scaff

auxprogs/utrrnaseq/src/Compute_UTRs.cpp:32

↓ 2 callersFunctionget_impl_ptr

get a pointer to the value (object)

include/json.hpp:19194

↓ 2 callersMethodget_numSeq

* @return The number of protein sequences used for the intron profile */

include/pp_profile.hh:182

↓ 2 callersMethodgraphOmegaOnCodonAli

src/codonevo.cc:625

↓ 2 callersFunctiongrisu2

include/json.hpp:15162

↓ 2 callersFunctiongrisu2_round

include/json.hpp:14880

↓ 2 callersFunctiongsl_minimizer

src/train_logReg_param.cc:421

↓ 2 callersMethodhasEvidence

src/graph.cc:1308

↓ 2 callersMethodhasFeatures

auxprogs/homGeneMapping/include/gene.hh:144

↓ 2 callersFunctionhasStopCodon

src/exoncand.cc:22

↓ 2 callersMethodincludeStopInCDS

auxprogs/homGeneMapping/src/gene.cc:148

↓ 2 callersMethodinitPredecessors

* initPredecessors */

src/statemodel.cc:41

↓ 2 callersMethodinitThresholds

src/pp_profile.cc:245

↓ 2 callersMethodinit_db

(cls, cmd_list)

tests/short/examples/test_examples.py:171

↓ 2 callersMethodinit_test_data

tests/short/examples/test_examples.py:68

↓ 2 callersMethodinsertMissingGFs

auxprogs/homGeneMapping/src/gene.cc:211

↓ 2 callersMethodintronsInRange

returns the number of introns with position (j,{0,1,2}), where start<=j<end

src/pp_simscore.cc:152

↓ 2 callersMethodisCoding

include/gene.hh:391

↓ 2 callersMethodisExon

include/graph.hh:95

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